Bioinformatic Characterization of Genes and Proteins Involved in Blood Clotting in Lampreys
Bioinformatic Characterization of Genes and Proteins Involved in Blood Clotting in Lampreys
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DOI：
10.1007/s00239-015-9701-0
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发表时间：
2015-10-01
影响因子：
3.9
通讯作者：
Doolittle, Russell F.
中科院分区：
文献类型：
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作者：
Doolittle, Russell F.
七鳃鳗和八目鳗是现存脊椎动物中最早分化的物种，也是研究哺乳动物中复杂生化系统起源的明显目标。目前，这种查询的最简单的方法是在全基因组序列（WGS）组件中搜索相关基因的存在。不幸的是，在过去，无论是七鳃鳗还是八目鳗，都没有高质量的完整基因组序列，排除了证明基因缺失的可能性。最近，两种七鳃鳗的改进但仍然不完整的基因组组装已经发布，并且，与NCBI跟踪档案中广泛收集的短序列一起，它们使得有可能对特定基因家族进行可靠的计数。特别是，多源策略已用于研究七鳃鳗血液凝固系统中已知存在于高等脊椎动物中的基因的存在和不存在。正如早期研究所表明的那样，七鳃鳗缺乏凝血因子VIII和IX的基因，这两种因子对“内在”凝血系统至关重要，并导致人类血友病。另一方面，他们有三个因子VII和X的基因，参与“外在”凝血系统。利用七鳃鳗的原始痕量序列“reads”和部分WGS组装的策略可以用于脊椎动物其他生化系统早期进化的研究。
Lampreys and hagfish are the earliest diverging of extant vertebrates and are obvious targets for investigating the origins of complex biochemical systems found in mammals. Currently, the simplest approach for such inquiries is to search for the presence of relevant genes in whole genome sequence (WGS) assemblies. Unhappily, in the past a high-quality complete genome sequence has not been available for either lampreys or hagfish, precluding the possibility of proving gene absence. Recently, improved but still incomplete genome assemblies for two species of lamprey have been posted, and, taken together with an extensive collection of short sequences in the NCBI trace archive, they have made it possible to make reliable counts for specific gene families. Particularly, a multi-source tactic has been used to study the lamprey blood clotting system with regard to the presence and absence of genes known to occur in higher vertebrates. As was suggested in earlier studies, lampreys lack genes for coagulation factors VIII and IX, both of which are critical for the "intrinsic" clotting system and responsible for hemophilia in humans. On the other hand, they have three each of genes for factors VII and X, participants in the "extrinsic" clotting system. The strategy of using raw trace sequence "reads" together with partial WGS assemblies for lampreys can be used in studies on the early evolution of other biochemical systems in vertebrates.