Article
Plant Sciences
Tijana Cvetkovic, Damien D. Hinsinger, Daniel C. Thomas, Jan J. Wieringa, Elango Velautham, Joeri S. Strijk
Summary: Dipterocarpoideae, the largest subfamily in the Meranti family, are dominant trees in wet tropical Asia facing increasing anthropogenic pressures. They have been the focus of numerous studies due to their economic value, historical biogeographical importance, and role in the evolution of the Asian tropical forest biome. Despite persistent taxonomic and evolutionary questions, a comprehensive phylogenomic hypothesis has been proposed, revising the tribal classification of the subfamily into four main clades based on plastome and nuclear cistron data.
Article
Evolutionary Biology
Yujing Yan, Charles C. Davis, Dimitar Dimitrov, Zhiheng Wang, Carsten Rahbek, Michael Krabbe Borregaard
Summary: The tea family, Theaceae, exhibits a unique distribution pattern with species mainly found in East Asia and some in the Americas. By integrating fossil evidence and phylogenetic analysis, the study revealed the historical biogeography of Theaceae species and highlighted the significance of combining fossil and molecular data for improving the reliability of biogeographic inferences.
SYSTEMATIC BIOLOGY
(2021)
Article
Plant Sciences
Ya-Ping Chen, Fei Zhao, Alan J. Paton, Purayidathkandy Sunojkumar, Lian-Ming Gao, Chun-Lei Xiang
Summary: This study aimed to elucidate the phylogenetic relationships within Isodon, especially in Clade IV, using plastome sequences with a broad taxon sampling. Results showed congruent topologies among 12 data sets, recovering major lineages of Isodon but also revealing incongruences among data sets and single plastid loci. These incongruences are likely due to insufficient phylogenetic signal, hybridization, and plastid capture, highlighting the need for additional nuclear genome data to resolve relationships within Isodon.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Xue-Min Xu, Zhen Wei, Jun-Zhe Sun, Qing-Fei Zhao, Yang Lu, Zhen-Long Wang, Shi-Xin Zhu
Summary: This study analyzed the chloroplast genomes of 43 Leontopodium and closely related genera. It found that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved, but differed in terms of length and certain regions. The molecular phylogenetic results were inconsistent with the previous taxonomic system based on morphology.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Jian He, Rudan Lyu, Yike Luo, Lele Lin, Min Yao, Jiamin Xiao, Lei Xie, Jun Wen, Linying Pei, Shuangxi Yan, Jin Cheng, Jinyu Li, Liangqian Li
Summary: The study reconstructed the evolutionary history of Clematis using plastome and nuclear ribosomal DNA sequences, revealing that the shrubby habit evolved independently in four lineages of Clematis in Asia and emerged since the very beginning of the Pliocene. Asian monsoon variation in the Pliocene and glacial period fluctuation in the Pleistocene were identified as driving forces for the origin and diversification of shrubby Clematis in Central Asia and adjacent dry areas.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jinliao Chen, Fei Wang, Chengyuan Zhou, Sagheer Ahmad, Yuzhen Zhou, Minghe Li, Zhongjian Liu, Donghui Peng
Summary: Aerides is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, comprising approximately 20 species. This study used next-generation sequencing technology to investigate the phylogeny and DNA barcoding of Aerides using genetic information from six Aerides plastid genomes. The findings provide assistance for species identification and DNA barcoding investigation in Aerides, as well as contribute to future research on the phylogenomics of Orchidaceae.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Priyanka Sharma, Ardashir Kharabian Masouleh, Bruce Topp, Agnelo Furtado, Robert J. Henry
Summary: Recent advances in sequencing and assembly of plant genomes have led to increased contiguity and accuracy, allowing for near complete chromosome level assemblies. The use of proximity analysis and highly accurate long reads has greatly improved the quality of genome assemblies, making de novo assembly of plant genomes feasible.
