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Nima uchun ba'zi daraxtlarning genomlari juda katta?

Nima uchun ba'zi daraxtlarning genomlari juda katta?



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Masalan, hozirgi eng katta ma'lum genom daraxtga tegishli: http://motherboard.vice.com/read/the-largest-genome-ever-sequenced-belongs-to-a-tree

Men daraxtlarga ma'lum genlarning ko'p nusxalarini talab qilishi mumkinligi sababli bo'lishi mumkinligini eshitdim, chunki ular butun hayoti davomida to'g'ridan-to'g'ri quyosh nuri ostida yashaydilar.

Nima uchun bunday bo'lishi mumkinligi haqida biron bir aniq ilmiy farazlar haqida kimdir biladimi?


Yaqinda ketma-ket kelgan qarag'ay turlarini o'rganish shuni ko'rsatadiki, genomning 82% takrorlanadi. Bu har qanday murakkab genomga, shu jumladan odamlarga xosdir. Bunday ketma-ketliklar ko'pincha "keraksiz DNK" deb hisoblangan, ammo har qanday olim sizga uning maqsadini bilmasligimiz uning yo'qligini anglatmasligini aytadi. Ya'ni, takroriy takrorlanishlarning yaxshi qismi ko'chiriladigan elementlarga, samarali hujayra ichidagi parazitlarga bog'liq bo'lib, ularning yagona maqsadi, ehtimol, o'z-o'zini kuchaytirish va ko'pincha zararli emas. Ushbu kesishgan takrorlanishlar inson genomining ~ 45% ni tashkil qiladi. Ushbu maqolada aytilishicha, ketma-ketlik homologiyasiga asoslanib, qarag'ay genomining ~ 65% bu takrorlanishlardan iborat (bu 15 milliard tayanch juftlik).

Qizig'i shundaki, qarag'ayning genomi insonnikidan ~7 baravar katta bo'lsa-da, u faqat ikki baravar ko'p. bashorat qilingan genlar. Qarag'ay daraxtida ~50 000 gipotetik gen mavjud, ammo mualliflar buni yuqori ishonch deb atashadi - atigi ~ 16 000. Odam genomi birinchi marta ketma-ketlikda 35 000 ga yaqin gipotetik genlar mavjud edi, ammo hozir, taxminan 10 yil o'tgach, atigi ~ 21 000 taxmin qilingan genlar mavjud. Ikkisini solishtirishga hali erta. Bu shuningdek, genlar soni organizmning murakkabligi bilan bog'liq emasligi haqidagi muhim fikrni keltirib chiqaradi: C. elegans qurti ~ 20 000 genga ega.

Qog'ozdan:

Katta genom hajmi, birinchi navbatda, bir-biri bilan o'ralgan takrorlanuvchi tarkibning katta hissasi bilan bog'liq (Morse va boshq. 2009; Kovach va boshq. 2010; Wegrzyn va boshq. 2013). Norvegiya archa genomining yig'ilishi shuni ko'rsatdiki, ayniqsa LTR retrotranspozonlari ko'pincha ba'zi gen oilalarining uzun intronlari ichida joylashgan (Nystedt va boshq. 2013). Bundan tashqari, genlarning ko'payishi, psevdogenlar va paraloglar uchun dalillar mavjud, garchi ularning darajasi aniq emas (Kovach va boshq. 2010; Pavy va boshq. 2012).

Men siz aytgan gipotezani hech qachon eshitmaganman (bu hech narsani anglatmaydi), lekin menimcha, buni aytishga erta.


"Homongous qo'ziqorin" sirlari

25 yil oldin Jeyms Anderson Yerdagi hayot imkoniyatlarini kengaytirgan qo'ziqorinni kashf etdi.

Bu a yagona jinsdagi qo'ziqorin Armillaria, taxminan 22,000 funtni tashkil etadi va ajoyib 15 gektarga tarqaldi. Organizm taxminan 1500 yil davomida o'sib borgan, u o'sgan er Michigan shtatiga aylanganidan ming yildan ko'proq vaqt oldin. Anderson va uning hamkorlari buni yozganlarida Tabiat, ular uni dunyodagi "eng katta va eng qadimgi tirik organizmlar qatorida" deb taxmin qilishdi.

Bu taklif, ustunlikdan foydalanishda, raqobatni keltirib chiqardi - tabiiyki. Tez orada butun dunyo olimlari ov qilishdi Armillaria, yoki asal qo'ziqorinlari, o'z o'rmonlarida. Dunyodagi eng katta qo'ziqorin unvoni oxir-oqibat Oregon shtatidagi Malheur milliy o'rmonidagi qo'ziqorin nomiga kirdi: 1000 gektarga yaqin katta, yoshi 8650 yil. Ba'zida "katta qo'ziqorin" deb ataladi, ba'zi ma'lumotlarga ko'ra, hozirgacha topilgan eng katta tirik organizmdir.

Qo'ziqorinlar odatda mitseliya shaklida o'sadi - siz muzlatgichda juda uzoq vaqt saqlanadigan ovqatda ko'rgan yumshoq, oq, paxta tuplari. Ulardan ba'zilari qo'ziqorinlarni ham hosil qiladi. Lekin Armillaria, biroz o'ziga xos, shuningdek, qalin, qora, ildizga o'xshash rizomorflar o'sishi mumkin, ularning tarmoqlari ovqatlanish uchun o'tin qidirish uchun tuproq bo'ylab milyaga cho'zilishi mumkin. Rizomorflar, olimlarning fikriga ko'ra, bitta bo'lishiga imkon beradi Armillaria organizm shunchalik katta bo'ladi. Keng qamrovli yangi genetik tadqiqot qanday qilib degan savolni oladi Armillaria rizomorflarini oldi.

Endi Toronto universitetida biologiya professori bo'lgan Anderson shunday deydi: "Aspirant bo'lganimdan beri men nashr etilgan tadqiqot bilan shug'ullanishni xohlardim". Anderson tadqiqot uchun bir nechta genomlarni o'z hissasini qo'shdi, ammo tadqiqot va tahlillarning asosiy qismini mos ravishda Sopron universiteti va Vengriya Fanlar akademiyasidan Dyordji Sipos va Laslo Nagy amalga oshirdi.

Sipos va Nagy nafaqat to'rtta turni ketma-ketlikda Armillaria, lekin ular qo'ziqorinning rizomorflari va qo'ziqorinlarida faol bo'lgan genlarni ham aniqladilar. Ushbu genlarni aniqlash uchun ular kamida bitta turni qanday etishtirishni aniqlashlari kerak edi Armillaria laboratoriyada.

Rizomorflar Armillaria mellea (Lairich Rig)

Rizomorflar oson qism edi. Bir marta Armillaria Ular guruch, talaş, pomidor va apelsinni o'stirishga kirishdilar - "bu qo'ziqorin haqiqatan ham g'alati ta'mga ega", deb ta'kidlaydi Nagi - ular o'z-o'zidan rizomorflarni hosil qilgan. Qo'ziqorinlar ancha hiyla-nayrang edi. Ular qo'ziqorinni kuzda deb o'ylash uchun aldashlari kerak edi, ular Nagy laboratoriyasida zamburug'larini asta-sekin kamroq yorug'lik bilan sovuqroq haroratga o'tkazish orqali qildilar. Siposning aytishicha, uning hamkasblari “haqiqatan ham ajoyib ish qilishdi. Ilgari bu qo‘ziqorindan qo‘ziqorin hosil qilish qiyin edi”. Ular bitta turni olishga muvaffaq bo'lishdi -Armillaria ostoyae, shuningdek, yirik Oregon qo'ziqorinining turlari - qo'ziqorinlarni ishlab chiqarish uchun.

