Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan.
PLoS One. 2018 Oct 26;13(10):e0206154. doi: 10.1371/journal.pone.0206154. eCollection 2018.
The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes' miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.
现代牛是从原牛驯化而来的，具有两种亚种，即 Bos taurus 和 Bos indicus。miRNAs（microRNAs）是一类约 22nt 的非编码短 RNA，在动物的许多细胞和生理过程的调节中起着关键作用。本研究旨在通过从头预测和同源性基于计算的方法预测和注释指示型 miRNA 在整个基因组中的潜在突变。通过同源性方法在可用的指示型组装中进行了全基因组映射，并从属于 521 个独特成熟 miRNA 家族的 808 个报告的 Taurine miRNA 中回收了 768 个 miRNA。由于缺乏二级 miRNA 结构、增加 miRNA 两个基因组之间的相似性或严格性，42 个前体被丢弃。在 chr5、chr7、chr8、chr12 和 chr21 上观察到 miRNA 发生率的增加趋势，指示型基因组中有 19 个多顺反子 miRNA 在 1kb 距离内。值得注意的是，12 个 miRNA 显示出拷贝数变异。在其成熟序列中发现了 18 个 miRNA 突变，其中 8 个位于其种子区域。而在基于从头的方法中，在指示型牛的 Y 染色体上发现了 12 个新的潜在 miRNA 以及 chrX 上的一个新 miRNA（bind-miR-1264）。最终数据集进行了注释，并解释了负责增强指示型免疫力、耐热性和疾病耐受性调节的潜在靶基因。该研究符合对指示型基因组的更好理解和感知方法。
