The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, USDA ARS, Madison, WI 53706, USA.
Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA), Italy.
Genomics. 2019 May;111(3):418-425. doi: 10.1016/j.ygeno.2018.02.018. Epub 2018 Mar 6.
This study sought to characterize differences in gene content, regulation and structure between taurine cattle and river buffalo (one subspecies of domestic water buffalo) using the extensively annotated UMD3.1 cattle reference genome as a basis for comparisons. We identified 127 deletion CNV regions in river buffalo representing 5 annotated cattle genes. We also characterized 583 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes. Transcriptome analysis in various tissue types on river buffalo confirmed the absence of four cattle genes. Four genes which may be related to phenotypic differences in meat quality and color, had upstream MEI predictions and were found to have significantly elevated expression in river buffalo compared with cattle. Our comparative alignment approach and gene expression analyses suggested a functional role for many genomic structural variations, which may contribute to the unique phenotypes of river buffalo.
本研究旨在利用广泛注释的 UMD3.1 牛参考基因组作为比较基础，描述牛磺酸牛和（家养水牛的一个亚种）河水牛之间在基因组成、调控和结构上的差异。我们在河水牛中鉴定出 127 个缺失的 CNV 区域，代表 5 个注释的牛基因。我们还描述了在注释的牛基因上游区域内的 583 个合并的移动元件插入（MEI）事件。对河水牛各种组织类型的转录组分析证实了四个牛基因的缺失。四个可能与肉质和颜色表型差异有关的基因，具有上游 MEI 预测，并且与牛相比在河水牛中表达显著升高。我们的比较比对方法和基因表达分析表明，许多基因组结构变异可能具有功能作用，这可能有助于河水牛独特的表型。
