民猪从头组装(de novo)的基因组序列特征分析

Genome Sequence Characteristics of De Novo Assembly of Min Pig

利用Hiseq 2000测序平台对1头雌性民猪采用从头组装(de novo)策略,绘制了其完整的基因组序列。测序深度达116.91×,N50 contig为57.3 kb,N50 scaffold为4.91 Mb,最终组装的基因组大小为2.64 Gb。组装的基因组中重复序列共占基因组大小的41.14%,其中占比最多的为长散在重复序列(Long interspersed nuclear elements,LINE),但存在1.22 Mb大小的缺失序列。共发现12079623个单核苷酸多态性(SNP)及1854337个插入缺失突变(InDels),检测到38867个缺失型结构变异(SV)和6867个插入型SV,以及575个倒位(INV)型变异。其中,缺失序列长多为60~300 bp,插入序列长多集中在1~8 bp,90%的插入片段长在1~30 bp。与11个其他猪种比较筛选后,发现民猪存在12个特异的SV位点,这些位点的形成机制以逆转录转座子元件的插入为主。预测到20853个基因,其中20651个基因有功能注释,占预测总数的99.03%。鉴定出22个基因受到正选择,包括与脂类代谢相关的多磷酸肌醇1-磷酸酶(INPP1)和缓激肽受体B1(BDKRB1);与繁殖性状相关的含HORMA结构域的蛋白1(HORMAD1)和核糖体蛋白大亚基8(RPL8);与耐寒性状相关的瞬时性受体电位通道香草酸受体5(TRPV5);与生长性状相关的甲基丙二酰辅酶A表异构酶MCEE和尤因肿瘤相关抗原1(ETAA1)以及与免疫性状相关的环指蛋白31(RNF31)。

In order to further analyze the genetic basis of Min pig germplasm characteristics,a whole genome sequence of a female pig was drawn by de novo strategy using Hiseq 2000 platform.The sequencing depth was 116.91×,N50 contig was 57.3 kb,N50 scaffold was 4.91 Mb,and the final assembled genome size was 2.64 Gb.In the assembled genome,repetitive sequences accounted for 41.14%of the total genome,of which the largest proportion was long interspersed nuclear elements(LINE),but there were 1.22 Mb lack of sequences.A total of 12079623 SNPs and 1854337 InDels were found.38867 deletion SV,6867 insertion SV and 575 inversion variants were detected.Most of the deletion sequences were 60-300 bp in length,and most of the insertion sequences were 1-8 bp in length.90%of the insertion fragments were between 1-30 bp in length.Compared with other 11 pig breeds,12 specific SV loci were found in Min pig.The formation mechanism of these loci was mainly the insertion of retrotransposon elements.20853 genes were predicted,of which 20651 genes had functional annotation,accounting for 99.03%of the total number.22 genes were positively selected,including INPP1 and BDKRB1,which were related to lipid metabolism.HORMAD1 and RPL8 were related to reproductive traits,TRPV5 was related to cold tolerance,MCEE and ETAA1 were related to growth traits and RNF31 was related to immune traits.