Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.
Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.
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DOI：
10.1093/jhered/esab036
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发表时间：
2021-11-01
期刊：
影响因子：
--
通讯作者：
Krasheninnikova K
中科院分区：
文献类型：
--
作者：
Tamazian G;Dobrynin P;Zhuk A;Zhernakova DV;Perelman PL;Serdyukova NA;Graphodatsky AS;Komissarov A;Kliver S;Cherkasov N;Scott AF;Mohr DW;Koepfli KP;O'Brien SJ;Krasheninnikova K
猫科动物家族中的美洲狮血统由3个物种组成，最后一次分享共同的祖先大约在490万年前。全基因组序列的两个物种的血统以前报道：猎豹（Acinonyx jubatus）和美洲狮（美洲狮concolor）。本报告描述了其余物种美洲虎（美洲狮）的全基因组组装。我们用10X Genomics连接的读数对雄性美洲虎的基因组进行了测序，并组装了全基因组序列。组装的基因组包含一系列达到染色体臂长度的支架，并且在支架邻接性方面与猎豹和美洲狮的基因组组装相似，重叠群N50 = 100.2 kbp，支架N50 = 49.27 Mbp。我们使用BUSCO评估了美洲虎基因组的组装序列，将测序的个体和另一个已发表的雌性美洲虎与组装的基因组进行了比对，注释了蛋白质编码基因、重复序列、基因组变异及其对蛋白质编码基因的影响，并分析了2种美洲虎与参考线粒体基因组的差异。美洲虎基因组组装和它的注释进行了比较，在质量，变异和功能，以前报道的美洲狮和猎豹的基因组组装。研究中使用的计算分析以透明和可重复的方式实现，以允许进一步重用和修改。
The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification.
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DOI：
10.1109/tvcg.2014.2346248
发表时间：
2014-12
影响因子：
5.2
作者：
Lex A;Gehlenborg N;Strobelt H;Vuillemot R;Pfister H
通讯作者：
Pfister H
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
14.9
作者：
Kriventseva EV;Kuznetsov D;Tegenfeldt F;Manni M;Dias R;Simão FA;Zdobnov EM
通讯作者：
Zdobnov EM
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
2.6
作者：
Challis, Richard;Richards, Edward;Blaxter, Mark
通讯作者：
Blaxter, Mark