Article
Plant Sciences
Kashish Kamra, Joonhyung Jung, Joo-Hwan Kim
Summary: The plastid genome is an effective tool for studying plant phylogenetics. In this study, we conducted comparative genomics of the Iridaceae family, revealing its structural characteristics and evolutionary relationships. We also identified genomic events and gene deletions in some species. This study provides valuable insights for further research on the evolution and phylogenetic relationships of Iridaceae.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Jianshuang Shen, Xueqin Li, Xia Chen, Xiaoling Huang, Songheng Jin
Summary: Carya cathayensis, an economically important nut tree endemic to eastern China, has a cp genome of 160,825 bp with 129 genes, showing signs of positive selection. Phylogenetic analysis reveals that C. cathayensis is closely related to Carya kweichowensis and Carya illinoinensis.
Article
Plant Sciences
Xu-Long Yang, Qing-Hui Sun, Diego F. Morales-Briones, Jacob B. Landis, Da-Juan Chen, Hong-Xin Wang, Jun Wen, Hua-Feng Wang
Summary: The discontinuous geographic distribution of plants in the north temperate zone has attracted significant research attention. This study investigates the distribution pattern of Lonicera and proposes revisions to its classification. The findings provide insights into the evolutionary history and diversification of Lonicera.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Plant Sciences
Zhi-Qiong Mo, Chao-Nan Fu, Ming-Shu Zhu, Richard Milne, Jun-Bo Yang, Jie Cai, Han-Tao Qin, Wei Zheng, Peter M. Hollingsworth, De-Zhu Li, Lian-Ming Gao
Summary: This study reconstructed the phylogeny of Rhododendron using plastid genomes with broad taxon sampling, revealing complex relationships within the genus. The research also uncovered the divergence times and diversification rates of different subgenera, as well as the ecological adaptability of species.
Article
Biochemistry & Molecular Biology
Cheng-Yuan Zhou, Meng-Yao Zeng, Xuyong Gao, Zhuang Zhao, Ruyi Li, Yuhan Wu, Zhong-Jian Liu, Diyang Zhang, Ming-He Li
Summary: Trichoglottis is a valuable ornamental orchid genus with rich variations in colors and shapes of flower. Plastome data is found to be a valuable source for molecular identification and evolutionary studies of Trichoglottis and its related genera.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Zhuang Zhao, Meng-Yao Zeng, Yu-Wei Wu, Jin-Wei Li, Zhuang Zhou, Zhong-Jian Liu, Ming-He Li
Summary: Epidendrum, an important genus in the Orchidaceae family, has significant horticultural and ornamental value and serves as a valuable research model. By sequencing and assembling the plastomes of five Epidendrum species, the characteristics and phylogenetic relationships of this genus were explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Lei Wei, Tong-Jian Liu, Gang Hao, Xue-Jun Ge, Hai-Fei Yan
Summary: This study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales. The mitogenomes possessed relatively high nucleotide diversity and showed considerable structural variation. The evolutionary history of MTPTs in Primula was found to be complicated, and various reasons for the size variation in Ericales mitogenomes were identified.
Article
Plant Sciences
Shi-Yu Lv, Xia-Ying Ye, Zhong-Hu Li, Peng-Fei Ma, De-Zhu Li
Summary: Fargesia, the largest genus in the temperate bamboo tribe Arundinarieae, is mainly found in the mountains of Southwest China with over 90 species. These bamboos are essential for subalpine forest ecosystems and provide food and habitat for endangered animals like the giant panda. However, identifying Fargesia species is challenging due to rapid radiation and slow molecular evolutionary rate. In this study, the discriminatory power of complete plastomes and nrDNA sequences were evaluated and found to be more effective than standard barcodes. Despite this, additional nuclear markers are needed for accurate species discrimination.
