Toward a genome sequence for every animal: Where are we now?
Toward a genome sequence for every animal: Where are we now?
复制标题
DOI：
10.1073/pnas.2109019118
复制
发表时间：
2021-12-28
影响因子：
11.1
通讯作者：
Frandsen PB
中科院分区：
文献类型：
--
作者：
Hotaling S;Kelley JL;Frandsen PB
在不到25年的时间里，动物基因组科学领域已经从一个寻求第一次瞥见生命之树基因组序列的学科转变为一个全球性的企业，其目标是为地球上所有的真核生物多样性进行基因组测序[H。a. Lewin等人，Proc. Natl. Acad. sci. U.S.A. 115，4325 - 4333（2018）]。随着该领域的快速发展，重要的是要评估已经取得的进展，以最好地告知学科的未来。在这个角度来看，我们提供了一个当代的，定量的概述动物基因组测序。我们确定了世界上最广泛的基因数据库GenBank中最好的可用基因组组装，涵盖24个门的3，278种独特动物物种。我们评估了主要分支的分类表示，组装质量和注释状态。我们表明，虽然发生了巨大的分类学进展，在基因组的代表性存在明显的差异，突出的系统性的脊椎动物和节肢动物的代表性不足。在组装质量方面，长读段测序极大地提高了连续性，而基因注释仅适用于34.3%的分类群。此外，我们表明，动物基因组科学近年来已经多样化，参与的研究人员不断扩大。然而，该领域似乎仍然由全球北方的机构主导，这些机构被列为77%的大会的提交机构。最后，我们提出了提高基因组资源可用性和研究价值的建议，同时也扩大了全球代表性。
In less than 25 y, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earth’s eukaryotic diversity [H. A. Lewin et al., Proc. Natl. Acad. Sci. U.S.A. 115, 4325–4333 (2018)]. As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the discipline’s future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies in GenBank, the world’s most extensive genetic database, for 3,278 unique animal species across 24 phyla. We assessed taxonomic representation, assembly quality, and annotation status for major clades. We show that while tremendous taxonomic progress has occurred, stark disparities in genomic representation exist, highlighted by a systemic overrepresentation of vertebrates and underrepresentation of arthropods. In terms of assembly quality, long-read sequencing has dramatically improved contiguity, whereas gene annotations are available for just 34.3% of taxa. Furthermore, we show that animal genome science has diversified in recent years with an ever-expanding pool of researchers participating. However, the field still appears to be dominated by institutions in the Global North, which have been listed as the submitting institution for 77% of all assemblies. We conclude by offering recommendations for improving genomic resource availability and research value while also broadening global representation.
登录
查看更多内容
影响因子：
56.9
作者：
Nurk, Sergey;Koren, Sergey;Rhie, Arang;Rautiainen, Mikko;Bzikadze, Andrey V;Mikheenko, Alla;Vollger, Mitchell R;Altemose, Nicolas;Uralsky, Lev;Gershman, Ariel;Aganezov, Sergey;Hoyt, Savannah J;Diekhans, Mark;Logsdon, Glennis A;Alonge, Michael;Antonarakis, Stylianos E;Borchers, Matthew;Bouffard, Gerard G;Brooks, Shelise Y;Caldas, Gina V;Chen, Nae-Chyun;Cheng, Haoyu;Chin, Chen-Shan;Chow, William;de Lima, Leonardo G;Dishuck, Philip C;Durbin, Richard;Dvorkina, Tatiana;Fiddes, Ian T;Formenti, Giulio;Fulton, Robert S;Fungtammasan, Arkarachai;Garrison, Erik;Grady, Patrick G S;Graves-Lindsay, Tina A;Hall, Ira M;Hansen, Nancy F;Hartley, Gabrielle A;Haukness, Marina;Howe, Kerstin;Hunkapiller, Michael