Shunga qaramay, barcha qiyinchiliklar o'z samarasini berdi. Jamoa ketma-ketlik ma'lumotlarini qaytarib olganida, ular bir xil gen tarmoqlari qo'ziqorin rizomorflarida ham, uning qo'ziqorinlarida ham faol ekanligini payqashdi. U ushbu jinsdagi rizomorflar uchun potentsial evolyutsion kelib chiqishini taklif qiladi: Armillaria O'zining rizomorflarini va shuning uchun keng tarqalish qobiliyatini - dastlab qo'ziqorinlarni etishtirish uchun ishlatilgan genlarni birgalikda tanlash orqali olishi mumkin edi. Nagyning fikriga ko'ra, rizomorflar qo'ziqorin poyalariga o'xshash bo'lishi mumkin, ular unib chiqa olmagan va qalpoqcha o'smagan, aksincha, er ostida uzun va ingichka o'sadi.

ning ko'tarilishi Armillaria daraxtlar hisobiga kelgan. Qo'ziqorin aslida daraxtlarga aylanadi va qobig'i ostida tarqaladi. Avvaliga ular tirik yog'ochni hazm qilishadi va etarlicha zarar etkazgandan so'ng, ular o'lik yog'ochda ziyofat qilishni davom ettiradilar. "Asosan siz butun tepaliklar vayron bo'lgan, butun o'rmonlar qirib tashlanganini ko'rishingiz mumkin", deydi Nagi. Oregon shtatidagi Malheur o'rmonida siz o'sha paytdan beri juda katta qo'ziqorinni ko'ra olmaysiz. Armillaria asosan er ostida, lekin u o'ldirgan barcha daraxtlarni ko'rishingiz mumkin.

O'lgan ignabargli o'rmon tomonidan zararlangan Armillaria Sibirda (Igor Pavlovning izni bilan)


Genomning qorong'u tomoni

Biz DNK tuzilishini 1953 yildan beri bilsak-da, biologik xilma-xillikni tushunish uchun undagi genomik ma'lumotlarni sharhlash qobiliyatimiz faqat so'nggi yillarda tez o'sdi.

Ammo genomning bir tomoni, ya'ni organizmdagi genetik ma'lumotlarning to'liq to'plami uzoq vaqtdan beri olimlarni hayratda qoldirdi.

Nega genomlar o'lchamlari bo'yicha juda xilma-xil bo'lib, turning har bir hujayradagi DNK miqdori (ya'ni genom hajmi) va organizmning murakkabligi o'rtasida aniq bog'liqlik yo'q?

Eng kichikdan eng katta o'simlik genomlarigacha

Gullaydigan o'simliklarda genom o'lchamlari hayratlanarli darajada 2400 marta o'zgarib turadi, bu har qanday taqqoslanadigan organizmlar guruhi uchun eng katta diapazondir.

Genlisea tuberosa, mayda mayda go'shtxo'r o'simlikning genomi biznikidan 50 barobar kichikroq. Parij Yaponiya, o'tsimon monokot esa biz odamlarga qaraganda har bir hujayrada 50 baravar ko'p DNKga ega.

Aslini olib qaraganda, P. yaponika tahlil qilingan har qanday organizmning eng katta genomiga ega.

Haqiqatan ham, agar biz DNKni bitta hujayradan ajratib olsak P. yaponika uning uzunligi 100 m, Kewdagi Pagoda balandligidan ikki baravar ko'p, bizning genomimiz esa atigi 2 m cho'zilgan bo'lar edi!

DNK ketma-ketligi ma'lumotlarini yaratishning tobora ortib borayotgan tezligi ko'plab turlarning, shu jumladan o'zimizning genomlardagi genlarning tarkibi, tuzilishi, ifodasi va evolyutsiyasi haqida chuqur ma'lumot berdi.

Biroq, genlar ko'pincha genomning faqat kichik qismini tashkil qiladi. Odamlarda bizning c. 23 000 gen bizning umumiy genom hajmining atigi 2-3% ni tashkil qiladi.

Xo'sh, genomning qolgan qismini nima tashkil qiladi?

Sirli DNK

Genomning qolgan qismini o'z ichiga olgan DNK haqida juda kam narsa ma'lum. Olimlar ba'zan bizning bilimimiz etishmasligini aks ettirish uchun bu DNKni "qorong'u materiya" deb atashadi.

Biz bilgan narsa shundaki, u harakatlanuvchi elementlardan tashkil topgan takrorlanuvchi DNK ketma-ketliklarini va harakatlanish va ko'payish qobiliyatiga ega bo'lgan boshqa ketma-ketliklarni o'z ichiga oladi.

Bizning genomimizda bu takrorlanuvchi ketma-ketliklar DNKning kamida 50% ni tashkil qilishi taxmin qilinadi.

Ular genetik xilma-xillikni yaratish orqali genomimizning ishlashi va evolyutsiyasiga chuqur ta'sir ko'rsatishi, shuningdek, saraton kabi kasalliklarni keltirib chiqarishi mumkin.

Qorong'u materiyaning dekodlanishi

O'simliklarda genom hajmi o'simliklarning qanday va qayerda o'sishiga ta'sir qiladi, shuning uchun genom hajmining o'zgarishiga hissa qo'shadigan takroriy ketma-ketliklarni tahlil qilish muhimdir.

Tadqiqotlar shuni ko'rsatadiki, takrorlanuvchi ketma-ketliklarning ko'pligidagi farqlar ularning kuchayish qobiliyati va genomdan olib tashlash tezligi o'rtasidagi muvozanatni aks ettiradi. Shunga qaramay, bizning deyarli barcha tushunchalarimiz kichik genomli turlarni o'rganishdan kelib chiqqan.

Shuning uchun biz o'simliklarda uchraydigan genom o'lchamlarining deyarli to'liq diapazonidagi turlarni ko'rib chiqib, genomning "qorong'i tomoni" ni tahlil qildik.

Katta genom, ko'proq takrorlash?

Natijalar hayratlanarli edi. Biz genom hajmi va takrorlanuvchi ketma-ketliklar o'rtasidagi bog'liqlikni ko'rishni kutgan edik - genom qanchalik katta bo'lsa, kichik va o'rta genomlarga ega turlarda ko'rinadigan takrorlanishlar shunchalik ko'p bo'ladi.

Buning o'rniga, biz 10 Gbp dan katta genomlarda (ya'ni, inson genomining 3x kattaligi) genom hajmi oshgani sayin takrorlanishlar ko'pligi kamaydi.

Bizning natijalarimiz shuni ko'rsatadiki, bu genom hajmiga qarab genomda takrorlanishlar qanday o'zgarishi bilan bog'liq.

Qulupnay, eman va romashka kabi kichik va oʻrta genomga ega (yaʼni 10 Gb/s dan kam) turlar dinamik genomlari bilan ajralib turadi, ular takroriy koʻpaytiriladi va tez yoʻq qilinadi va potentsial ravishda koʻplab genomik xilma-xillikni keltirib chiqaradi. .

Bundan farqli o'laroq, kattaroq genomga ega bo'lgan turlar (ya'ni, taxminan 10 Gbp dan katta), masalan, ko'k qo'ng'iroqlar, ilon boshi va ökse o'ti, DNKni yo'q qilish tezligida ancha sust ko'rinadi.

Natijada takrorlanishlar genomda "tupoq" bo'lib qoladi, bu erda ular vaqt o'tishi bilan sekin mutatsiyaga uchraydilar, shunda ular endi takrorlanish sifatida tanib bo'lmaydi. Shunday qilib, genom kengayadi va ular asta-sekin yo'q bo'lib ketish tomon harakat qilishlari mumkin.

Turlarning evolyutsiyasiga ta'sir qilishda genom hajmi muhim rol o'ynashi aniq.

Biz bilamizki, genom hajmi bir nechta jarayonlarga ta'sir qiladi.

