State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
BMC Genomics. 2018 Dec 20;19(1):950. doi: 10.1186/s12864-018-5346-x.
Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the divergence of species, RNA editing and phylogeny. In this study, we sequenced and analyzed the complete chloroplast (cp) genome sequence of B. platyphylla.
The complete cp genome of B. platyphylla was 160,518 bp in length, which included a pair of inverted repeats (IRs) of 26,056 bp that separated a large single copy (LSC) region of 89,397 bp and a small single copy (SSC) region of 19,009 bp. The annotation contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. There were 3 genes using alternative initiation codons. Comparative genomics showed that the sequence of the Fagales species cp genome was relatively conserved, but there were still some high variation regions that could be used as molecular markers. The IR expansion event of B. platyphylla resulted in larger cp genomes and rps19 pseudogene formation. The simple sequence repeat (SSR) analysis showed that there were 105 SSRs in the cp genome of B. platyphylla. RNA editing sites recognition indicated that at least 80 RNA editing events occurred in the cp genome. Most of the substitutions were C to U, while a small proportion of them were not. In particular, three editing loci on the rRNA were converted to more than two other bases that had never been reported. For synonymous conversion, most of them increased the relative synonymous codon usage (RSCU) value of the codons. The phylogenetic analysis suggested that B. platyphylla had a closer evolutionary relationship with B. pendula than B. nana.
In this study, we not only obtained and annotated the complete cp genome sequence of B. platyphylla, but we also identified new RNA editing sites and predicted the phylogenetic relationships among Fagales species. These findings will facilitate genomic, genetic engineering and phylogenetic studies of this important species.
白桦是中国北方常见的树种，具有很高的经济和药用价值。我们的实验室大约 10 年来一直致力于白桦的基因组研究。作为主要的细胞器基因组，叶绿体的完整基因组序列对于研究物种的分化、RNA 编辑和系统发育非常重要。在这项研究中，我们对白桦的完整叶绿体（cp）基因组进行了测序和分析。
白桦的完整 cp 基因组长度为 160518bp，包括一对长为 26056bp 的反向重复（IR），它们分隔了长单一拷贝（LSC）区的 89397bp 和短单一拷贝（SSC）区的 19009bp。注释共包含 129 个基因，包括 84 个蛋白质编码基因、37 个 tRNA 基因和 8 个 rRNA 基因。有 3 个基因使用了替代起始密码子。比较基因组学表明，壳斗目物种 cp 基因组的序列相对保守，但仍存在一些可作为分子标记的高度变异区。白桦的 IR 扩展事件导致了更大的 cp 基因组和 rps19 假基因的形成。简单序列重复（SSR）分析表明，白桦的 cp 基因组中存在 105 个 SSR。RNA 编辑位点识别表明，cp 基因组中至少发生了 80 次 RNA 编辑事件。大多数取代是 C 到 U，而一小部分则不是。特别是，rRNA 上的三个编辑位点被转换为从未报道过的其他两个以上的碱基。对于同义转换，大多数增加了密码子的相对同义密码子使用（RSCU）值。系统发育分析表明，白桦与欧洲白桦的进化关系比与北美白桦更近。
在这项研究中，我们不仅获得并注释了白桦的完整 cp 基因组序列，还鉴定了新的 RNA 编辑位点，并预测了壳斗目物种的系统发育关系。这些发现将促进对这一重要物种的基因组学、遗传工程和系统发育研究。
