Glagoleva Anastasia Y, Ivanisenko Nikita V, Khlestkina Elena K
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Novosibirsk State University, Novosibirsk, Russia.
BMC Genet. 2019 Mar 18;20(Suppl 1):30. doi: 10.1186/s12863-019-0727-y.
Flavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids; it is involved in biosynthesis of all classes of flavonoid compounds. Nevertheless, the Chs gene family in bread wheat (Triticum aestivum L.) has been not characterized yet. The aim of the current study was to investigate structural and functional organization of the Chs genes and evolution of this gene family in bread wheat and relative species.
The nucleotide sequences of the eight Chs copies in T. aestivum were identified. Among them, two homoeologous sets of the Chs genes were located on the short (Chs-A1, -B1, -D1) and the long (Chs-A4, -B4, -D4) arms of homoeologous group 2 chromosomes. Two paralogous gene copies in the B-genome (Chs-B2, -B3) were located in the distal regions of 2BS chromosome. To clarify the origin of Chs duplications in the B-genome the phylogenetic analysis with the Chs sequences of Triticum and Aegilops species carrying ancestral genomes was conducted. It was estimated that the first duplication event occurred in the genome of the common ancestor of Triticum and Aegilops genera about 10-12 million years ago (MYA), then another copy was formed in the ancestor of the B-genome about 6-7 MYA. A homology modeling revealed high sequence similarity of bread wheat CHS enzymes. A number of short deletions in coding regions of some Chs sequences are not expected to have any significant functional effects. Estimation of transcriptional activity of the Chs copies along with a comparative analysis of their promoters structure suggested their functional specialization, which likely contributed to the maintaining of the duplicated Chs genes in wheat genome.
From possible ten Chs copies in bread wheat genome, eight members of this family retained their intact structure and activity, while two copies appear to be lost at the level of diploid and tetraploid ancestors. Transcriptional assay along with a comparative analysis of the cis-regulatory elements revealed their functional diversification. The multiple functions supported by the Chs family are assumed to be a driving force for duplications of the Chs gene and their retention in plant genome.
类黄酮化合物是植物的次生代谢产物，在植物发育、抵御病原体和不利环境因素方面具有重要作用。查尔酮合酶（CHS）是类黄酮生物合成中的关键酶，参与所有类黄酮化合物的生物合成。然而，普通小麦（Triticum aestivum L.）中的Chs基因家族尚未得到表征。本研究的目的是探究普通小麦中Chs基因的结构和功能组织以及该基因家族在普通小麦及其近缘物种中的进化情况。
鉴定出了普通小麦中8个Chs拷贝的核苷酸序列。其中，两组同源的Chs基因分别位于2号同源群染色体的短臂（Chs-A1、-B1、-D1）和长臂（Chs-A4、-B4、-D4）上。B基因组中的两个旁系同源基因拷贝（Chs-B2、-B3）位于2BS染色体的远端区域。为了阐明B基因组中Chs重复的起源，对携带祖先基因组的小麦和山羊草属物种的Chs序列进行了系统发育分析。据估计，第一次重复事件发生在小麦和山羊草属共同祖先的基因组中，大约在1000-1200万年前（百万年前），然后在B基因组的祖先中大约在600-700万年前形成了另一个拷贝。同源建模显示普通小麦CHS酶具有高度的序列相似性。一些Chs序列编码区的一些短缺失预计不会产生任何显著的功能影响。对Chs拷贝转录活性的估计以及对其启动子结构的比较分析表明了它们的功能特化，这可能有助于维持小麦基因组中重复的Chs基因。
在普通小麦基因组中可能存在的10个Chs拷贝中，该家族的8个成员保留了完整的结构和活性，而在二倍体和四倍体祖先水平上似乎有两个拷贝丢失了。转录分析以及对顺式调控元件的比较分析揭示了它们的功能多样化。Chs家族支持的多种功能被认为是Chs基因重复及其在植物基因组中保留的驱动力。