Misol uchun, katta genomli o'simliklar DNKni ko'paytirish va hujayralarini bo'lish uchun ko'proq vaqt talab etadi va kattaroq hujayralarga ega bo'lish bilan cheklanadi, bu esa fotosintez tezligining pasayishiga va suvdan foydalanish samaradorligining o'zgarishiga olib keladi.

Bu katta genomli o'simliklar sekin o'sib borishini va uzoq umr ko'rishini anglatadi. Ular, shuningdek, kichikroq genomli turlarga qaraganda biomassani qo'yish yoki suv stressiga javob berishda samarasiz bo'lishi mumkin.

Shunday qilib, gigant genomlari bo'lgan turlarning tez-tez yo'qolib ketish xavfi ostida turgan o'simliklar orasida topilishi ajablanarli emas, bu qisman kichikroq genomli turlarga nisbatan o'zgaruvchan muhitga moslashish qobiliyatining cheklanganligi sababli.

Qog'ozni o'qing

Ushbu tadqiqot Qirolicha Meri, London universiteti, CAS Biologiya markazi (Chexiya) va Kew Qirollik botanika bog'lari olimlari tomonidan olib borilgan va quyidagi maqolada nashr etilgan:


Ta'kidlash joizki, uni katta qilish: Salamanderlar DNKni yaqin va aziz tutadilar

Qadimgi ma'lumotlarga ko'ra, salamandrlar olovdan o'z-o'zidan sakrashga qodir sehrli mavjudotlar edi. Yong'indan zarar ko'rishdan ko'ra, ular olov bilan oziqlangan. Da Vinchi o'zining kamroq ilmiy lahzalaridan birida salamandr "olovdan boshqa ovqat olmaydi" deb yozgan edi, u doimiy ravishda po'stlog'ini yangilab turadi.

Garchi bu kuchlar, afsuski, to'g'ri bo'lmasa-da, boshqa sabablarga ko'ra salamandrlarning deyarli sehrli ekanligini bilish taskin beradi. Tabiatshunoslar va maktab o'quvchilari orasida bu ko'pincha ajoyib rangli amfibiyalar kesilgan oyoq-qo'llarini qayta tiklash qobiliyati bilan mashhur. Biroq, molekulyar evolyutsionist Reychel Lokridj Myullerni o'ziga tortgan narsa bu jonzotlarning aql bovar qilmaydigan, katta bo'lmagan genomlari edi. Salamanderlar taxminan 250 million yil oldin qurbaqalar bilan umumiy ajdoddan ajralib chiqishgan, ammo ularning genomlari o'rtacha to'qqiz baravar katta. Qushlar, baliqlar va sutemizuvchilar kabi boshqa hayvonlar bilan solishtirganda, salamander genomlari 15-x0201340 marta kattaroqdir.

"Bu g'alati hodisa", deydi Kolorado shtat universitetidan Myuller. "Bizni qiziqtiradi, chunki genomlar juda katta bo'lishi kamdan-kam uchraydi."

Yaqinda nashr etilgan tadqiqotda Genom biologiyasi evolyutsiyasi, Myuller va uning hamkasblari salamandrning genomik xususiyatlarini o'rganib chiqdilar va ular DNKga yopishib olishda kamdan-kam mahoratga ega ekanligini aniqladilar.

Barcha genomlar o'lchamlari bo'yicha o'zgarib turadi. Biroq, salamandrlar uchun o'chirishlar nisbatan kam uchraydi va ular sodir bo'lganda, boshqa umurtqali hayvonlar bilan solishtirganda o'rtachadan kamroq tayanch juftlari chiqariladi. Myullerning so'zlariga ko'ra, salamandrlar o'xshatish yo'li bilan yig'uvchilarning genetik ekvivalentidir. Ular boshqa turlarga qaraganda ko'proq "do'kon" qilmasliklari (yoki DNK to'plashlari) mumkin emas, lekin ular shkaflarini kamroq tozalaydilar va qachonki ular kichikroq sumkalarni tejamkor do'konga olib boradilar.

Ushbu tadqiqotda Kolorado jamoasi to'rtta salamander turining ko'chiriladigan elementlariga kiritish, o'chirish va almashtirish naqshlarini o'rganib chiqdi. Taqqoslash uchun ular boshqa beshta genomdan: primatlar (odamlar), kaltakesaklar, baliqlar, qushlar va boshqa amfibiyalar guruhidan (qurbaqalar) transpozisatsiya qilinadigan elementlarning yo'qotish darajasini taxmin qilishdi. Ba'zan "xudbin DNK" yoki "sakrab o'tuvchi genlar" deb ataladigan transposable elementlar DNK ketma-ketligi bo'lib, ular genomning qolgan qismidan ajralib turadigan o'z hayotiga ega. Ular o'zlarining nusxalarini yaratadilar, butun genomga tarqaladilar, lekin organizm uchun ko'p narsa qilmaydi. Aytishimiz mumkinki, ular oqsillarni kodlamaydi va (ushbu tadqiqotda ishlatiladigan segmentlar uchun) oqsillar ularga bog'lanmaydi. Ular mutatsiyaga uchraydi va betaraf rivojlanadi, go'yo selektsiya bosimisiz. Ko'chma elementlar ko'plab biotexnika va biomedikal ilovalarda qo'llanilganligi sababli, Myuller ularni chuqurroq tushunish tadqiqotchilarga ular bilan shug'ullanishga yordam beradi deb umid qiladi.

Yo'q qilish mutatsiyalarining sabablari bo'yicha olib borilgan tadqiqotlar shuni ko'rsatadiki, ular DNK replikatsiyasi va rekombinatsiyadagi xatolar, xromosomalar meioz paytida bo'limlarni almashtirganda. "Bu DNKni avloddan-avlodga saqlab qolish bilan shug'ullanadigan asosiy mexanizm", deydi Myuller. "Ushbu asosiy mexanizm bilan bog'liq muammolar mavjud bo'lganda, o'chirish hodisalari paydo bo'ladi."

Salamanderning yuqori DNKga sodiqligi mexanizmi noma'lum bo'lsa-da, Myuller salamanderlarda rekombinatsiya boshqa hayvonlarga qaraganda bir oz boshqacha ishlashi mumkinligiga shubha qiladi. "Bu kichik maslahat," deydi u, "yadro DNK mexanizmlaridagi farqlarga ishora qiladi - [butun hayot uchun] juda muhim narsaning o'zgarishi haqida o'ylash juda ajoyibdir."

Ushbu topilmalar Kiwoong Nam va Hans Ellegren (2012) tomonidan qilingan so'nggi ishlarga uyg'unlashtiruvchi akkord beradi, bu rekombinatsiya genomlarni ingichkalashini ko'rsatadi. Misol uchun, qushlar nisbatan kichik genomlarga ega va ular rekombinatsiya hodisalari orqali ko'p materiallarni yo'qotishga moyil bo'lib, ularning kichik genom hajmini yanada kuchaytiradi. Butun hayvonot olamida, aslida, DNKni yo'qotish darajasi va genom hajmi o'rtasida bog'liqlik borga o'xshaydi (shunga o'xshash naqshlar hasharotlarda ham topilgan).

1990-yillarda Garvard populyatsiyasi genetiki Den Hartl va uning hamkasblari tomonidan birinchi marta taklif qilinganida, bu fikr munozarali edi. "Shunday qilib, u o'tirdi. Endi odamlar unga qaytishmoqda", deydi Xartl. O'zining va boshqalarning g'oyalarini tasdiqlashdan tashqari, Xartl Myullerning ishini genomikadagi ba'zi hozirgi tafakkurlarga, xususan, ENCODE loyihasiga qiziqarli qarama-qarshilik deb biladi. ENCODE 2003 yilda Milliy Inson genomi tadqiqot instituti tomonidan inson genomidagi barcha funktsional elementlarni topish uchun ishga tushirilgan. 2012-yil sentabr oyida loyiha “[inson] genomining 80% biokimyoviy funksiyalarini” tayinlovchi natijalarni eʼlon qildi.

