Reference genome of the Virginia rail, Rallus limicola.
Reference genome of the Virginia rail, Rallus limicola.
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DOI：
10.1093/jhered/esad026
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发表时间：
2023-06-22
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--
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弗吉尼亚秧鸡（Rallus limicola）是秧鸡科（Rallidae）的一员，该科还包括许多其他种类的秘密和研究不足的湿地鸟类。牠们在北美洲广泛分布，被认为是单一物种，在那里牠们被当作猎鸟，通常有慷慨的收获限制，尽管缺乏系统的人口调查，以及许多地区由于湿地丧失和退化而减少的证据。为了帮助进一步了解这一难以捉摸的物种的地理学，生物学和生态学，我们报告了弗吉尼亚州铁路的第一个参考基因组组装，作为加州保护基因组学项目（CCGP）的一部分。我们使用Pacific Biosciences HiFi长读段和Hi-C染色质邻近测序技术进行了从头基因组组装，估计测序错误率为0.191%。组装体由跨越1.39 Gb的1，102个支架组成，其中重叠群N50为11.0 Mb，支架N50为25.3 Mb，最大重叠群为45 Mb，最大支架为128.4 Mb。它具有96.9%的高BUSCO完整性评分，代表了Rallus属的第一个基因组组装。这种基因组组装将有助于解决有关铁轨复杂进化历史的问题，并评估铁轨在气候变化和栖息地丧失和破碎化日益增长的威胁下进行适应性进化的潜力。它还将通过量化弗吉尼亚铁路的灵活性、人口连通性和有效人口规模，为铁路保护工作提供宝贵的资源。
The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.
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影响因子：
46.9
作者：
Cheng, Haoyu;Jarvis, Erich D.;Fedrigo, Olivier;Koepfli, Klaus-Peter;Urban, Lara;Gemmell, Neil J.;Li, Heng
通讯作者：
Li, Heng
影响因子：
2.6
作者：
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通讯作者：
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通讯作者：
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影响因子：
9.2
作者：
Korlach J;Gedman G;Kingan SB;Chin CS;Howard JT;Audet JN;Cantin L;Jarvis ED
通讯作者：
Jarvis ED
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