Article
Plant Sciences
Alexa S. Tyszka, Eric C. Bretz, Holly M. Robertson, Miles D. Woodcock-Girard, Karolis Ramanauskas, Drew A. Larson, Gregory W. Stull, Joseph F. Walker
Summary: Chloroplasts and mitochondria have their own genomes and have been important for inferring land plant phylogeny. This study examined the genomes of 226 land plants to investigate the similarity between the evolutionary histories of these organelles. The results showed mostly concordant topologies, except for a few conflicting relationships that need further investigation. The findings suggest significant differences in molecular evolution between the chloroplast and mitochondrial genomes, indicating the need for separate evolutionary models.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Dhafer A. Alzahrani
Summary: Abutilon fruticosum, an endemic plant in Saudi Arabia, has a complete chloroplast genome with 114 unique genes. Comparative analyses show similarities with other Malvaceae species in gene content and structure, and variability in gene position. Phylogenetic analysis suggests a close relationship with Althaea officinalis, contradicting previous systematic positions. This study provides valuable insights for further phylogenetic and evolutionary studies within the Malvaceae family.
Article
Multidisciplinary Sciences
Xinyu Sun, Ying Zhan, Songlin Li, Yu Liu, Qiang Fu, Xin Quan, Jinyu Xiong, Huixin Gang, Lijun Zhang, Huijuan Qi, Aoxue Wang, Junwei Huo, Dong Qin, Chenqiao Zhu
Summary: This study assembled the complete chloroplast genomes of blackcurrant, red currant, white currant, and gooseberry for the first time, providing valuable genomic data for their systematic classification and molecular breeding. The phylogenetic analysis revealed the relationships within Grossulariaceae and the Ribes genus, challenging the current classification based on morphology.
Article
Plant Sciences
Salvador Guzman-Diaz, Fabian Augusto Aldaba Nunez, Emily Veltjen, Pieter Asselman, Isabel Larridon, Marie-Stephanie Samain
Summary: Chloroplast genomes in Magnoliaceae are considered highly conserved but intergenic regions show significant nucleotide diversity, contributing to phylogenetically informative data. The gene content is consistent across species, with a length of about 160kb, and differences between genera are greater than within genera. Phylogenetic analyses confirm that the current infrageneric classification in Magnolia does not reflect natural relationships.
Article
Plant Sciences
Yun Song, Fan Jiang, Junxia Shi, Chaonan Wang, Ning Xiang, Shuifang Zhu
Summary: This study examined the classification and phylogenetic relationships of Phytolacca using the whole chloroplast genome and three markers. The results showed that Phytolacca is monophyletic and that Central America is the center of species diversity. Birds may play a key role in the dispersal of Phytolacca due to the fleshy fruiting of the genus.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Joonhyung Jung, Changkyun Kim, Joo-Hwan Kim
Summary: This study provides detailed information on 15 complete plastid genomes of Commelinoideae taxa, revealing structural variations and resolving problematic positions among genera in the family.
Article
Biotechnology & Applied Microbiology
Nan Lin, Rui Liu, Yakun Wang, Peng Guo, Yihan Wang, Yanpei Liu, Fude Shang
Summary: The complete chloroplast genome of Ulmus mianzhuensis was sequenced and compared with other Ulmus species, revealing a highly conserved gene structure. It was also found that U. mianzhuensis should be considered as a subspecies of U. parvifolia. This study highlights the valuable information provided by the chloroplast genome in genetic variation and phylogenetic analysis of Ulmus species.
Article
Biotechnology & Applied Microbiology
Kewang Xu, Chenxue Lin, Shiou Yih Lee, Lingfeng Mao, Kaikai Meng
Summary: This study compared the chloroplast genomes of Ilex species and estimated their phylogenetic relationships. The results showed shared genomic structures and gene rearrangements among Ilex species. Hypervariable and repetitive regions were also identified, which could be useful for future phylogenetic and population genetic studies.
Article
Plant Sciences
Bartosz Ulaszewski, Sandra Jankowska-Wroblewska, Katarzyna Swilo, Jaroslaw Burczyk
Summary: The study found that Aria edulis, Chamaemespilus alpina, and Torminalis glaberrima were more closely related to each other rather than to Sorbus s.s., providing additional support for considering them as separate genera.
