Article
Genetics & Heredity
Chao Luo, Wulue Huang, Huseyin Yer, Troy Kamuda, Xinyi Li, Yang Li, Yuhong Rong, Bo Yan, Yonghui Wen, Qiong Wang, Meijuan Huang, Haiquan Huang
Summary: This study sequenced the complete chloroplast genomes of three Impatiens ornamental species and compared them with previously published data. The results showed similar genomic features among the species, as well as identified highly variable nucleotide hotspots that could be used as markers for species identification and taxonomy. The phylogenetic analysis revealed a close relationship among the Impatiens species studied.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Shujie Dong, Zhiqi Ying, Shuisheng Yu, Qirui Wang, Guanghui Liao, Yuqing Ge, Rubin Cheng
Summary: The study sequenced and compared the complete chloroplast genome of Stephania plants, revealing genome structures, genetic diversity hotspots, and phylogenetic relationships. This provides important references for future studies in DNA barcode, species identification, intraspecific and interspecific variability, and phylogenetic relationships of Stephania plants.
Article
Biotechnology & Applied Microbiology
Qijing Xia, Hongbin Zhang, Dong Lv, Yousry A. El-Kassaby, Wei Li
Summary: This study systematically analyzed and summarized the chloroplast genomes of 33 published pine species, confirming the traditional evolutionary theory and classification, and reclassifying some controversial species. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.
Article
Biochemistry & Molecular Biology
Jinliao Chen, Fei Wang, Zhuang Zhao, Minghe Li, Zhongjian Liu, Donghui Peng
Summary: In this study, the chloroplast genomes of three species of Paraphalaenopsis were reported and comprehensively analyzed. The genomes exhibited a quadripartite structure and varied in length from 147,311 bp to 149,240 bp. Unique genes including protein-coding genes, tRNA genes, and rRNA genes were identified in each genome. Six hypervariable regions were discovered as potential DNA molecular markers. Phylogenetic analysis indicated that Paraphalaenopsis is closely related to the Holcoglossum-Vanda clade within the Aeridinae subfamily. This study provides a foundation for future phylogenetic analysis of Aeridinae.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Forestry
Heng Liang, Juan Chen
Summary: The study investigated the plastome variation in nine species representing five genera of Zingibereae, confirming the relationship between Stahlianthus and Curcuma, and grouping Kaempferia, Boesenbergia, and Zingiber together as the Kaempferia group. Pyrgophyllum was found to be embedded within the Hedychium clade, not allied with the Curcuma clade. The findings demonstrate the power of plastid phylogenomics in improving phylogenetic relationships within Zingibereae.
Article
Horticulture
Yaxuan Xin, Wen-Bin Yu, Wichan Eiadthong, Zhengying Cao, Qishao Li, Zhenxin Yang, Wenzhi Zhao, Peiyao Xin
Summary: In this study, the chloroplast genomes of Mangifera species were analyzed, resulting in the identification of three highly variable regions that could be used as DNA barcodes for species determination. Phylogenetic analysis divided Mangifera into three clades, providing a theoretical basis for species determination and evolutionary studies.
Article
Biology
Xi Xia, Jingyu Peng, Lin Yang, Xueli Zhao, Anan Duan, Dawei Wang
Summary: In this study, the chloroplast genomes of eight Ficus species were sequenced and analyzed, revealing similar genome structures and repetitive sequences. The study also provided new insights into the subgeneric classification and species identification of Ficus.
Article
Genetics & Heredity
Haiyu Chen, Xinke Zhang, Guoshuai Zhang, Zhi Zhang, Guoxu Ma, Zhaocui Sun, Chang Liu, Linfang Huang
Summary: This study successfully obtained the chloroplast genome of Nepeta bracteata using Next-generation sequencing. The genome consists of 130 genes and exhibits a typical quadripartite structure. Comparative analysis with other species from the Nepeta genus identified five hypervariable regions. Phylogenetic analysis showed a close relationship between N. bracteata and Nepeta stewartiana. These findings enrich the resources available for chloroplast genomes in the Nepeta genus and highlight the potential of hypervariable regions as molecular markers.
