The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.
The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.
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DOI：
10.1093/gigascience/giy141
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发表时间：
2018-12-01
期刊：
影响因子：
9.2
通讯作者：
Hiller M
中科院分区：
文献类型：
--
作者：
Roscito JG;Sameith K;Pippel M;Francoijs KJ;Winkler S;Dahl A;Papoutsoglou G;Myers G;Hiller M
爬行动物是一个物种丰富的群体，具有很大的表型和生活史的多样性，但在脊椎动物物种的基因组测序高度不足。在这里，我们报告了一个高质量的基因组组装的tegu蜥蜴，萨尔瓦多meritrium，第一lacertoid与测序的基因组。我们结合了74X Illumina短读、29.8X Pacific Biosciences长读和光学映射数据，以生成具有55.4 Mb的支架N50值的高质量组装体。该集合体的重叠群N50值为521 Kb，使其成为迄今为止最连续的爬行动物集合体。我们发现，泰加大会具有最高的完整性的编码基因和保守的非外显子元件（CNEs）相比，其他爬行动物。此外，泰古大会有最高数量的进化保守的CNE对，证实了高的组装邻接基因间区域。与其他爬行动物一样，长散布的核元件构成了最丰富的转座子类。我们使用转录组学数据、同源性和从头基因预测来注释22，413个编码基因，其中16，995个（76%）可能具有CESAR衍生基因映射推断的人类直系同源物。最后，我们产生了一个多基因组比对，包括10个有鳞动物和7个其他的物种，并确定了保守的区域，在进化的约束。CNE覆盖泰加基因组的38 Mb（1.8%），其中3.3 Mb的这些元素是鳞状细胞特异性的。与胎盘哺乳动物特异性CNE相反，这些鳞状细胞特异性CNE（<20 Kb）中很少与转座子重叠，突出了谱系特异性CNE如何在这两个分支中起源的差异。泰古蜥蜴基因组与多基因组比对和全面的保守元件数据集一起为爬行动物和其他爬行动物的比较基因组研究提供了宝贵的资源。
Reptiles are a species-rich group with great phenotypic and life history diversity but are highly underrepresented among the vertebrate species with sequenced genomes. Here, we report a high-quality genome assembly of the tegu lizard, Salvator merianae, the first lacertoid with a sequenced genome. We combined 74X Illumina short-read, 29.8X Pacific Biosciences long-read, and optical mapping data to generate a high-quality assembly with a scaffold N50 value of 55.4 Mb. The contig N50 value of this assembly is 521 Kb, making it the most contiguous reptile assembly so far. We show that the tegu assembly has the highest completeness of coding genes and conserved non-exonic elements (CNEs) compared to other reptiles. Furthermore, the tegu assembly has the highest number of evolutionarily conserved CNE pairs, corroborating a high assembly contiguity in intergenic regions. As in other reptiles, long interspersed nuclear elements comprise the most abundant transposon class. We used transcriptomic data, homology- and de novo gene predictions to annotate 22,413 coding genes, of which 16,995 (76%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. CNEs cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being squamate specific. In contrast to placental mammal-specific CNEs, very few of these squamate-specific CNEs (<20 Kb) overlap transposons, highlighting a difference in how lineage-specific CNEs originated in these two clades. The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provide a valuable resource for comparative genomic studies of reptiles and other amniotes.
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影响因子：
3.3
作者：
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通讯作者：
Mikheyev AS
影响因子：
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作者：
Li, Heng
通讯作者：
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影响因子：
14.9
作者：
Chakraborty, Mahul;Baldwin-Brown, James G.;Emerson, J. J.
通讯作者：
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测序，从头组装和注释濒临灭绝的中国鳄鱼蜥蜴shinisaurus鳄鱼的基因组。
影响因子：
9.2
作者：
Gao J;Li Q;Wang Z;Zhou Y;Martelli P;Li F;Xiong Z;Wang J;Yang H;Zhang G
通讯作者：
Zhang G
DOI：
10.1098/rspb.2014.1122
发表时间：
2014-09-22
影响因子：
4.7
作者：
Gilbert, C.;Meik, J. M.;Schaack, S.
通讯作者：
Schaack, S.