ENCODE ning asosiy taxmini shundan iboratki, agar oqsil DNK bo'limiga bog'lansa, bu muhim ahamiyatga ega. "Bu mutlaqo to'g'ri emas", deydi Xartl. "Bu funktsional bo'lishi mumkin, ammo bu DNKning ko'p qismi passiv ravishda olib borilganidan dalolat beradi. Kimdir menga salamandrlar faqat salamandr bo'lish uchun bu materiallarning barchasiga muhtojligini aytadimi?"

Ehtimol, yo'q va ularning mamont o'lchamidagi genomlari kutilgan noqulaylik tug'diradigan belgilarni keltirib chiqaradi. Katta genomga ega hayvonlar, masalan, ularning ko'p DNKlarini joylashtirish uchun kattaroq hujayralarga ega bo'lishi kerak. Bu rivojlanish uchun zarur bo'lgan vaqtni oshiradi va miyaning ma'lum bir o'lchamda qanchalik murakkablashishi mumkinligini kamaytiradi. "Siz ko'p sabablarga ko'ra katta genomlar tanlanishini kutgan edingiz", deydi Jokush. "Ammo evolyutsiya katta genomni yo'q qilgani yo'q. Bu juda intuitivdir."

Kodlanmagan DNKning roli va genom hajmining to'sqinlik yoki yordam berish darajasi hali ham ochiq savollar bo'lib qolmoqda va ehtimol bir muncha vaqt bo'ladi. Hozircha salamandrning ajoyib sahna ortidagi genetikasi ularning afsonaviy jozibali kuchlarini qo'shishi kifoya.


Sutemizuvchilarning eng katta genomi poliploid emas

Taxminan 40 million yil oldin, Janubiy Amerikada, qadimgi dunyodan kaviomorf kemiruvchilarning umumiy ajdodi kelganidan so'ng, katta o'zgarishlar yuz berdi.
Xususan, kaviomorf kolonistlari morfologiyasi, ekologiyasi va hayot tarixida sezilarli xilma-xillikni ko'rsatadigan 250 ga yaqin turdagi va 13 ta endemik Janubiy Amerika kemiruvchilar oilasining saqlanib qolgan evolyutsion naslini keltirib chiqara boshladilar (Fikr qiling, Yangi Dunyo kirpilari, chinchillalar va Gvineya). cho'chqalar). Qizig'i shundaki, kaviomorflar, shuningdek, sezilarli genomik o'zgarishlar (ya'ni, xromosomalarning soni, shakli va joylashishi kabi genom hajmi va tuzilishining evolyutsiyasi) tashuvchisi hisoblanadi. Xromosomalarning funktsional soni 10-118 gacha o'zgarib turadi, bundan tashqari, kaviomorflardagi genomik evolyutsiyaning eng ekstremal holatlari eng yuqori diversifikatsiya darajasiga ega bo'lgan guruhlarda uchraydi. Sutemizuvchilarda bu naqsh (turlanish va genomik evolyutsiyaning o'zaro bog'liq tezligi) kam uchraydi va uning kaviomorflarda mavjudligi genomik evolyutsiya, turlanish va molekulyar moslashuv o'rtasidagi bog'liqlik haqidagi tushunchamizdagi doimiy teshiklarni takrorlaydi.
Ushbu kaviomorf xromosoma kombinatoriyasining hozirgi (va taniqli) turi bu nom bilan ataladi. Tympanoctomys barrerae, yoki qizil vizkacha kalamush (1-rasm). Qizil vizkacha kalamushlar kichik kemiruvchilardir (agar siz Shimoliy Amerikada cho'lda yashovchi bo'lsangiz, kenguru kalamushning o'lchamini o'ylab ko'ring) yuqori kengliklarda yashaydi. cis-G'arbiy Argentinaning And cho'llari, ular asosan past osilgan sho'r mevalari bilan kun kechiradilar. Ajablanarlisi shundaki, hujayralar T. berrarae o'rtacha sutemizuvchilardan ikki baravar ko'proq va inson genomidan deyarli uch baravar katta bo'lgan yadro genomlari. Bu DNK massasi 102 ta katta xromosomaga qadoqlangan bo'lib, ular eng katta ma'lum bo'lgan sutemizuvchilar karyotipini (boliviya bambuk kalamushiga tegishli bo'lgan sharaf) o'z ichiga olmasa ham, uning eng yaqin qarindoshlaridan ikki baravar ko'pdir. Ma'lum bo'lgan eng yirik sutemizuvchilar genomiga ega bo'lish "evolyutsion qiziquvchanlik" maqomiga ega bo'lish uchun etarli, ammo bu bilan bog'liq asosiy savollar hali ham mavjud. Qanaqasiga va nima uchun qizil vizkacha kalamushning genomi juda katta bo'ldi.

“Evolyutsion munosabatlar, xromosoma soni (2n) va genom hajmi pikogrammada (C-qiymati) vizkacha kalamushlari va Octodontidae oilasining boshqa a'zolari (chapda). Qizil vizkacha kalamush T. barrerae El-Nixuil, Mendosa, Argentina (foto krediti: Fernanda Kuevas).” Evansning izohi va boshqalar. 2017.


Kaliforniya gigantlari: Qizil o'rmonlar va kitlar qanday qilib juda katta bo'ldi

Virjiniya shtatida yashovchi ekolog Jeff Atkins Muir-Vuds milliy yodgorligidagi ulkan qizil daraxt daraxtlarini ziyorat qilganida, u aqlini hayratda qoldirgan narsani ko'rdi.

“Men chodirning tepasidan suv tomchilari tushishini ko‘rganimni eslayman”, — deb yozdi u Twitter’da. "Va ularning qulashi uchun abadiy kerak bo'ldi. Men FOREVER demoqchiman!"

Qizil daraxtlar shunchalik balandki, o'rmon tagida turib, tepalarni ko'ra olmaysiz.

&ldquoSiz boshingizni orqaga tortasiz va yuqoriga, yuqoriga, yuqoriga, yuqoriga qaraysiz va tojga kirganingizda bu loyqa bo'lib qoladi "deydi Lyusi Kerxulas, Gumboldt shtat universitetining o'rmon fiziologiyasi professori. Siz nima bo'layotganini aniq bilolmaysiz. u erda, Agar aslida yuqoriga borib ko'tarilishni ekan,&rdquo qaysi Kerhoulas bor.

Kaliforniyadagi yoz gigantlar bilan dam olish uchun ajoyib vaqt: Yosemit milliy bog'idagi ulkan sekvoyalar yoki Big Surdan Oregon chegarasigacha bo'lgan o'rmonlardagi ulkan qizil daraxt daraxtlari. Mashhur kulrang kit migratsiya mavsumi allaqachon tugagan bo'lsa-da, yozgi kit kuzatuvchilari dunyodagi eng katta tirik hayvon: ko'k kitni ko'rishlari mumkin.

Ko‘k kit skeleti Kaliforniya Fanlar akademiyasida yillar davomida osilib turdi - yangi ko‘rgazma klassik namunaga e’tiborni qaratish uchun mo‘ljallangan. (Ketrin Uitni/Kaliforniya fanlar akademiyasi)

Kaliforniya gigantlari va nima uchun shtat bu gigantlarning vatani bo'lganligi haqida bilishning eng yaxshi usullaridan biri bu Kaliforniya Fanlar akademiyasining yangi ko'rgazmasiga tashrif buyurishdir. Quruqlik va dengiz gigantlari.

Kaliforniya va bizning sohilimiz yaqinidagi suvlar bu gigantlarning vatani ekanligi tasodifdir. Yangi eksponat tushuntirganidek, kattalik qisman bu yerdagi hayotning tafsilotlari va okean oqimlari va bizning mashhur tumanimizdan kelib chiqadi.