Article
Biochemistry & Molecular Biology
Hui Shang, Michael Sundue, Ran Wei, Xue-Ping Wei, Jun-Jie Luo, Li Liu, Pedro Schwartsburd, Yue-Hong Yan, Xian-Chun Zhang
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2018)
Article
Biochemistry & Molecular Biology
Ran Wei, Atsushi Ebihara, Yan-Mei Zhu, Cun-Feng Zhao, Sabine Hennequin, Xian-Chun Zhang
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2018)
Article
Plant Sciences
Lijuan He, Harald Schneider, Peter Hovenkamp, Jeannine Marquardt, Ran Wei, Xueping Wei, Xianchun Zhang, Qiaoping Xiang
Article
Plant Sciences
Si-Qi Liang, Ronald L. L. Viane, Xian-Chun Zhang, Ran Wei
Summary: The Asplenium pekinense complex includes multiple ploidy species, with A. sarelii and A. pekinense being more common, while A. anogrammoides and A. altajense are rare species often misidentified. The A. varians complex is composed of the widespread A. tenuicaule, rare A. semivarians, and three other tetraploid species. Both species complexes are known for their taxonomic difficulty due to their history of reticulate evolution.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2021)
Article
Evolutionary Biology
Cun-Feng Zhao, Ran Wei, Xian-Chun Zhang, Qiao-Ping Xiang
Article
Plant Sciences
Cun-Feng Zhao, Ran Wei, Qiao-Ping Xiang, Xian-Chun Zhang
Correction
Evolutionary Biology
Cun-Feng Zhao, Ran Wei, Xian-Chun Zhang
Article
Evolutionary Biology
Ran Wei, Jie Yang, Li-Juan He, Hong-Mei Liu, Jia-Yu Hu, Si-Qi Liang, Xue-Ping Wei, Cun-Feng Zhao, Xian-Chun Zhang
Summary: This study investigated the deep phylogenetic relationships within Polypodiaceae by utilizing 81 plastid genomes, improving the resolution of backbone phylogeny. The research identified potential phylogenetic artefacts affecting the incongruence of phylogenetic inferences and provided a robust framework for future subfamilial taxonomy within Polypodiaceae.
Article
Biochemistry & Molecular Biology
Ran Wei, Cun-Feng Zhao, Qiao-Ping Xiang, Xian-Chun Zhang
Summary: The establishment of Ellipinema was to accommodate Lepisorus jakonensis in the plastid gene tree. However, new nuclear data revealed that Ellipinema and allied genera are deeply nested within Lepisorus. The incongruent phylogenetic placement between nuclear and plastid results may suggest ancient hybridization events.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Meng-Hua Zhang, Ran Wei, Qiao-Ping Xiang, Atsushi Ebihara, Xian-Chun Zhang
Summary: The Eurasian and Mediterranean Selaginella helvetica group is taxonomically challenging, with 10 taxa identified through phylogenetic analyses. Nuclear DNA markers are more informative than chloroplast DNA markers in delineating closely related species within Selaginella.
Article
Biochemistry & Molecular Biology
Si-Qi Liang, Xian-Chun Zhang, Ran Wei
Summary: This study investigates the spatial genetic structure of the Athyrium sinense complex and identifies geographical distance, environment, climatic history, and external dispersal constraints as driving forces. The findings reveal a clear north-south divergence in East Asia, with climate fluctuations playing a crucial role in the formation of this divergence. The present genetic structure is attributed to adaptation to heterogeneous environments and the effects of gene flow are constrained by factors such as canopy density, wind direction, and habitat continuity.
Article
Biochemistry & Molecular Biology
Meng-Hua Zhang, Qiao-Ping Xiang, Xian-Chun Zhang
Summary: This study provides a comprehensive analysis of the plastomes of Selaginellaceae, revealing conflicts and uncertainties in their phylogenetic relationships and exploring the underlying causes. The results demonstrate that the coalescent method is more effective in overcoming issues caused by outlier genes and extreme RNA editing events.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Editorial Material
Plant Sciences
Ran Wei, Cunfeng Zhao
Article
Plant Sciences
Zi-Yue Liu, Hong-Jin Wei, Hui Shang, Ran Wei, Ying Wang, Bao-Dong Liu, Yue-Hong Yan