PDF(Pubmed)
Abstract：
UNASSIGNED: Genomic resource development for non-model organisms is rapidly progressing, seeking to uncover molecular mechanisms and evolutionary adaptations enabling thriving in diverse environments. Limited genomic data for bat species hinder insights into their evolutionary processes, particularly within the diverse Myotis genus of the Vespertilionidae family. In Mexico, 15 Myotis species exist, with three-M. vivesi, M. findleyi, and M. planiceps-being endemic and of conservation concern.
UNASSIGNED: We obtained samples of Myotis vivesi, M. findleyi, and M. planiceps for genomic analysis. Each of three genomic DNA was extracted, sequenced, and assembled. The scaffolding was carried out utilizing the M. yumanensis genome via a genome-referenced approach within the ntJoin program. GapCloser was employed to fill gaps. Repeat elements were characterized, and gene prediction was done via ab initio and homology methods with MAKER pipeline. Functional annotation involved InterproScan, BLASTp, and KEGG. Non-coding RNAs were annotated with INFERNAL, and tRNAscan-SE. Orthologous genes were clustered using Orthofinder, and a phylogenomic tree was reconstructed using IQ-TREE.
UNASSIGNED: We present genome assemblies of these endemic species using Illumina NovaSeq 6000, each exceeding 2.0 Gb, with over 90% representing single-copy genes according to BUSCO analyses. Transposable elements, including LINEs and SINEs, constitute over 30% of each genome. Helitrons, consistent with Vespertilionids, were identified. Values around 20,000 genes from each of the three assemblies were derived from gene annotation and their correlation with specific functions. Comparative analysis of orthologs among eight Myotis species revealed 20,820 groups, with 4,789 being single copy orthogroups. Non-coding RNA elements were annotated. Phylogenomic tree analysis supported evolutionary chiropterans\' relationships. These resources contribute significantly to understanding gene evolution, diversification patterns, and aiding conservation efforts for these endangered bat species.
UNASSIGNED: We obtained samples of Myotis vivesi, M. findleyi, and M. planiceps for genomic analysis. Each of three genomic DNA was extracted, sequenced, and assembled. The scaffolding was carried out utilizing the M. yumanensis genome via a genome-referenced approach within the ntJoin program. GapCloser was employed to fill gaps. Repeat elements were characterized, and gene prediction was done via ab initio and homology methods with MAKER pipeline. Functional annotation involved InterproScan, BLASTp, and KEGG. Non-coding RNAs were annotated with INFERNAL, and tRNAscan-SE. Orthologous genes were clustered using Orthofinder, and a phylogenomic tree was reconstructed using IQ-TREE.
UNASSIGNED: We present genome assemblies of these endemic species using Illumina NovaSeq 6000, each exceeding 2.0 Gb, with over 90% representing single-copy genes according to BUSCO analyses. Transposable elements, including LINEs and SINEs, constitute over 30% of each genome. Helitrons, consistent with Vespertilionids, were identified. Values around 20,000 genes from each of the three assemblies were derived from gene annotation and their correlation with specific functions. Comparative analysis of orthologs among eight Myotis species revealed 20,820 groups, with 4,789 being single copy orthogroups. Non-coding RNA elements were annotated. Phylogenomic tree analysis supported evolutionary chiropterans\' relationships. These resources contribute significantly to understanding gene evolution, diversification patterns, and aiding conservation efforts for these endangered bat species.
摘要：
■非模式生物的基因组资源开发正在迅速发展，寻求揭示分子机制和进化适应，从而在不同的环境中蓬勃发展。蝙蝠物种有限的基因组数据阻碍了对其进化过程的认识，特别是在Vespertilionidae家族的各种Myotis属中。在墨西哥,有15种Myotis，与三MVivesi,M.Findleyi,和M.planiceps-是地方性和保护关注。
■我们获得了Myotisvevesi的样本，M.Findleyi,和M.planiceps进行基因组分析。提取三个基因组DNA中的每一个，测序，和组装。通过ntJoin程序内的基因组参考方法,利用Yumanensis基因组进行支架。GapCloser被用来填补空白。重复元素被表征，基因预测是通过MAKER管道的从头算和同源性方法进行的。功能注释涉及InterproScan，BLASTp,和KEGG。非编码RNA用INFERNAL注释，和tRNAscan-SE。使用Orthofinder对直系同源基因进行聚类，并使用IQ-TREE重建了系统发育树。
■我们使用IlluminaNovaSeq6000展示了这些特有物种的基因组组装，每个都超过2.0Gb，根据BUSCO分析，超过90%代表单拷贝基因。转座元素，包括线路和犯罪，占每个基因组的30%以上。Helitron,与Vespertilionids一致，已确定。来自三个组件中每一个的约20,000个基因的值来自基因注释及其与特定功能的相关性。八个Myotis物种之间的直系同源物的比较分析显示20,820组，4,789是单副本正交组。注释了非编码RNA元件。系统发育树分析支持进化翼龙关系。这些资源大大有助于理解基因进化，多样化模式，并协助保护这些濒临灭绝的蝙蝠物种。
■我们获得了Myotisvevesi的样本，M.Findleyi,和M.planiceps进行基因组分析。提取三个基因组DNA中的每一个，测序，和组装。通过ntJoin程序内的基因组参考方法,利用Yumanensis基因组进行支架。GapCloser被用来填补空白。重复元素被表征，基因预测是通过MAKER管道的从头算和同源性方法进行的。功能注释涉及InterproScan，BLASTp,和KEGG。非编码RNA用INFERNAL注释，和tRNAscan-SE。使用Orthofinder对直系同源基因进行聚类，并使用IQ-TREE重建了系统发育树。
■我们使用IlluminaNovaSeq6000展示了这些特有物种的基因组组装，每个都超过2.0Gb，根据BUSCO分析，超过90%代表单拷贝基因。转座元素，包括线路和犯罪，占每个基因组的30%以上。Helitron,与Vespertilionids一致，已确定。来自三个组件中每一个的约20,000个基因的值来自基因注释及其与特定功能的相关性。八个Myotis物种之间的直系同源物的比较分析显示20,820组，4,789是单副本正交组。注释了非编码RNA元件。系统发育树分析支持进化翼龙关系。这些资源大大有助于理解基因进化，多样化模式，并协助保护这些濒临灭绝的蝙蝠物种。
