Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish.
Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish.
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DOI：
10.1186/1471-2164-14-65
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发表时间：
2013-01-31
期刊：
影响因子：
4.4
通讯作者：
He S
中科院分区：
文献类型：
--
作者：
Yang L;Zou M;Fu B;He S
尽管基因组和转录组序列数据的可用性不断增加，但硬骨鱼表型复杂性的基因组基础仍然不清楚。考虑到灭绝的基生射线鳍鱼类数量相对较多，鱼类特异性基因组复制无法为硬骨鱼的形态复杂性提供充分的解释。在本研究中，我们进行了比较基因组分析，以发现斑马鱼内保守的硬骨鱼特异性基因（CTSG）和孤儿基因，并发现这两组谱系特异性基因可能在斑马鱼胚胎发生过程中发挥重要作用。斑马鱼中的谱系特异性基因与其他物种中的对应基因具有许多相同的特征：长度较短、外显子数量较少、GC 含量较高，并且具有转录本支持的基因较少。染色体定位分析表明，CTSGs和孤儿基因在斑马鱼染色体上的分布都不均匀。由基因本体论（GO）注释或从头开始预测的 CTSG 中免疫蛋白的显着富集可能意味着对病原体的防御可能是硬骨鱼多样化的重要原因。谱系特异性基因的进化起源已被确定，并且很高比例的谱系特异性基因是通过基因复制产生的。通过表达序列标签（EST）和RNA-seq数据获得的谱系特异性基因的时间和空间表达谱揭示了两个新的特性：除了高度组织偏好的表达之外，谱系特异性基因在时间上也受到高度限制，即它们的表达时间窗口比进化上保守的基因更窄，并且在胚胎后期和早期幼虫阶段特别富集。我们的研究首次系统地鉴定了斑马鱼内两组不同的谱系特异性基因，并为更好地理解硬骨鱼表型复杂性的基因组基础的分子机制提供了有价值的信息，以供未来的研究使用。
The genomic basis of teleost phenotypic complexity remains obscure, despite increasing availability of genome and transcriptome sequence data. Fish-specific genome duplication cannot provide sufficient explanation for the morphological complexity of teleosts, considering the relatively large number of extinct basal ray-finned fishes. In this study, we performed comparative genomic analysis to discover the Conserved Teleost-Specific Genes (CTSGs) and orphan genes within zebrafish and found that these two sets of lineage-specific genes may have played important roles during zebrafish embryogenesis. Lineage-specific genes within zebrafish share many of the characteristics of their counterparts in other species: shorter length, fewer exon numbers, higher GC content, and fewer of them have transcript support. Chromosomal location analysis indicated that neither the CTSGs nor the orphan genes were distributed evenly in the chromosomes of zebrafish. The significant enrichment of immunity proteins in CTSGs annotated by gene ontology (GO) or predicted ab initio may imply that defense against pathogens may be an important reason for the diversification of teleosts. The evolutionary origin of the lineage-specific genes was determined and a very high percentage of lineage-specific genes were generated via gene duplications. The temporal and spatial expression profile of lineage-specific genes obtained by expressed sequence tags (EST) and RNA-seq data revealed two novel properties: in addition to being highly tissue-preferred expression, lineage-specific genes are also highly temporally restricted, namely they are expressed in narrower time windows than evolutionarily conserved genes and are specifically enriched in later-stage embryos and early larval stages. Our study provides the first systematic identification of two different sets of lineage-specific genes within zebrafish and provides valuable information leading towards a better understanding of the molecular mechanisms of the genomic basis of teleost phenotypic complexity for future studies.
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