W;Jain, Chirag;Jain, Miten;Jarvis, Erich D;Kerpedjiev, Peter;Kirsche, Melanie;Kolmogorov, Mikhail;Korlach, Jonas;Kremitzki, Milinn;Li, Heng;Maduro, Valerie V;Marschall, Tobias;McCartney, Ann M;McDaniel, Jennifer;Miller, Danny E;Mullikin, James C;Myers, Eugene W;Olson, Nathan D;Paten, Benedict;Peluso, Paul;Pevzner, Pavel A;Porubsky, David;Potapova, Tamara;Rogaev, Evgeny I;Rosenfeld, Jeffrey A;Salzberg, Steven L;Schneider, Valerie A;Sedlazeck, Fritz J;Shafin, Kishwar;Shew, Colin J;Shumate, Alaina;Sims, Ying;Smit, Arian F A;Soto, Daniela C;Sovic, Ivan;Storer, Jessica M;Streets, Aaron;Sullivan, Beth A;Thibaud-Nissen, Francoise;Torrance, James;Wagner, Justin;Walenz, Brian P;Wenger, Aaron;Wood, Jonathan M D;Xiao, Chunlin;Yan, Stephanie M;Young, Alice C;Zarate, Samantha;Surti, Urvashi;McCoy, Rajiv C;Dennis, Megan Y;Alexandrov, Ivan A;Gerton, Jennifer L;O'Neill, Rachel J;Timp, Winston;Zook, Justin M;Schatz, Michael C;Eichler, Evan E;Miga, Karen H;Phillippy, Adam M
通讯作者：
Phillippy, Adam M
影响因子：
5.4
作者：
Danovaro R;Dell'Anno A;Pusceddu A;Gambi C;Heiner I;Kristensen RM
通讯作者：
Kristensen RM
影响因子：
64.8
作者：
Meyer A;Schloissnig S;Franchini P;Du K;Woltering JM;Irisarri I;Wong WY;Nowoshilow S;Kneitz S;Kawaguchi A;Fabrizius A;Xiong P;Dechaud C;Spaink HP;Volff JN;Simakov O;Burmester T;Tanaka EM;Schartl M
通讯作者：
Schartl M
影响因子：
7.7
作者：
Greenhalgh R;Dermauw W;Glas JJ;Rombauts S;Wybouw N;Thomas J;Alba JM;Pritham EJ;Legarrea S;Feyereisen R;Van de Peer Y;Van Leeuwen T;Clark RM;Kant MR
通讯作者：
Kant MR
影响因子：
64.8
作者：
Rhie A;McCarthy SA;Fedrigo O;Damas J;Formenti G;Koren S;Uliano-Silva M;Chow W;Fungtammasan A;Kim J;Lee C;Ko BJ;Chaisson M;Gedman GL;Cantin LJ;Thibaud-Nissen F;Haggerty L;Bista I;Smith M;Haase B;Mountcastle J;Winkler S;Paez S;Howard J;Vernes SC;Lama TM;Grutzner F;Warren WC;Balakrishnan CN;Burt D;George JM;Biegler MT;Iorns D;Digby A;Eason D;Robertson B;Edwards T;Wilkinson M;Turner G;Meyer A;Kautt AF;Franchini P;Detrich HW 3rd;Svardal H;Wagner M;Naylor GJP;Pippel M;Malinsky M;Mooney M;Simbirsky M;Hannigan BT;Pesout T;Houck M;Misuraca A;Kingan SB;Hall R;Kronenberg Z;Sović I;Dunn C;Ning Z;Hastie A;Lee J;Selvaraj S;Green RE;Putnam NH;Gut I;Ghurye J;Garrison E;Sims Y;Collins J;Pelan S;Torrance J;Tracey A;Wood J;Dagnew RE;Guan D;London SE;Clayton DF;Mello CV;Friedrich SR;Lovell PV;Osipova E;Al-Ajli FO;Secomandi S;Kim H;Theofanopoulou C;Hiller M;Zhou Y;Harris RS;Makova KD;Medvedev P;Hoffman J;Masterson P;Clark K;Martin F;Howe K;Flicek P;Walenz BP;Kwak W;Clawson H;Diekhans M;Nassar L;Paten B;Kraus RHS;Crawford AJ;Gilbert MTP;Zhang G;Venkatesh B;Murphy RW;Koepfli KP;Shapiro B;Johnson WE;Di Palma F;Marques-Bonet T;Teeling EC;Warnow T;Graves JM;Ryder OA;Haussler D;O'Brien SJ;Korlach J;Lewin HA;Howe K;Myers EW;Durbin R;Phillippy AM;Jarvis ED
通讯作者：
Jarvis ED