Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
Department of Biological Sciences, The Bayousphere Research Lab, Nicholls State University, Thibodaux, LA 70310, USA.
Comp Biochem Physiol Part D Genomics Proteomics. 2018 Mar;25:19-25. doi: 10.1016/j.cbd.2017.10.002. Epub 2017 Oct 13.
With the advent of high-throughput DNA sequencing technology, the genomic sequence of many disparate species has led to the relatively new discipline of genomics, the study of genome structure, function and evolution. Much work has been focused on the role of whole genome duplications (WGD) in the architecture of extant vertebrate genomes, particularly those of teleost fishes which underwent a WGD early in the teleost radiation >230 million years ago (mya). Our past work has focused on the fate of duplicated copies of a multigene family coding for the intracellular lipid-binding protein (iLBP) genes in the teleost fishes. To define the evolutionary processes that determined the fate of duplicated genes and generated the structure of extant fish genomes, however, requires comparative genomic analysis with a fish lineage that diverged before the teleost WGD, such as the spotted gar (Lepisosteus oculatus), an ancient, air-breathing, ray-finned fish. Here, we describe the genomic organization, chromosomal location and tissue-specific expression of a subfamily of the iLBP genes that code for fatty acid-binding proteins (Fabps) in spotted gar. Based on this work, we have defined the minimum suite of fabp genes prior to their duplication in the teleost lineages ~230-400 mya. Spotted gar, therefore, serves as an appropriate outgroup, or ancestral/ancient fish, that did not undergo the teleost-specific WGD. As such, analyses of the spatio-temporal regulation of spotted gar genes provides a foundation to determine whether the duplicated fabp genes have been retained in teleost genomes owing to either sub- or neofunctionalization.
随着高通量 DNA 测序技术的出现，许多不同物种的基因组序列导致了相对较新的基因组学领域的出现，即研究基因组的结构、功能和进化。人们已经对全基因组复制（WGD）在现存脊椎动物基因组结构中的作用进行了大量研究，特别是那些在 2 亿 3000 多万年前的硬骨鱼辐射早期经历了 WGD 的硬骨鱼。我们过去的工作主要集中在多基因家族编码的细胞内脂质结合蛋白（iLBP）基因在硬骨鱼中的复制副本的命运上。然而，为了确定决定复制基因命运并产生现存鱼类基因组结构的进化过程，需要与在硬骨鱼 WGD 之前分化的鱼类谱系进行比较基因组分析，例如斑点雀鳝（Lepisosteus oculatus），这是一种古老的、能呼吸空气的、有鳍鱼类。在这里，我们描述了斑点雀鳝中编码脂肪酸结合蛋白（Fabps）的 iLBP 基因亚家族的基因组组织、染色体位置和组织特异性表达。基于这项工作，我们在 2.3 亿至 4 亿年前的硬骨鱼谱系中确定了 Fabp 基因复制之前的最小基因套件。因此，斑点雀鳝作为一个合适的外群或祖先/古老鱼类，没有经历过硬骨鱼特有的 WGD。因此，分析斑点雀鳝基因的时空调控为确定复制的 Fabp 基因是否由于亚功能化或新功能化而保留在硬骨鱼基因组中提供了基础。
