PDF(Pubmed)
Abstract：
The mammalian Leukocyte Receptor Complex (LRC) chromosomal region may contain gene families for the killer cell immunoglobulin-like receptor (KIR) and/or leukocyte immunoglobulin-like receptor (LILR) collections as well as various framing genes. This complex region is well described in humans, mice, and some domestic animals. Although single KIR genes are known in some Carnivora, their complements of LILR genes remain largely unknown due to obstacles in the assembly of regions of high homology in short-read based genomes.
As part of the analysis of felid immunogenomes, this study focuses on the search for LRC genes in reference genomes and the annotation of LILR genes in Felidae. Chromosome-level genomes based on single-molecule long-read sequencing were preferentially sought and compared to representatives of the Carnivora.
Seven putatively functional LILR genes were found across the Felidae and in the Californian sea lion, four to five genes in Canidae, and four to nine genes in Mustelidae. They form two lineages, as seen in the Bovidae. The ratio of functional genes for activating LILRs to inhibitory LILRs is slightly in favor of inhibitory genes in the Felidae and the Canidae; the reverse is seen in the Californian sea lion. This ratio is even in all of the Mustelidae except the Eurasian otter, which has a predominance of activating LILRs. Various numbers of LILR pseudogenes were identified.
The structure of the LRC is rather conservative in felids and the other Carnivora studied. The LILR sub-region is conserved within the Felidae and has slight differences in the Canidae, but it has taken various evolutionary paths in the Mustelidae. Overall, the process of pseudogenization of LILR genes seems to be more frequent for activating receptors. Phylogenetic analysis found no direct orthologues across the Carnivora which corroborate the rapid evolution of LILRs seen in mammals.
As part of the analysis of felid immunogenomes, this study focuses on the search for LRC genes in reference genomes and the annotation of LILR genes in Felidae. Chromosome-level genomes based on single-molecule long-read sequencing were preferentially sought and compared to representatives of the Carnivora.
Seven putatively functional LILR genes were found across the Felidae and in the Californian sea lion, four to five genes in Canidae, and four to nine genes in Mustelidae. They form two lineages, as seen in the Bovidae. The ratio of functional genes for activating LILRs to inhibitory LILRs is slightly in favor of inhibitory genes in the Felidae and the Canidae; the reverse is seen in the Californian sea lion. This ratio is even in all of the Mustelidae except the Eurasian otter, which has a predominance of activating LILRs. Various numbers of LILR pseudogenes were identified.
The structure of the LRC is rather conservative in felids and the other Carnivora studied. The LILR sub-region is conserved within the Felidae and has slight differences in the Canidae, but it has taken various evolutionary paths in the Mustelidae. Overall, the process of pseudogenization of LILR genes seems to be more frequent for activating receptors. Phylogenetic analysis found no direct orthologues across the Carnivora which corroborate the rapid evolution of LILRs seen in mammals.
摘要：
哺乳动物白细胞受体复合物(LRC)染色体区可含有杀伤细胞免疫球蛋白样受体(KIR)和/或白细胞免疫球蛋白样受体(LILR)集合的基因家族以及各种成帧基因。这个复杂的区域在人类中有很好的描述，老鼠,和一些家畜。尽管在一些食肉动物中已知单个KIR基因，LILR基因的互补序列在很大程度上仍然未知,因为在基于短读的基因组中,高同源性区域的组装存在障碍.
■作为felid免疫基因组分析的一部分，这项研究的重点是在参考基因组中寻找LRC基因，并在Felidae中注释LILR基因。优先寻找基于单分子长读数测序的染色体水平基因组，并与食肉动物的代表进行比较。
■在Felidae和加利福尼亚海狮中发现了七个假定的功能性LILR基因，犬科有4到5个基因,还有4到9个基因.它们形成两个谱系，如在Bovidae中看到的。激活LILRs的功能基因与抑制性LILRs的比例略大于Felidae和Canidae中的抑制性基因；在加利福尼亚海狮中看到了相反的情况。这个比例甚至在除欧亚水獭以外的所有Mustelidae中，具有激活LILR的优势。鉴定了各种数量的LILR假基因。
■在猫科动物和其他食肉动物中，LRC的结构相当保守。LILR亚区在Felidae中保守，在犬科中略有差异，但是它在Mustelidae中采取了各种进化路径。总的来说,LILR基因的假化过程似乎更频繁地激活受体。系统发育分析发现，食肉动物中没有直接的直向同源物，这证实了哺乳动物中LILR的快速进化。
■作为felid免疫基因组分析的一部分，这项研究的重点是在参考基因组中寻找LRC基因，并在Felidae中注释LILR基因。优先寻找基于单分子长读数测序的染色体水平基因组，并与食肉动物的代表进行比较。
■在Felidae和加利福尼亚海狮中发现了七个假定的功能性LILR基因，犬科有4到5个基因,还有4到9个基因.它们形成两个谱系，如在Bovidae中看到的。激活LILRs的功能基因与抑制性LILRs的比例略大于Felidae和Canidae中的抑制性基因；在加利福尼亚海狮中看到了相反的情况。这个比例甚至在除欧亚水獭以外的所有Mustelidae中，具有激活LILR的优势。鉴定了各种数量的LILR假基因。
■在猫科动物和其他食肉动物中，LRC的结构相当保守。LILR亚区在Felidae中保守，在犬科中略有差异，但是它在Mustelidae中采取了各种进化路径。总的来说,LILR基因的假化过程似乎更频繁地激活受体。系统发育分析发现，食肉动物中没有直接的直向同源物，这证实了哺乳动物中LILR的快速进化。
