Lee Sung-Il, Nkongolo Kabwe, Park Doori, Choi Ik-Young, Choi Ah-Young, Kim Nam-Soo
Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266, Sinjeong, Jeongeup, 500-185, Republic of Korea.
Department of Biology, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
Genes Genomics. 2019 Mar;41(3):305-316. doi: 10.1007/s13258-018-0762-5. Epub 2018 Nov 19.
Betulaceae is a relatively small birch family that comprises about 160 deciduous trees and shrubs. Chloroplast (cp) genome sequencing of Alnus rubra and Betula cordifolia was carried out to elucidate their molecular features and phylogenetic relationship among species in Betulaceae family.
Chloroplast genome sequencing was carried out using next generation sequencing method. Molecular and genomic features of the two cp genomes were characterized with other cp genomes in Betulaceae. Also, molecular phylogenetic analysis was performed using the whole cp genome sequences.
The average cp genome length was 160,136 bp among the Betulaceae species. Base compositions of the cp genomes were skewed toward a high AT ratio, with an average of 63.4%. We identified 117 different genes 83 with protein coding, 4 with ribosomal RNA, and 30 with tRNA. Eighteen genes contained introns which were conserved among the cp genomes of all Betulaceae. We mined 82 SSRs from the cp genomes of A. rubra, A. cordifolia, and A. nana. The SSRs were variable in motif repeat numbers and presence/absence among the cp genomes.
Chloroplast genome-wide sequence comparison from 11 Betulaceae species and one cp genome of evergreen oak revealed that the patterns of sequence variations were congruent with two subfamily classification Betuloideae (Alnus and Betula) and Corylaceae (Corylus, Ostrya, and Carpinus). Subsequent phylogenetic analysis also supports the sub-classifications of these species.
桦木科是一个相对较小的桦木家族，包含约160种落叶乔木和灌木。对红桤木和心叶桦进行叶绿体（cp）基因组测序，以阐明它们的分子特征以及桦木科物种间的系统发育关系。
采用下一代测序方法进行叶绿体基因组测序。用桦木科的其他cp基因组对这两个cp基因组的分子和基因组特征进行了表征。此外，使用整个cp基因组序列进行了分子系统发育分析。
桦木科物种的cp基因组平均长度为160,136 bp。cp基因组的碱基组成偏向于高AT比例，平均为63.4%。我们鉴定出117个不同的基因，其中83个为蛋白质编码基因，4个为核糖体RNA基因，30个为tRNA基因。18个基因含有内含子，这些内含子在所有桦木科cp基因组中都是保守的。我们从红桤木、心叶桦和矮桤木的cp基因组中挖掘出82个简单序列重复（SSR）。这些SSR在基序重复数以及cp基因组之间的存在/缺失情况上存在差异。
对11种桦木科物种的叶绿体全基因组序列比较以及一种常绿栎的一个cp基因组序列比较显示，序列变异模式与两个亚科分类一致，即桦亚科（桤木属和桦木属）和榛科（榛属、铁木属和鹅耳枥属）。随后的系统发育分析也支持这些物种的亚分类。