Article
Biotechnology & Applied Microbiology
Dongzhu Jiang, Xiaodong Cai, Min Gong, Maoqin Xia, Haitao Xing, Shanshan Dong, Shuming Tian, Jialin Li, Junyao Lin, Yiqing Liu, Hong-Lei Li
Summary: This study conducted comparative genomics and phylogenetic analysis on the Zingiber genus. The results showed that the chloroplast genomes of Zingiber species have typical structures and conservative characteristics. Positive selection was identified in certain genes. The study also provided the complete chloroplast genome sequences of Zingiber species, which can be used for future research on molecular evolutionary dynamics and population variation.
Correction
Biotechnology & Applied Microbiology
Gurusamy Raman, Kyu Tae Park, Joo-Hwan Kim, SeonJoo Park
Summary: A revised version of this article has been published and is available through the original article.
Article
Plant Sciences
Zhengying Cao, Linyi Yang, Yaxuan Xin, Wenbin Xu, Qishao Li, Haorong Zhang, Yuxiang Tu, Yu Song, Peiyao Xin
Summary: This study conducted comparative genomic and phylogenetic analyses on seven Neocinnamomum taxa, revealing the genetic structure and evolutionary characteristics of these species. The chloroplast genome of Neocinnamomum has a size range of 150,753-150,956 bp and contains 128 annotated genes. The study identified 31 preferred codons and three highly variable regions. The results of this study will serve as a reference for molecular marker development and phylogenetic research in Neocinnamomum.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lin Li, Wanyao Wang, Guoqiang Zhang, Kunlin Wu, Lin Fang, Mingzhi Li, Zhongjian Liu, Songjun Zeng
Summary: This study sequenced and analyzed the chloroplast genomes of 13 species of Pholidota and revealed the systematic classification and mutation patterns of their chloroplast genomes. Six mutational hotspots were identified as potential molecular markers, providing important information for future genetic and genomic studies.
Article
Plant Sciences
Yu Feng, Xin-Fen Gao, Jun-Yi Zhang, Li-Sha Jiang, Xiong Li, Heng-Ning Deng, Min Liao, Bo Xu
Summary: The study provides insights into the chloroplast genome evolution and phylogenetic relationships of Campylotropis species through comparative genomics and phylogenomic analysis. It reveals the similarities among Campylotropis chloroplast genomes and identifies highly variable regions for species identification and phylogenetic studies. The study also reports a pseudogene in the matK gene of the legume family. Additionally, the phylogenetic analysis confirms the monophyly of Campylotropis and its relationship with other genera. The identification of positively selected genes and fast-evolving genes may contribute to understanding the adaptation of Campylotropis species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agricultural Engineering
Bingchao Wu, Jie Zhu, Xixi Ma, Jiyuan Jia, Dan Luo, Qiong Ding, Xiaoshan Wang, Linkai Huang
Summary: By comparing the chloroplast genomes of upland and lowland ecotypes of switchgrass, this study reveals conservation in terms of repetitive sequences, codon usage, and the identification of a lowland-specific hotspot. The phylogenetic analysis also highlights the complexity of the evolutionary process of switchgrass.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Biotechnology & Applied Microbiology
Chao Luo, Wulue Huang, Huayu Sun, Huseyin Yer, Xinyi Li, Yang Li, Bo Yan, Qiong Wang, Yonghui Wen, Meijuan Huang, Haiquan Huang
Summary: This study investigated the chloroplast genomes of Impatiens species and provided insights into nucleotide diversity hotspots, repeat sequences, and phylogenetic relationships within the Balsaminaceae family. The findings offer valuable genomic resources for molecular marker development and systematic evolution studies of Balsaminaceae species.