Article
Plant Sciences
Kuan Liu, Rong Wang, Xiu-Xiu Guo, Xue-Jie Zhang, Xiao-Jian Qu, Shou-Jin Fan
Summary: This study sequenced and analyzed the chloroplast genomes of 13 Eragrostideae species, identifying useful molecular markers for phylogenetic analysis. The study revealed Enneapogon as the earliest diverging lineage, Eragrostis as the sister to Uniola including Harpachne, and discussed the classification of Harpachne harpachnoides based on morphological and molecular evidence.
Article
Horticulture
Anna Pikunova, Svetlana Goryunova, Olga Golyaeva, Maria Dolzhikova, Anna Pavlenko, Oleg Kurashev, Evgeniia Sotnikova, Oksana Polivanova, Anastasia Sivolapova, Oleg Kazakov, Denis Goryunov
Summary: The complete chloroplast genomes of red currant and gooseberry cultivars were sequenced and assembled, revealing differences in genome length and protein-coding genes. Phylogenetic analysis showed that Ribes species clustered together, with Ribes fasciculatum being the most distant. All Ribes species share a similar set of protein-coding genes in their plastome sequences. Negative selection was observed for most genes in both the Ribes group and Saxifragales, while positive selection was observed for ycf4 and clpP genes in the Ribes group. Pseudogenization events of ycf genes may reflect their importance in Ribes' adaptation. The study provides valuable genomic resources and clarifications for marker development and phylogenomics of the Ribes genus.
Article
Genetics & Heredity
Samaila Samaila Yaradua, Kowiyou Yessoufou
Summary: This study sequenced the complete chloroplast genome of Hypoestes forskaolii and explored its evolutionary patterns and phylogenetic relationships within Justiceae. The results showed highly conserved genomic structure and gene contents within Justiceae, with slight differences in gene locations. Variable hotspots in the cp genome were identified as potential DNA barcodes for evolutionary analysis.
Article
Genetics & Heredity
Jialong Pei, Yong Wang, Juan Zhuo, Huibin Gao, Naresh Vasupalli, Dan Hou, Xinchun Lin
Summary: This study sequenced and analyzed the complete chloroplast genome of Dendrocalamus farinosus, a bamboo species used for food and timber in southwestern China. The genome structure, gene content, repeat sequences, and phylogenetic relationship with other Dendrocalamus species were investigated. Comparative analysis showed differences between the genomes, with higher divergence in non-coding regions and greater conservation in inverted repeat regions. The study also identified a potential gene marker for distinguishing bamboo species and provided insights into the evolutionary pathways of bamboo species based on their geographic distribution and rhizome types.
Article
Biology
Lin Yang, Jinhong Tian, Liu Xu, Xueli Zhao, Yuyang Song, Dawei Wang
Summary: This study sequenced six new chloroplast genomes of the endangered Magnoliaceae family and analyzed the phylogenetic relationships of 37 published chloroplast genomes in the family. The findings showed the typical quadripartite structure of chloroplast genomes in Magnoliaceae and provided insights into the intergeneric relationships of the family. These findings will contribute to adjusting the phylogenetic position of Magnoliaceae at the molecular level.
Article
Plant Sciences
Rongrong Yan, Yanfei Geng, Yuhuan Jia, Chunlei Xiang, Xinxin Zhou, Guoxiong Hu
Summary: This study explored the phylogenetic relationships and genome evolution of the Linderniaceae family through plastid phylogenomic and comparative genomic analyses. The findings provide new evidence for the classification of certain genera within Linderniaceae and confirm Linderniaceae as a distinctive lineage. Comparative analyses revealed the highly conservative nature of the Linderniaceae plastomes in terms of structure, gene order, and gene content.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Ecology
Ya-Huang Luo, Liang-Liang Ma, Sebastian Seibold, Marc W. W. Cadotte, Kevin S. S. Burgess, Shao-Lin Tan, Lin-Jiang Ye, Wei Zheng, Jia-Yun Zou, Zhi-Fa Chen, De-Tuan Liu, Guang-Fu Zhu, Xiao-Chun Shi, Wei Zhao, De-Zhu Li, Jie Liu, Lian-Ming Gao
Summary: This study assessed the effects of different mycorrhizal types on forest carbon storage and the biodiversity-ecosystem functioning (BEF) relationships in the Gaoligong Mountains, Southwest China. It was found that different mycorrhizal types have significant impacts on forest carbon storage and species diversity. Furthermore, future global changes could potentially alter the mycorrhizal-mediated BEF relationships in mountain forests.