Quruqlik va dengiz gigantlari 15-iyun kuni ochilgan. Eng muhim voqealar quyidagilardan iborat:

  • Uzunligi 85 fut bo'lgan ko'k kit skeleti.
  • Mehmonlar qizil daraxt bo'lish nimani anglatishini his qilishlari mumkin bo'lgan immersiv tuman xonasi.
  • Qizil daraxtning ildizidan to tojigacha ekologiyasini aks ettiruvchi filmlar seriyasi, 6K aniqlikda dron tomonidan suratga olingan.
  • Dengiz sutemizuvchilarning bosh suyagi va skeletlari, shu jumladan massiv shimoliy fil muhri.

Kuchli shamollar okeanni qirg'oq bo'ylab yuqoriga ko'tarib, okeanning pastki qatlamlaridan yer yuzasiga ozuqa moddalarini olib chiqadi. Plankton va krill juda ko'p ko'payib, ko'k kitni oziq-ovqat bilan ta'minlaydi.

Xuddi shu shamollar Arktika kengliklaridan janubga sovuq suv olib keladi. Yozning iliq harorati o'sha sovuq suvga tushganda, tuman qatlami hosil bo'ladi. Tuman quruqlikka qarab tortilib, qirg'oq bo'yidagi qirmizi daraxtlarni ko'p miqdorda suv bilan ta'minlaydi. Qizil daraxtlar tumanga tegib, namlikning bir qismini barglari orqali o'zlashtirib, ildizlariga ko'proq o'tish qobiliyatini rivojlantirdi. Shunday qilib, okean oqimlari va ob-havo tizimlari Kaliforniyada kattalikni rivojlantirish uchun yaratilgan ekologik tizimda birlashadi.

Shunga qaramay, UC Devis paleontologi Geerat Vermeijning aytishicha, ekologiya gigantlar qanday qilib bunchalik kattalashgani haqida butun hikoyani aytib bera olmaydi. O'simliklar va hayvonlar kattalikni rivojlantira olishlari uchungina rivojlanmaydilar, xuddi mashina oldida yo'l borligi uchun oldinga siljishi va kimdir haydovchi o'rindig'iga o'tirib, uni yoqishi kerak. Boshqacha qilib aytganda, evolyutsion haydovchi ham bo'lishi kerak. Kattaroq bo'lishning afzalligi bo'lishi kerak.

Moviy kit 2008-yil 16-iyul kuni Kaliforniya shtatining Long-Bich sohilidagi Tinch okeanida havo teshigidan nafas chiqarmoqda. Uzunligi 33 metr (110 fut) va og‘irligi 181 metrik tonna (200 qisqa tonna) yoki undan ortiq. , er yuzida yashagan eng katta hayvon ekanligiga ishonishadi. (ROBYN BEK/AFP/Getty Images)

Dengiz devlari

Stenforddagi paleobiolog Uill Geartining fikricha, u ko'plab dengiz sutemizuvchilarni kattalashishga nima undaganini biladi: ular isinishlari kerak edi. Suv tanadan issiqlikni havoga qaraganda tezroq olib tashlaydi va nima uchun 60 darajali suvda gipotermiya bo'lishi mumkinligini tushuntiradi. Dengiz sutemizuvchisi har kuni bu bilan shug'ullanishi kerak va issiqlik yo'qotilishining oldini olishning eng yaxshi usullaridan biri kattaroq bo'lishdir.

&ldquoIchkidagi narsalar bilan solishtirganda teri miqdori kamayadi,&rdquo Gearty, "va shuning uchun ular kamroq issiqlikni yo'qotadilar".

Gearty sutemizuvchining suvda iliq bo'lishi uchun optimal o'lchamga ega bo'lishi kerakligini hisoblab chiqdi va ma'lum bo'lishicha, u taxminan manatee kattaligiga teng. Ko'pgina quruqlikdagi sutemizuvchilarga nisbatan, bu juda katta va biz ko'rib turgan ko'plab dengiz sutemizuvchilari bilan solishtirish mumkin. Ammo u ko'k kitdan ancha kichikroq.

O'tgan yili chop etilgan tadqiqotlar shuni ko'rsatdiki, eng katta kitlarning evolyutsiyasiga oziq-ovqat mavjudligi emas, balki oziq-ovqat zichligi sabab bo'lgan. Katta kitlar kichik kitlarga qaraganda zich krill cho'ntaklarini samaraliroq iste'mol qilishgan.

Ammo Vermeij boshqa farazni ma'qullaydi: qotil kitlar va ulkan akulalar.

&ldquoMa'lum bo'lishicha, eng katta kitlarning evolyutsiyasi qotil kitlar evolyutsiyasiga juda to'g'ri keladi&rdquo u.

Qotil kitlar juda katta, ammo ular ijtimoiy ovchilardir, bu ularga haqiqatan ham katta o'ljani yo'q qilishga imkon beradi. Boshqa erta kitlar Megalodon, burundan dumgacha 59 futga cho'zilgan ulkan akula bilan uchrashgan bo'lishi mumkin. Megalodondan kattaroq bo'lish kitlarga o'lja bo'lishdan qochishga yordam bergan bo'lar edi.

Qizil daraxt ko'pincha balandligi 300 futdan oshadi. (Ketrin Uitni/Kaliforniya fanlar akademiyasi)

Quruqlikda gigantlar

Ma'lum bo'lishicha, qizil daraxt ikkinchi xususiyatga ega bo'lib, ular tumandan suvni yutish qobiliyatiga o'xshab, ularga ulkan daraxtlar kabi gullab-yashnashiga imkon beradi: Qizil daraxt o'lmaydi.


Barcha 70 000 umurtqali hayvonlarning genomlarini o'qish loyihasi birinchi kashfiyotlar haqida xabar beradi

Bu bugungi kunda biologiyadagi eng jasoratli loyihalardan biri -- har bir qush, sutemizuvchi, kaltakesak, baliq va boshqa barcha umurtqali jonzotlarning butun genomini o'qish.

Va endi umurtqali hayvonlar genomi loyihasidan (VGP) birinchi katta foyda keladi: 25 turdagi to'liq, yuqori sifatli genomlarga yaqin, Govard Xyuz tibbiyot instituti (HHMI) tadqiqotchisi Erich Jarvis ko'plab mualliflar hisoboti bilan 2021 yil 28 aprelda jurnalda Tabiat. Bu turlarga katta taqa ko'rshapalak, Kanada silovsisi, platypus va kākāpō to'tiqush kiradi -- yo'qolib ketish xavfi ostida turgan umurtqali hayvonlarning birinchi yuqori sifatli genomlaridan biri.

Hujjat, shuningdek, olimlarga aniqlik va to'liqlikning yangi darajasiga erishish imkonini beradigan texnik yutuqlarni bayon qiladi va bugungi kunda yashovchi 70 000 ga yaqin umurtqali hayvonlarning genomlarini dekodlash uchun yo'l ochadi, deydi HHMI tergovchisi va tadqiqot muallifi Devid Xaussler, hisoblash genetiki Kaliforniya universiteti, Santa Kruz (UCSC). "Biz tabiatning barcha ekotizimlarni hayvonlarning aql bovar qilmaydigan xilma-xilligi bilan qanday to'ldirgani haqida ajoyib rasmga ega bo'lamiz."

Bir qator qo'shimcha hujjatlar bilan birgalikda ish ushbu va'dani amalga oshirishni boshlaydi. Loyiha jamoasi, masalan, zebra ispinozi genomida ilgari noma'lum bo'lgan xromosomalarni va marmoset va inson miyasi o'rtasidagi genetik farqlar haqida ajablantiradigan topilmani topdi. Yangi tadqiqot, shuningdek, kākāpō to'tiqush va yo'qolib ketish arafasida turgan vakita delfinini yo'q bo'lib ketishdan saqlab qolishga umid beradi.

