College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160, China.
College of Horticulture and Gardening, Yangtze University, Jingzhou, 433200, China.
BMC Genomics. 2023 Jan 18;24(1):30. doi: 10.1186/s12864-023-09115-9.
The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100-150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse.
We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986-88,200 bp), a small single copy (SSC, 15,498-15,891 bp) and a pair of inverted repeats (IRs, 29,765-29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis.
This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.
姜科姜属分布于热带、亚热带和远东亚洲。该属约有 100-150 种，许多种具有重要的农业、药用和园艺资源价值。然而，目前用于物种鉴定的基因组资源和合适的分子标记仍然很匮乏。
我们对姜属物种进行了比较基因组学和系统发育分析。姜属叶绿体基因组（大小范围 162507-163711bp）具有典型的四分体结构，由一个大的单拷贝（LSC，86986-88200bp）、一个小的单拷贝（SSC，15498-15891bp）和一对反向重复（IRs，29765-29934bp）组成。基因组包含 113 个独特的基因，包括 79 个蛋白编码基因、30 个 tRNA 和 4 个 rRNA 基因。姜属基因组的结构、基因组成、氨基酸频率、密码子使用模式、RNA 编辑位点、简单序列重复和长重复均具有保守性。序列分歧分析表明，以下基因经历了正选择（ccsA、ndhA、ndhB、petD、psbA、psbB、psbC、rbcL、rpl12、rpl20、rpl23、rpl33、rpoC2、rps7、rps12 和 ycf3）。鉴定出 8 个高度可变区，包括 7 个内含子区（petA-pabJ、rbcL-accD、rpl32-trnL-UAG、rps16-trnQ-UUG、trnC-GCA-psbM、psbC-trnS-UGA 和 ndhF-rpl32）和 1 个基因区（ycf1）。系统发育分析表明，姜组与隐瓣姜组而不是 Pleuranthesis 组亲缘关系最近。
本研究报道了 14 种姜属植物的完整叶绿体基因组。总的来说，本研究为姜属提供了一个可靠的系统发育框架。我们在基因组测序中发现的多态性为姜属生成 DNA 标记提供了一个难得的机会。这些结果为未来的研究提供了基础，这些研究旨在了解姜属的分子进化动态或个体种群变异。