JOURNAL OF BIOGEOGRAPHY
(2023)
Review
Biochemistry & Molecular Biology
Cen Guo, Yang Luo, Lian-Ming Gao, Ting-Shuang Yi, Hong-Tao Li, Jun-Bo Yang, De-Zhu Li
Summary: The advancement of next-generation sequencing and long-read sequencing technologies has greatly influenced plant phylogenetic studies. Numerous phylogenetic studies using hundreds to thousands of genes across various clades have emerged in the past decade, bringing plant phylogenetics and evolution into a new era. This review focuses on the application of genomic data in phylogenetic and evolutionary investigations, describes the methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at different taxonomic levels. Challenges, such as systematic errors and underlying biological factors, are discussed, suggesting that a bifurcating tree may not be the most suitable model for the tree of life. Finally, promising avenues for future plant phylogenomic studies are discussed.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Plant Sciences
Sheng-Yuan Qin, Kai Chen, Wen-Ju Zhang, Xiao-Guo Xiang, Zheng-Yu Zuo, Cen Guo, Yao Zhao, Lin-Feng Li, Yu-Guo Wang, Zhi-Ping Song, Ji Yang, Xiao-Qiang Yang, Jian Zhang, Wei-Tao Jin, Qiang Wen, Song-Zi Zhao, Jia-Kuan Chen, De-Zhu Li, Jun Rong
Summary: This study sequenced and assembled the transcriptomes and plastomes of various species in the Camellia genus, providing a comprehensive taxonomic sampling for Camellia sect. Oleifera and C. sect. Paracamellia. Phylogenetic analyses showed that C. sect. Oleifera should be merged with C. sect. Paracamellia. Hybridization was found among polyploid species and their relatives. The divergence of major clades in C. sect. Paracamellia occurred during the middle to late Miocene, and the Quaternary period witnessed rapid diversification likely due to hybridization and polyploidization. This study also suggested that the hexaploid Camellia oleifera may have originated from hybridization between closely related diploid and tetraploid species.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Review
Ecology
Zeng-Yuan Wu, Richard I. Milne, Jie Liu, Ran Nathan, Richard T. Corlett, De-Zhu Li
Summary: Long-distance dispersal (LDD) beyond a species' range is crucial for ecological and evolutionary patterns, but postdispersal establishment has not received enough attention. This review summarizes the current understanding of post-LDD establishment in plant colonization, identifies key determinants of establishment success, develops a general framework for quantifying post-LDD establishment, and outlines future research challenges and opportunities. These include improving LDD detection and understanding using novel approaches, investigating mechanistic modeling and inference to understand establishment success, and comparing establishment between past and present. By addressing knowledge gaps, this review aims to enhance our understanding of the impacts of LDD on plant distributions and long-term consequences.
TRENDS IN ECOLOGY & EVOLUTION
(2023)
Article
Plant Sciences
Zhi-Hua Zeng, Qian Yu, Qing-Hong Feng, Xin-Jia Wang, Li Zhong, Hua-Ying Sun, Hong Wang, De-Zhu Li, Spencer C. H. Barrett, Wei Zhou
Summary: This study demonstrates the functional consequences of height dimorphism reversal in dioecious plants, shedding light on the reproductive strategies of males and females in terms of pollen and seed dispersal.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Sheng-Yuan Qin, Zheng-Yu Zuo, Cen Guo, Xin-Yu Du, Shui-Yin Liu, Xiang-Qin Yu, Xiao-Guo Xiang, Jun Rong, Bing Liu, Zhi-Fang Liu, Peng-Fei Ma, De-Zhu Li
Summary: This study focuses on the Litsea complex, which is a key lineage of evergreen broadleaved forests (EBLFs) in East Asia, aiming to explore the shift of evergreen versus deciduous trait and understand the origin and historical dynamics of EBLFs under Cenozoic climate change. The results show that the prototype of EBLFs in East Asia probably appeared in the Early Eocene period (about 55-50 million years ago) facilitated by greenhouse warming. With the cooling and drying climate in the Middle to Late Eocene period (48-38 million years ago), deciduous habits evolved. The development of East Asian monsoon in the Early Miocene period (23 million years ago) increased the extreme seasonal precipitation and promoted the emergence of evergreen habits.
