基于全基因组的龟鳖目Hox基因序列特征及进化分析

EVOLUTIONARY ANALYSES AND SEQUENCE FEATURE OF HOX GENES IN TURTLES

为对Hox基因在龟鳖目物种中进行系统地序列比较分析和进化研究,文章对目前具有染色体水平的龟鳖目基因组进行了Hox基因的鉴定,序列特征、进化和转录组分析。研究结果表明龟鳖物种的Hox基因簇是高度保守的。非重复序列的缺失导致鳖科HoxB9—HoxB13基因间区相对龟科短了10 kb。大量Hox基因编码区发生了鳖科或龟科特异的序列替换、插入和缺失。胸部骨骼发育相关的Hox基因在鳖科祖先发生了快速进化和受到正选择。Hox基因的表达具有组织、时期特异性,主要在胚胎时期的顶端外胚层嵴、背甲嵴和性腺表达。研究为龟鳖目Hox基因不同胚胎时期的多组学及表达调控分析提供了靶标,也为进一步厘清龟鳖物种演化创新提供了参考。

Hox genes,as a family of transcription factors,play a central role in the specification of regional identities along the anterior-posterior body axis,skeletal development,and limb morphogenesis in vertebrates.Previous analyses of Hox genes revealed an unexpected diversity in gene number,genomic organization,and expression patterns in different vertebrate groups.However,the Hox genes have not been systematically analyzed in terms of sequence and evolutionary features in turtles.In this study,we performed Hox gene identification,sequence characterization and evolutionary analyses in turtles with the publicly available chromosomal-level genome sequences and RNA-seq data,and found that the Hox gene clusters in turtles are highly conserved.Turtles possess the same Hox inventory(39 genes,lost HoxC3)as birds,crocodiles,and placental mammals.The HoxB9-HoxB13 intergenic region in soft-shell turtles is about 10 kb shorter than that in hard-shell turtles,which resulted from the deletion of the non-repetitive sequences.There are hard-shell/soft-shell turtle specific nucleotide substitutions,insertions,and deletions located in the coding regions of tens of Hox genes.However,these sequence mutations are not in functional domains,nor do they lead to changes in protein spatial structure.The Hox genes related to thoracic skeletal development have been undergone rapid evolution and positive selection in the ancestor of soft-shell turtles.The Hox gene expression is tissue-and stage-specific,and mainly expressed in the apical ectoderm ridge,carapace ridge and gonad during the embryonic stages in turtles.We speculate that the phenotypic differences between soft-shell and hard-shell turtles might be related to non-coding regulatory elements located in the HoxB9-HoxB13 intergenic region,and the HoxB5 and HoxC6,which are positively selected in the ancestors of soft-shell turtles.This study provides a target for the analyses of multi-omics,gene expression and regulatory mechanism of Hox genes across different embryonic stages in turtles,also provides a reference for further clarifying the evolutionary innovation in turtles.