"Ushbu 25 ta genom muhim bosqichni anglatadi", deb tushuntiradi Jarvis, VGP rahbari va Rokfeller universitetining neyrogenetik mutaxassisi. "Biz kutganimizdan ham ko'proq narsani o'rganmoqdamiz", deydi u. "Bu ish kelajakdagi narsalar uchun printsipial dalildir."

10K dan 70K gacha

VGPning muhim bosqichi yillar davomida ishlab chiqilmoqda. Loyihaning kelib chiqishi 2000-yillarning oxiriga borib taqaladi, o‘shanda Xaussler, genetik Stiven O'Brayen va San-Diego hayvonot bog‘ining tabiatni muhofaza qilish genetikasi bo‘yicha direktori Oliver Rayder katta o‘ylash vaqti keldi deb hisoblashgan.

Odamlar va meva chivinlari kabi bir nechta turlarni tartiblash o'rniga, nega "Genome 10K" dadil harakatda o'n ming hayvonlarning to'liq genomlarini o'qib chiqmaysiz? Biroq, o'sha paytda, narx yorlig'i yuzlab million dollarlarni tashkil etdi va reja hech qachon amalga oshmadi. "Hamma bu ajoyib g'oya ekanligini bilar edi, lekin hech kim buning uchun pul to'lashni xohlamadi", deb eslaydi HHMI tergovchisi va HHMI professori Bet Shapiro, UCSC evolyutsion biologi va hammuallifi. Tabiat qog'oz.

Bundan tashqari, olimlarning hayvonlar genomidagi barcha DNK harflarini talaffuz qilish yoki “ketmalash” bo‘yicha dastlabki urinishlari xatolarga to‘la edi. 2003 yilda birinchi qo'pol inson genomini to'ldirishda qo'llanilgan asl yondashuvda olimlar DNKni bir necha yuz harfdan iborat bo'lgan qisqa bo'laklarga bo'lishdi va bu harflarni o'qishdi. Keyin bo'laklarni to'g'ri tartibda yig'ish kabi dahshatli qiyin ish keldi. Usullar to'g'ri kelmadi, natijada noto'g'ri yig'ilishlar, katta bo'shliqlar va boshqa xatolar yuzaga keldi. Ko'pincha genlarni individual xromosomalarga solishtirish ham mumkin emas edi.

Qisqaroq o'qish bilan yangi ketma-ketlik texnologiyalarini joriy etish minglab genomlarni o'qish g'oyasini amalga oshirishga yordam berdi. Ushbu tez rivojlanayotgan texnologiyalar xarajatlarni pasaytirdi, lekin genom yig'ish strukturasining sifatini ham pasaytirdi. Keyin 2015-yilda Xaussler va uning hamkasblari qushlarga boshqalarning qo‘shiqlarini tinglagandan so‘ng yangi kuylarni chalishlariga imkon beruvchi murakkab neyron zanjirlarni ochish bo‘yicha kashshof Jarvisni olib kelishdi. Jarvis allaqachon katta va murakkab harakatlarni boshqarish qobiliyatini namoyish etgan edi. 2014-yilda u yuzdan ortiq hamkasblari bilan 48 turdagi qushlarning genomlarini ketma-ketlashtirdi, bu esa vokal o‘rganishda ishtirok etuvchi yangi genlarni aniqladi. "Devid va boshqalar mendan Genome 10K loyihasiga rahbarlik qilishimni so'rashdi", deb eslaydi Jarvis. "Ular mening shaxsiyatim borligini his qilishdi." Yoki, Shapiro aytganidek: "Erich juda tajovuzkor lider, chiroyli ma'noda. U nima bo'lishini xohlasa, amalga oshiradi".

Jarvis barcha umurtqali hayvonlar genomlarini o'z ichiga olgan Genome 10K g'oyasini kengaytirdi va rebrending qildi. U, shuningdek, Rokfellerda yangi sekvensiya markazini ishga tushirishga yordam berdi, u Germaniyadagi Maks Plank institutida sobiq HHMI Janelia tadqiqot kampus guruhi rahbari Gen Myers boshchiligida va boshqasi Buyuk Britaniyadagi Sanger institutida Richard Durbin va Mark Blaxter boshchiligida. , hozirda VGP genom ma'lumotlarining ko'p qismini ishlab chiqaradi. U Milliy Inson genomi tadqiqot institutining (NHGRI) yetakchi genom mutaxassisi Adam Fillipidan VGP yig'ish guruhiga raislik qilishni so'radi. Keyin u 60 ga yaqin eng yaxshi olimlarni o'zlari qiziqtirgan genomlarni hal qilish uchun markazlardagi ketma-ketlik xarajatlarini to'lash uchun o'zlarining grant mablag'laridan foydalanishga tayyor. kākāpō va vaquita namunalarini “xalqaro hamkorlikning go'zal namunasi” sifatida olish, deydi Rokfellerdagi VGP dasturi direktori Sadye Paez.

Eshiklarni ochish

Katta tadqiqotchilar jamoasi bir qator texnologik yutuqlarni qo'lga kiritdi. Yangi ketma-ketlik mashinalari ularga atigi bir necha yuz emas, 10 000 yoki undan ortiq harf uzunlikdagi DNK qismlarini o'qish imkonini beradi. Tadqiqotchilar, shuningdek, ushbu segmentlarni alohida xromosomalarga yig'ishning aqlli usullarini ishlab chiqdilar. Ular qaysi genlar ona va otadan meros bo'lib qolganligini aniqlashga muvaffaq bo'lishdi. Bu "noto'g'ri takrorlash" deb nomlanuvchi, ayniqsa, murakkab muammoni hal qiladi, bu erda olimlar bir xil genning ona va ota nusxalarini ikkita alohida gen sifatida noto'g'ri belgilashadi.

"I think this work opens a set of really important doors, since the technical aspects of assembly have been the bottleneck for sequencing genomes in the past," says Jenny Tung, a geneticist at Duke University, who was not directly involved with the research. Having high-quality sequencing data "will transform the types of question that people can ask," she says.

The team's improved accuracy shows that previous genome sequences are seriously incomplete. In the zebra finch, for example, the team found eight new chromosomes and about 900 genes that had been thought to be missing. Previously unknown chromosomes popped up in the platypus as well, as members of the team reported online in Tabiat earlier this year. The researchers also plowed through, and correctly assembled, long stretches of repetitive DNA, much of which contain just two of the four genetic letters. Some scientists considered these stretches to be non-functional "junk" or "dark matter." Noto'g'ri. Many of the repeats occur in regions of the genome that code for proteins, says Jarvis, suggesting that the DNA plays a surprisingly crucial role in turning genes on or off.

That's just the start of what the Tabiat paper envisions as "a new era of discovery across the life sciences." With every new genome sequence, Jarvis and his collaborators uncover new -- and often unexpected -- findings. Jarvis's lab, for example, has finally nabbed the regulatory region of a key gene parrots and songbirds need to learn tunes next, his team will try to figure out how it works. The marmoset genome yielded several surprises. While marmoset and human brain genes are largely conserved, the marmoset has several genes for human pathogenic amino acids. That highlights the need to consider genomic context when developing animal models, the team reports in a companion paper in Tabiat. And in findings also published last year in Tabiat, a group led by Professor Emma Teeling at University College Dublin in Ireland discovered that some bats have lost immunity-related genes, which could help explain their ability to tolerate viruses like SARS-CoV-2, which causes COVID-19.

