Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada.
BMC Genomics. 2020 Oct 19;21(1):722. doi: 10.1186/s12864-020-07121-9.
The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in some plant species, but no systematic evolutionary analysis is available for the flax genome.
Here we describe the ABC transporter and HMA gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domains' composition. Nine of these genes, i.e., LuABCC9, LuABCC10, LuABCG58, LuABCG59, LuABCG71, LuABCG72, LuABCG73, LuHMA3, and LuHMA4, were orthologous with the Cd associated genes in Arabidopsis, rice and maize. Ten motifs were identified from all ABC transporter and HMA genes. Also, several motifs were conserved among genes of similar length, but each subfamily each had their own motif structures. Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis. While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal duplications, suggesting that segmental duplications contributed the most to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were for the most part lower than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diversified expression profiling patterns of the genes and revealed their functional or sub-functional conservation and neo-functionalization.
Characterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.
最近发布的亚麻基因组序列参考组装，这是一种具有 15 对染色体的自花授粉作物，进入染色体规模的拟南芥基因组，使基因家族的特征得以实现。ABC 转运蛋白和 HMA 基因家族在控制作物中镉（Cd）积累方面很重要。迄今为止，这些两个基因家族的全基因组分析已经在一些植物物种中成功进行，但亚麻基因组没有系统的进化分析。
本文描述了亚麻中的 ABC 转运蛋白和 HMA 基因家族，提供了其进化的全面概述，并为其成员的功能注释提供了一些支持。在亚麻基因组中鉴定的 198 个 ABC 转运蛋白和 12 个 HMA 基因根据其系统发育分析和结构域组成分为八个 ABC 转运蛋白和四个 HMA 亚家族。其中 9 个基因，即 LuABCC9、LuABCC10、LuABCG58、LuABCG59、LuABCG71、LuABCG72、LuABCG73、LuHMA3 和 LuHMA4，与拟南芥、水稻和玉米中的 Cd 相关基因是同源的。从所有 ABC 转运蛋白和 HMA 基因中鉴定出 10 个基序。此外，相似长度的基因之间存在一些基序保守，但每个亚家族都有自己的基序结构。亚麻的 ABC 转运蛋白和 HMA 基因家族在亚家族之间以及与拟南芥的基因家族高度保守。虽然观察到四种不同频率的基因复制类型，但全基因组或片段复制是最常见的，有 162 个基因，其次是 29 个分散的、14 个串联的和 4 个邻近的复制，这表明片段复制对亚麻中这两个基因家族的扩张贡献最大。配对重复基因的非同义到同义（Ka/Ks）突变率大部分低于 1，表明主要是纯化选择。只有 5 对基因的 Ka/Ks 比值大于 1，表明明显受到正选择。基因本体论分析表明，大多数亚麻 ABC 转运蛋白和 HMA 基因具有 ATP 结合、运输、催化活性、ATP 酶活性和金属离子结合的作用。八个不同器官的 RNA-Seq 分析表明，基因表达谱具有多样化的表达模式，并揭示了它们的功能或亚功能的保守性和新功能化。
对 ABC 转运蛋白和 HMA 基因家族的特征描述将有助于亚麻和其他作物物种候选基因的功能分析。
