Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA.
BMC Evol Biol. 2010 Feb 12;10:41. doi: 10.1186/1471-2148-10-41.
The availability of genome and transcriptome sequences for a number of species permits the identification and characterization of conserved as well as divergent genes such as lineage-specific genes which have no detectable sequence similarity to genes from other lineages. While genes conserved among taxa provide insight into the core processes among species, lineage-specific genes provide insights into evolutionary processes and biological functions that are likely clade or species specific.
Comparative analyses using the Arabidopsis thaliana genome and sequences from 178 other species within the Plant Kingdom enabled the identification of 24,624 A. thaliana genes (91.7%) that were termed Evolutionary Conserved (EC) as defined by sequence similarity to a database entry as well as two sets of lineage-specific genes within A. thaliana. One of the A. thaliana lineage-specific gene sets share sequence similarity only to sequences from species within the Brassicaceae family and are termed Conserved Brassicaceae-Specific Genes (914, 3.4%, CBSG). The other set of A. thaliana lineage-specific genes, the Arabidopsis Lineage-Specific Genes (1,324, 4.9%, ALSG), lack sequence similarity to any sequence outside A. thaliana. While many CBSGs (76.7%) and ALSGs (52.9%) are transcribed, the majority of the CBSGs (76.1%) and ALSGs (94.4%) have no annotated function. Co-expression analysis indicated significant enrichment of the CBSGs and ALSGs in multiple functional categories suggesting their involvement in a wide range of biological functions. Subcellular localization prediction revealed that the CBSGs were significantly enriched in proteins targeted to the secretory pathway (412, 45.1%). Among the 107 putatively secreted CBSGs with known functions, 67 encode a putative pollen coat protein or cysteine-rich protein with sequence similarity to the S-locus cysteine-rich protein that is the pollen determinant controlling allele specific pollen rejection in self-incompatible Brassicaceae species. Overall, the ALSGs and CBSGs were more highly methylated in floral tissue compared to the ECs. Single Nucleotide Polymorphism (SNP) analysis showed an elevated ratio of non-synonymous to synonymous SNPs within the ALSGs (1.99) and CBSGs (1.65) relative to the EC set (0.92), mainly caused by an elevated number of non-synonymous SNPs, indicating that they are fast-evolving at the protein sequence level.
Our analyses suggest that while a significant fraction of the A. thaliana proteome is conserved within the Plant Kingdom, evolutionarily distinct sets of genes that may function in defining biological processes unique to these lineages have arisen within the Brassicaceae and A. thaliana.
许多物种的基因组和转录组序列的出现，使得我们能够鉴定和描述保守的和分化的基因，如谱系特异性基因，这些基因与其他谱系的基因没有可检测的序列相似性。虽然分类群之间保守的基因提供了对物种核心过程的深入了解，但谱系特异性基因提供了对进化过程和生物功能的深入了解，这些功能可能是特定于分支或物种的。
使用拟南芥基因组和植物界 178 个其他物种的序列进行的比较分析，鉴定了 24624 个拟南芥基因（91.7%），这些基因被称为进化保守基因（EC），其定义是与数据库条目具有序列相似性，以及拟南芥中的两组谱系特异性基因。拟南芥谱系特异性基因的一组与芸薹科家族内的物种的序列具有相似性，被称为保守芸薹科特异性基因（914，3.4%，CBSG）。另一组拟南芥谱系特异性基因，即拟南芥谱系特异性基因（1324，4.9%，ALSG），与拟南芥以外的任何序列都没有序列相似性。虽然许多 CBSG（76.7%）和 ALSG（52.9%）都有转录，但大多数 CBSG（76.1%）和 ALSG（94.4%）没有注释功能。共表达分析表明，CBSG 和 ALSG 在多个功能类别中显著富集，表明它们参与了广泛的生物学功能。亚细胞定位预测显示，CBSG 显著富集于靶向分泌途径的蛋白质（412，45.1%）。在 107 个具有已知功能的推定分泌性 CBSG 中，有 67 个编码假定的花粉外壳蛋白或富含半胱氨酸的蛋白，与 S 座位富含半胱氨酸的蛋白具有序列相似性，S 座位富含半胱氨酸的蛋白是控制自交不亲和芸薹科物种花粉特异性花粉排斥的花粉决定因子。总的来说，与 EC 相比，ALSG 和 CBSG 在花组织中甲基化程度更高。单核苷酸多态性（SNP）分析显示，ALSG（1.99）和 CBSG（1.65）中的非同义 SNP 与同义 SNP 的比值高于 EC 组（0.92），主要是由于非同义 SNP 的数量增加，表明它们在蛋白质序列水平上快速进化。
我们的分析表明，虽然拟南芥蛋白质组的很大一部分在植物界中是保守的，但在芸薹科和拟南芥中出现了进化上不同的基因集，这些基因可能在定义这些谱系特有的生物学过程中发挥作用。