The new information also may boost efforts to save rare species. "It is a critically important moral duty to help species that are going extinct," Jarvis says. That's why the team collected samples from a kākāpō parrot named Jane, part of a captive breeding program that has brought the parrot back from the brink of extinction. In a paper published in the new journal Cell Genomics, of the Cell family of journals, Nicolas Dussex at the University of Otago and colleagues described their studies of Jane's genes along with other individuals. The work revealed that the last surviving kākāpō population, isolated on an island off New Zealand for the last 10,000 years, has somehow purged deleterious mutations, despite the species' low genetic diversity. A similar finding was seen for the vaquita, with an estimated 10-20 individuals left on the planet, in a study published in Molecular Ecology Resources, led by Phil Morin at the National Oceanic and Atmospheric Administration Fisheries in La Jolla, California. "That means there is hope for conserving the species," Jarvis concludes.

A clear path

VGP is now focused on sequencing even more species. The project team's next goal is finishing 260 genomes, representing all vertebrate orders, and then snaring enough funding to tackle thousands more, representing all families. That work won't be easy, and it will inevitably bring new technical and logistical challenges, Tung says. Once hundreds or even thousands of animals readily found in zoos or labs have been sequenced, scientists may face ethical hurdles obtaining samples from other species, especially when the animals are rare or endangered.

But with the new paper, the path ahead looks clearer than it has in years. The VGP model is even inspiring other large sequencing efforts, including the Earth Biogenome Project, which aims to decode the genomes of all eukaryotic species within 10 years. Perhaps for the first time, it seems possible to realize the dream that Haussler and many others share of reading every letter of every organism's genome. Darwin saw the enormous diversity of life on Earth as "endless forms most beautiful," Haussler observes. "Now, we have an incredible opportunity to see how those forms came about."


What is junk DNA, and what is it worth?

Our genetic blueprint consists of 3.42 billion nucleotides packaged in 23 pairs of linear chromosomes. Most mammalian genomes are of comparable size&mdashthe mouse script is 3.45 billion nucleotides, the rat's is 2.90 billion, the cow's is 3.65 billion&mdashand code for a similar number of genes: about 35,000. Of course, extremes exist: the bent-winged bat (Miniopterus schreibersi) has a relatively small 1.69-billion-nucleotide genome the red viscacha rat (Tympanoctomys barrerae) has a genome that is 8.21 billion nucleotides long. Among vertebrates, the highest variability in genome size exists in fish: the green puffer fish (Chelonodon fluviatilis) genome contains only 0.34 billion nucleotides, while the marbled lungfish (Protopterus aethiopicus) genome is gigantic, with almost 130 billion. Interestingly, all animals have a large excess of DNA that does not code for the proteins used to build bodies and catalyze chemical reactions within cells. In humans, for example, only about 2 percent of DNA actually codes for proteins.

For decades, scientists were puzzled by this phenomenon. With no obvious function, the noncoding portion of a genome was declared useless or sometimes called "selfish DNA," existing only for itself without contributing to an organism's fitness. In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome.

Typically these sections of junk DNA come about through transposition, or movement of sections of DNA to different positions in the genome. As a result, most of these regions contain multiple copies of transposons, which are sequences that literally copy or cut themselves out of one part of the genome and reinsert themselves somewhere else.

Elements that use copying mechanisms to move around the genome increase the amount of genetic material. In the case of "cut and paste" elements, the process is slower and more complicated, and involves DNA repair machinery. Nevertheless, if transposon activity happens in cells that give rise to either eggs or sperm, these genes have a good chance of integrating into a population and increasing the size of the host genome.

Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage? Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. It appears that these transposable elements are not useless DNA. Instead, they interact with the surrounding genomic environment and increase the ability of the organism to evolve by serving as hot spots for genetic recombination and by providing new and important signals for regulating gene expression.

Genomes are dynamic entities: new functional elements appear and old ones become extinct. And so, junk DNA can evolve into functional DNA. The late evolutionary biologist Stephen Jay Gould and paleontologist Elisabeth Vrba, now at Yale University, employed the term "exaptation" to explain how different genomic entities may take on new roles regardless of their original function&mdasheven if they originally served no purpose at all. With the wealth of genomic sequence information at our disposal, we are slowly uncovering the importance of non-protein-coding DNA.

In fact, new genomic elements are being discovered even in the human genome, five years after the deciphering of the full sequence. Last summer developmental biologist Gill Bejerano, then a postdoctoral fellow at the University of California, Santa Cruz, and now a professor at Stanford University, and his colleagues discovered that during vertebrate evolution, a novel retroposon&mdasha DNA fragment, reverse-transcribed from RNA, that can insert itself anywhere in the genome&mdashwas exapted as an enhancer, a signal that increases a gene's transcription. On the other hand, anonymous sequences that are nonfunctional in one species may, in another organism, become an exon&mdasha section of DNA that is eventually transcribed to messenger RNA. Izabela Makalowska of Pennsylvania State University recently showed that this mechanism quite often leads to another interesting feature in the vertebrate genomes, namely overlapping genes&mdashthat is, genes that share some of their nucleotides.

These and countless other examples demonstrate that repetitive elements are hardly "junk" but rather are important, integral components of eukaryotic genomes. Risking the personification of biological processes, we can say that evolution is too wise to waste this valuable information.


Xulosa

So far, studies in genomics have only scratched the surface of microbial diversity and have revealed how little is known about microbial species. In the next few years, more than 100 projects for sequencing microbial genomes should be completed, providing the scientific community with information on more than 300,000 predicted genes. A significant number of these genes will be novel and of unknown function. These novel genes represent exciting new opportunities for future research and potential sources of biological resources to be explored and exploited. The benefits of comparative genomics in understanding biochemical diversity, virulence and pathogenesis, and the evolution of species has been unequivocally demonstrated and the usefulness of comparative techniques will improve as more genomes become available. One of the major challenges is to develop techniques for assessing the function of novel genes on a large scale and integrating information on how genes and proteins interact at the cellular level to create and maintain a living organism. It is not unreasonable to expect that, by expanding our understanding of microbial biology and biodiversity, great strides can be made in the diagnosis and treatment of infectious diseases and in the identification of useful functions in the microbial world that could be applied to agricultural and industrial processes.


What makes a tree a tree?

Several years ago, after Thanksgiving dinner at my parents’ house in Vermont, lightning struck a backyard maple tree. There was a ferocious crack and the darkness outside the kitchen windows briefly turned day-bright. It wasn’t until spring that we knew for certain the tree was dead.

This maple was a youngster, its trunk the diameter of a salad plate. Were its life not cut short by catastrophe, the tree might have lived 300 years. But death by disaster is surprisingly common in trees. Sometimes it results from a tragic human blunder, as with the 3,500-year-old Florida bald cypress that was killed in 2012 by an intentionally lit fire. More often, calamity strikes via extreme weather — drought, wind, fire or ice. Of course, trees also are susceptible to pests and disease adversaries like wood-decaying fungi can significantly shorten a tree’s life. But the ones that manage to evade such foes can live for an incredibly long time.

If one is pressed to describe what makes a tree a tree, long life is right up there with wood and height. While many plants have a predictably limited life span (what scientists call “programmed senescence”), trees don’t, and many persist for centuries. In fact, that trait — indefinite growth — could be science’s tidiest demarcation of treeness, even more than woodiness. Yet it’s only helpful to a point. We think we know what trees are, but they slip through the fingers when we try to define them.

Centuries of pondering — and squabbling about — trees

Getting it ripe

Plant, reap, repeat — and now rethink

Trees don’t cluster into one clear group: They emerge in multiple lineages and have adopted multiple strategies to become what they are. Take longevity. A classic example of the Methuselah-ness of trees is the current record-holder, a 5,067-year-old great bristlecone pine that grows high in the White Mountains of California. (That tree was almost 500 years old when the first pyramids were built in Egypt.) Scientists speculate that the hardy bristlecones owe their endurance largely to location: They avoid fires that sweep through lower elevations and pests that can’t stomach the harsh terrain of the subalpine zone. The giant sequoias, a short way down the mountains from the bristlecones, take an entirely different longevity tack. These beasts — their trunks can be more than 30 feet across — live thousands of years, fighting fire and pestilence with thick, resistant bark and plentiful in-house repellent compounds.