Editorial Material
Plant Sciences
Dechang Cao, Jerry M. Baskin, Carol C. Baskin, De-Zhu Li
Summary: Smoke cues released from decaying leaves after drying are crucial for seed germination.
TRENDS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lin-Jiang Ye, Michael Moller, Ya-Huang Luo, Jia-Yun Zou, Wei Zheng, Jie Liu, De-Zhu Li, Lian-Ming Gao
Summary: Selection along environmental gradients in alpine ecosystems can drive adaptive evolution in plants. However, the genetic variation and adaptation in plants along environmental gradients remain poorly understood. To address this gap, we studied the transcriptomic profiles of Rhododendron sanguineum var. haemaleum at different elevations in the Gaoligong Mountains. We found that gene expression patterns in flower and leaf organs showed parallel shifts but with different functionality, indicating flexibility in response strategies to the heterogeneous environments.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Chun-Jiao Li, Xin-Tong Xie, Hong-Xin Liu, Ruo-Nan Wang, De-Zhu Li
Summary: This study sequenced and assembled the plastomes of East Asian lobelias, revealing variations in plastome gene structure among different taxonomic sections. The study also assessed the variability of several genes and simple sequence repeats, which can be used as important research tools in DNA barcoding and species delineation. The study further identified key genes related to the evolutionary history and adaptive evolution of East Asian lobelias. These findings will contribute to further advancements in taxonomy, evolutionary biology, and the utilization of medicinal plant resources.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Bing Han, Yelan Li, Di Wu, De-Zhu Li, Aizhong Liu, Wei Xu
Summary: Genomic imprinting plays a significant role in the endosperm development, storage compound accumulation, and seed germination in castor bean. The study reveals that DNA methylation has a limited role in controlling genomic imprinting, while histone modifications play a more significant role in regulating the expression of most imprinted genes.
Article
Plant Sciences
Jiu-Xia Zhao, Shu Wang, Jiazhi Liu, Xiao-Dong Jiang, Jing Wen, Zhi-Quan Suo, Jie Liu, Mi-Cai Zhong, Qin Wang, Zhirong Gu, Changning Liu, Yunfei Deng, Jin-Yong Hu, De-Zhu Li
Summary: This study generated a transcriptome resource for two Strobilanthes species, providing valuable information for understanding the molecular mechanisms of perennial monocarpic mass flowering. The differential expression of transcription factors potentially involved in the photoperiod and circadian-clock pathway suggests their role in regulating flowering time diversity.
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
Plant Sciences
Jing-Xia Liu, Zu-Chang Xu, Yu-Xiao Zhang, Meng-Yuan Zhou, De-Zhu Li
Summary: Three woody bamboo species collected in Hainan, China in 1940, previously described as Dinochloa, are found to be closely related to Melocalamus through molecular phylogenetic analysis and morphological comparison. Therefore, it is suggested to transfer these three species to the genus Melocalamus.
Article
Plant Sciences
Rivontsoa A. Rakotonasolo, Soejatmi Dransfield, Thomas Haevermans, Helene Ralimanana, Maria S. Vorontsova, Meng-Yuan Zhou, De-Zhu Li
Summary: The Hickeliinae is an important subtribe of tropical bamboos, mainly found in Madagascar, Comoros, Reunion Island, and a small part of Tanzania. Molecular phylogenetic analysis of newly sequenced plastid genomes revealed conserved structures and provided informative data for phylogenetic reconstructions. The analysis showed that all genera of Hickeliinae are monophyletic, except for Nastus, which forms two distant clades. This study provides significant resources for further genetic and phylogenomic research on this under-studied subtribe.
Article
Plant Sciences
Ji-Dong Ya, Wan -Ting Wang, Yun-Long Liu, Hong Jiang, Zhou-Dong Han, Ting Zhang, Hua Huang, Jie Cai, De-Zhu Li
Summary: Five new orchid species from Yunnan Province and Tibet have been described and illustrated. The study sequenced the complete plastomes of these species and their related species to confirm their identities and determine their phylogenetic relationships. The results showed that the N. lihengiae species is closely related to the N. grandiflora and N. pinetorum clade, while N. chawalongensis is sister to N. alternifolia. Additionally, the relationships among species in the genus Gastrochilus were inconsistent, but the two new species, G. lihengiae and G. bernhardtianus, were supported by all datasets.