Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

Su Chen,Guan-Zheng Qu,Sui Wang,Chuanping Yang,Xiyang Zhao

doi:10.1186/s12864-018-5346-x

Abstract

BackgroundBetula 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.ResultsThe 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.ConclusionsIn 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.

Highlights

Betula platyphylla is a common tree species in northern China that has high economic and medicinal value
Chloroplast genome assembly Based on the National Center for Biotechnology Information (NCBI) Organelle Genome Resources database, we extracted approximately 128.8 Mbp of pairedend reads for cp genome assembly
With the help of Edena, a first assembly consisting of 35 contigs was obtained (Table 1)

Summary

Introduction

Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. The complete genome sequences of chloroplasts are important to study the divergence of species, RNA editing and phylogeny. Deletion or switching bases, such as cytidine (C) to uridine (U), is an essential repair mechanism, and many mutations at the cp genome level may lead to strong deleterious phenotypes [17]. Because they have fairly stable structures, moderate evolutionary rates and uniparental inheritance in most angiosperms, the cp genomes have made significant contributions to phylogenetic studies [16, 18]

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