Perhaps the world’s largest trees by volume, giant sequoias can live thousands of years, thanks in part to fire-resistant, fibrous bark, which can be two feet thick.

CREDIT: INGE JOHNSSON / ALAMY STOCK PHOTO

Some 400 miles to the east, a spindly wisp of a tree has both the bristlecones and the sequoias beat when it comes to lifespan — through another strategy altogether. The quaking aspen (Populus tremuloides) — a tree you can wrap your arms around that rarely grows taller than 50 feet — excels at sending up new shoots from its base. This results in giant stands of “trees” that are, in fact, one genetic individual connected beneath the ground. A Utah colony of quaking aspen is estimated to be 80,000 years old. Neanderthals were around back then.

While individuals in this Utah grove of aspen typically don’t live more than 50 years, each trunk is part of a giant clone estimated to be 80,000 years old.

Once you add clones to the mix, trees quickly lose their claim on old age. King’s holly (Lomatia tasmanica) is a shiny green shrub native to Tasmania (shrubs, technically speaking, aren’t trees because they don’t have a central, dominant stem). There is only one population of king’s holly in the world, and scientists think it’s entirely clonal: Although it does occasionally flower, its fruit has never been seen. Recent radiocarbon dating suggests that it (they?) is at least 43,000 years old. Up there too is a scrubby ring of creosote bush out in the Mojave Desert of California, called “King Clone,” with an estimated age of 11,700 years. Longevity is wholly unsatisfying in a search for a unified “treeness of trees,” as forester Ronald Lanner terms it in a 2002 essay in Ageing Research Reviews.

Geneticist Andrew Groover of the US Forest Service Pacific Southwest Research Station in Davis, California, also spends a lot of time thinking about trees. He is quick to acknowledge that defining them is problematic. “Visit your favorite plant nursery and you will find plants categorized by their appearance and function, including a group categorized as ‘trees’,” he writes in a 2005 paper in O‘simlikshunoslikdagi yo‘nalishlar, “ What genes make a tree a tree?” “This categorization is intuitive and practical but contrived.”

Groover points to wood, surely a defining feature of trees, as a case in point. “True” trees (we’ll get to that later) make wood through what scientists call secondary growth this allows trees to grow out (thicken), in addition to growing up. Secondary growth emerges from a ring of specialized cells that encircle the stem. Called the vascular cambium, these cells divide in two directions: toward the outside of the tree, yielding bark, and toward the center of the tree, yielding wood. Year after year, this wood is deposited in new inner rings of growth that are doped with cellulose and the long, rigid polymer called lignin. After this cellular stiffening, the wood cells are killed and dismantled, for the most part, until nothing but their rigid walls remain.

Part of what makes a tree a tree is the ability to make wood, a process that originates with the band of cells called the vascular cambium, seen here between the bark (blue, outer cells) and wood (whitish middle bands of cells).

CREDIT: BERKSHIRE COMMUNITY COLLEGE BIOSCIENCE IMAGE LIBRARY

In plants that exist today, secondary growth probably had a single evolutionary origin, although the now-diminutive club mosses and horsetails invented their own version some 300 million years ago, enabling the extinct Lepidodendron, for example, to grow more than 100 feet tall. But secondary growth doesn’t automatically lead to treeness: Despite that single origin, woodiness pops up scattershot across the plant family tree. Some groups of plants have lost the ability to form wood woodiness has reappeared in lineages where it had vanished. It seems to evolve fairly quickly after plants colonize islands. Hawaii, for example, has woody violets, and the Canary Islands have dandelion trees.

The very concept of woodiness is quite flexible, belying its literal robustness — think of the stiff stems of garden salvia or lavender. It’s not a matter of present or absent, but a matter of degree. “Non-woody herbs and large woody trees can be thought to represent two ends of a continuum, and the degree of woodiness expressed by a given plant can be influenced by environmental conditions,” Groover and a colleague write in a 2010 review in Yangi fitolog. “Indeed, the terms ‘herbaceous’ and ‘woody’, while practical, do not acknowledge the vast anatomical variation and degrees of woodiness among plants variously assigned to these classes.”

Molecular biology offers some insights into why the ability to make wood is maintained and reappears so often in plant evolution. Genes that are involved in regulating the growing shoot — the upward, “primary” growth of trees and non-trees alike — are also active during the secondary growth that yields wood. This suggests that these already-existing and essential shoot-growth genes were co-opted during the evolution of woodiness. And it might explain why the ability to become woody is maintained in non-woody plants and why it’s relatively easy, from an evolutionary standpoint, to dial woodiness back up.

That said, you don’t need wood to be a tree. Monocots, an enormous group of plants that lost the ability to undergo secondary growth, have several arborescent members that aren’t “true” trees but sure look like them. Bananas grow tall with what appears to be a trunk but is really a “pseudostem” mass of tightly packed, overlapping leaf bases or sheaths. The true stem of a banana plant emerges only when it’s time to flower, pushing itself up and out through the leaf sheaths. Yet banana trees can be more than 10 feet tall. The family of palms, also monocots, grow tall by extending their initial, fat shoot topped by an enormous bud (note that palm stems don't widen as they grow tall).

A banana tree’s trunk doesn’t have the wood-making cells typical of most trees. It’s made up of overlapping fleshy leaf bases (shown here in cross section).

CREDIT: NIGEL CATTLIN / ALAMY STOCK PHOTO

Given all this, perhaps it’s not surprising that a recent analysis of tree genomes tells us little about the defining features of trees. Geneticist David Neale of UC Davis and colleagues pored over results from the 41 genomes (including grape) that have been sequenced, beginning with black cottonwood in 2006. Their analysis, published last year in the O'simliklar biologiyasining yillik sharhi, did find that trees making edible fruits often have an outsized number of genes devoted to making and transporting sugars, compared with non-edible-fruit trees. Then again, so do grapes and tomatoes. Several trees, including spruce, apple and some eucalyptus, have expanded genetic toolkits for dealing with environmental stresses such as drought or cold. But so do many herbaceous plants, including spinach and Arabidopsis, that weedy little lab rat of the plant world that is about as un-treelike as you can get.

So far, there is no standout gene or set of genes that confers treeness, nor any particular genome feature. Complexity? Nope: Full-on, whole-genome duplication (an often-used proxy for complexity) is prevalent throughout the plant kingdom. Genome size? Nope: Both the largest and smallest plant genomes belong to herbaceous species (Paris japonica va Genlisea tuberosa, respectively — the former a showy little white-flowered herb, the latter a tiny, carnivorous thing that traps and eats protozoans).

A chat with Neale confirms that tree-ness is probably more about what genes are turned on than what genes are present. “From the perspective of the genome, they basically have all the same stuff as herbaceous plants,” he says. “Trees are big, they’re woody, they can get water from the ground to up high. But there does not seem to be some profound unique biology that distinguishes a tree from a herbaceous plant.”

Notwithstanding the difficulty in defining them, being a tree has undeniable advantages — it allows plants to exploit the upper reaches where they can soak up sunlight and disperse pollen and seeds with less interference than their ground-dwelling kin. So maybe it’s time to start thinking of daraxt as a verb, rather than a noun — tree-ing, or tree-ifying. It’s a strategy, a way of being, like swimming or flying, even though to our eyes it’s happening in very slow motion. Tree-ing with no finish in sight — until an ax, or a pest, or a bolt of Thanksgiving lightning strikes it down.

Rachel Ehrenberg covers the intersection of plants, food and policy from Boston. Reach her at [email protected] or on twitter: @Rachelwrit.


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