Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case
Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case
复制标题
七鳃鳗基因未解决的直系同源性和特殊编码序列特性：以 KCNA 基因家族作为测试案例
作者：
H. Qiu;F. Hildebrand;Shigehiro Kuraku;A. Meyer
背景在了解脊椎动物的进化过程中，环口动物(七目鳗和七鳃鳗)占有至关重要的地位。解决环口基因与颌口(颌形脊椎动物)基因的分子系统发育关系是破译物种树和基因树所不可缺少的。然而，分子系统发育分析，特别是那些包括七鳗鱼基因的分析，已经在基因家族之间产生了高度不一致的结果。为了有效地利用早期脊椎动物的部分基因组组合来研究这一问题，我们将重点放在钾电压门控振动器相关(KCNA)家族上，该家族的成员大多是单外显子。结果鉴定出7个七鳃鳗KCNA基因和6个象鲨基因，并评估了它们与骨质脊椎动物亚群的同源性。与得到强有力支持的象鲨基因与颌口亚群的正交性相反，任何海鳗基因的明确正交性都无法建立。值得注意的是，七鳃鳗KCNA序列显示出独特的密码子使用模式和氨基酸组成，可能与其编码区异常高的GC-含量有关。该基因家族以外的基因也普遍观察到编码序列的这种七鳗鱼特有的特性。结论我们的结果表明，七鳗鱼谱系特有的序列特性的二次修改可能是阻碍七鳗鱼基因进行稳健的正交学评估的因素之一，这一点值得进一步的全基因组验证。在解决早期脊椎动物进化的关键问题时，需要考虑七鳃鳗谱系特有的蛋白质编码序列属性的改变。
BackgroundIn understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon.ResultsSeven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family.ConclusionsOur results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.
小鼠第三和第六号染色体上钾通道基因簇的物理图谱。
影响因子：
4.4
作者：
Street,VA;Tempel,BL
通讯作者：
Tempel,BL
影响因子：
5.6
作者：
Burge, C;Karlin, S
通讯作者：
Karlin, S