Taşkin Kemal Melik, Özbilen Aslıhan, Sezer Fatih, Hürkan Kaan, Güneş Şebnem
Çanakkale Onsekiz Mart University, Faculty of Arts and Sciences, Department of Biology, 17100 Çanakkale, Turkey.
Çanakkale Onsekiz Mart University, Faculty of Arts and Sciences, Department of Biology, 17100 Çanakkale, Turkey.
Comput Biol Chem. 2017 Apr;67:15-21. doi: 10.1016/j.compbiolchem.2016.12.002. Epub 2016 Dec 20.
In this study, we determined the structure of DNA methyltransferase (DNMT) genes in apomict and sexual Boechera species and investigated the expression levels during seed development. Protein and DNA sequences of diploid sexual Boechera stricta DNMT genes obtained from Phytozome 10.3 were used to identify the homologues in apomicts, Boechera holboellii and Boechera divaricarpa. Geneious R8 software was used to map the short-paired reads library of B. holboellii whole genome or B. divaricarpa transcriptome reads to the reference gene sequences. We determined three DNMT genes; for Boechera spp. METHYLTRANSFERASE1 (MET1), CHROMOMETHYLASE 3 (CMT3) and DOMAINS REARRANGED METHYLTRANSFERASE 1/2 (DRM2). We examined the structure of these genes with bioinformatic tools and compared with other DNMT genes in plants. We also examined the levels of expression in silique tissues after fertilization by semi-quantitative PCR. The structure of DNMT proteins in apomict and sexual Boechera species share common features. However, the expression levels of DNMT genes were different in apomict and sexual Boechera species. We found that DRM2 was upregulated in apomictic Boechera species after fertilization. Phylogenetic trees showed that three genes are conserved among green algae, monocotyledons and dicotyledons. Our results indicated a deregulation of DNA methylation machinery during seed development in apomicts.
在本研究中，我们确定了无融合生殖和有性生殖的博伊彻拉属物种中DNA甲基转移酶（DNMT）基因的结构，并研究了种子发育过程中的表达水平。从植物基因组数据库10.3中获取的二倍体有性生殖博伊彻拉窄叶种DNMT基因的蛋白质和DNA序列，用于鉴定无融合生殖种博伊彻拉全缘叶种和博伊彻拉叉分种中的同源物。使用Geneious R8软件将博伊彻拉全缘叶种全基因组的短配对 reads 文库或博伊彻拉叉分种转录组 reads 映射到参考基因序列。我们确定了三个DNMT基因；对于博伊彻拉属物种，分别是甲基转移酶1（MET1）、染色质甲基化酶3（CMT3）和结构域重排甲基转移酶1/2（DRM2）。我们用生物信息学工具检查了这些基因的结构，并与植物中的其他DNMT基因进行了比较。我们还通过半定量PCR检测了受精后角果组织中的表达水平。无融合生殖和有性生殖的博伊彻拉属物种中DNMT蛋白的结构具有共同特征。然而，无融合生殖和有性生殖的博伊彻拉属物种中DNMT基因的表达水平不同。我们发现受精后，DRM2在无融合生殖的博伊彻拉属物种中上调。系统发育树表明，这三个基因在绿藻、单子叶植物和双子叶植物中是保守的。我们的结果表明，在无融合生殖种的种子发育过程中，DNA甲基化机制失调。
