Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul.
Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul.
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DOI：
10.1093/nargab/lqad033
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发表时间：
2023-06
影响因子：
4.6
通讯作者：
中科院分区：
文献类型：
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作者：
帕拉斯猫，或称野猫（Otocolobus manul），是一种原产于中亚草原和大草原的小型猫科动物。蒙古和中国的人口据点面临着气候变化、栖息地破碎化、偷猎和其他来源带来的日益严峻的挑战。这些威胁，加上O. manul在动物园收藏的受欢迎程度和进化生物学的价值，有必要改善物种基因组资源。我们使用独立的纳米孔测序方法组装了一个2.5 Gb， 61个序列的核组装和17097 bp的有丝分裂基因组。初级核组装的测序覆盖率为56x， N50为118mb，对食肉动物特异性基因的BUSCO完整性评分为94.7%。在Felidae内的高基因组共线性允许基于比对的脚手架到钓鱼猫（Prionailurus viverrinus）参考基因组上。人工组合跨越所有19个大田染色体，推断总间隙长度小于400千碱基。修改碱基调用和变异相位产生交替的假单倍型组装和等位基因特异性DNA甲基化调用；在单倍型之间鉴定出61个差异甲基化区域。最接近的特征包括经典的印迹基因、非编码rna和假定的新型印迹位点。组装的有丝分裂基因组成功地解决了存在于猫科动物核系统发育和mtDNA系统发育之间的不一致。使用7个minION流式细胞从158gb序列中生成所有组装草图。
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul’s zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
DOI：
10.1093/jhered/esab036
发表时间：
2021-11-01
期刊：
The Journal of heredity
影响因子：
--
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
通讯作者：
Krasheninnikova K
影响因子：
4.6
作者：
Yasir M;Turner AK;Lott M;Rudder S;Baker D;Bastkowski S;Page AJ;Webber MA;Charles IG
通讯作者：
Charles IG