Article
Plant Sciences
Shuya Liu, Qing Xu, Kuiyan Liu, Yongfang Zhao, Nansheng Chen
Summary: In this study, complete chloroplast genomes of five Skeletonema species were constructed, showing high synteny and conservation with similar gene numbers. The presence of duplicate petF genes in both the chloroplast and nuclear genomes was observed. Selection analysis indicated purifying selection on protein-coding genes, while divergent regions were identified as potential markers for phylogenetic inference and genetic polymorphism detection. Furthermore, divergence times estimated using protein-coding genes suggest the establishment of these species around 33 million years ago, consistent with previous estimates using mitochondrial DNA. Overall, this study provides insights into the molecular evolution of Skeletonema chloroplast genomes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Rong Huang, Xuena Xie, Fang Li, Enwei Tian, Zhi Chao
Summary: The chloroplast genomes of Mediterranean Bupleurum species were reported for the first time, supporting them as a basal clade of Bupleurum with important insights into their evolutionary history and species classification. Chloroplast genome information is essential in advancing our understanding on phylogenetic study.
Article
Environmental Sciences
Ziyan He, Yang Chen, Yichao Wang, Kuiyan Liu, Qing Xu, Yang Li, Nansheng Chen
Summary: This study reports the full-length chloroplast genomes of nine Pseudo-nitzschia species and investigates their genomic structures and features. The findings provide critical genomic resources for future research on the biodiversity and speciation of Pseudo-nitzschia species.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Plant Sciences
Hoi-Yan Wu, Kwan-Ho Wong, Bobby Lim-Ho Kong, Tin-Yan Siu, Grace Wing-Chiu But, Stacey Shun-Kei Tsang, David Tai-Wai Lau, Pang-Chui Shaw
Summary: The pantropical genus Dalbergia consists of 269 species of trees, shrubs, and woody lianas. Due to illegal logging and trafficking driven by the high economic value of its heartwood, this genus is listed in CITES Appendices. However, species identification of Dalbergia timber and herbs is challenging but essential for CITES implementation. In this study, the chloroplast genomes of five Dalbergia species native to Hong Kong, including four medicinal plants, were sequenced and analyzed. Four divergence hotspots in the chloroplast genomes were identified as potential genetic markers for the identification of medicinal Dalbergia species.
Article
Multidisciplinary Sciences
Yihui Wang, Yifei Xie, Jiayi Jin, Jinyue Li, Xiangdong Qiu, Yang Tong, Zhongyang Li, Zhixiang Zhang, Wenling Lai
Summary: This study investigates the chloroplast genome characteristics and phylogenetic relationships of Elaeocarpaceae species. The results provide new insights into the evolutionary history of this plant family.
Article
Biotechnology & Applied Microbiology
Mengjia Zhang, Nansheng Chen
Summary: This study constructed the complete chloroplast genomes of seven Thalassionema strains, revealing genetic differences within and between species. Additionally, the study identified genomic differences between Thalassionema species and other diatoms. The study also provided insights into the phylogenetic position and emergence time of Thalassionema species.
Article
Forestry
Tao Yu, Zhiyuan Jia, Buddhi Dayananda, Junqing Li, Xiaolei Guo, Liang Shi, Xiaowen Yuan, Yan Gao
Summary: In this study, the authors analyzed the sequences of chloroplast genomes of four Pinus species to investigate hybrid speciation. The results showed that P. sylvestris was the paternal parent in hybridization events and identified divergent hotspot regions and simple sequence repeats. The findings provide new insights into the phylogenetic relationships within Pinus genus.
JOURNAL OF FORESTRY RESEARCH
(2022)
Article
Microbiology
Qing Xu, Zongmei Cui, Nansheng Chen
Summary: This study constructed full-length chloroplast genomes for seven Chaetoceros species, revealing their conserved genome arrangement and specific divergence. The availability of these cpDNAs provides valuable reference sequences for studying the evolutionary relationships among Chaetoceros species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Qiyu Chen, Chunling Chen, Bo Wang, Zehuan Wang, Wenfen Xu, Yuan Huang, Qingwen Sun
Summary: This study assembled and analyzed the chloroplast genomes of the genus Sabia, revealing a relatively conserved genome structure with multiple variable loci. Phylogenetic analysis indicated that the two sections of Sabia did not form separate monophyletic groups. Divergence time calculations showed that the evolutionary branches of Sabia and Meliosma began approximately 85.95 million years ago, with species within Sabia diverging around 7.65 million years ago.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Xiaomin Wang, Shengyi Bai, Zhaolei Zhang, Fushun Zheng, Lina Song, Lu Wen, Meng Guo, Guoxin Cheng, Wenkong Yao, Yanming Gao, Jianshe Li
Summary: In this study, the chloroplast genomes of 29 tomato germplasms were sequenced and analyzed to compare and understand their phylogenetic relationships. The analysis revealed highly conserved characteristics among the cp genomes, including structure, gene and intron number, inverted repeat regions, and repeat sequences. Candidate SNP markers for future studies were selected based on highly polymorphic SNP loci. The phylogenetic tree showed that the cp genomes of tomatoes were clustered into two major clades, with S. pimpinellifolium and S. lycopersicum showing a close genetic relationship. Only rps15 gene exhibited the highest average K-A/K-S ratio in the analysis of adaptive evolution, indicating strong positive selection. This study provides valuable information for further research on phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Ning Wang, Wan-Lin Dong, Xiao-Jing Zhang, Tong Zhou, Xiao-Juan Huang, Bao-Guo Li, Jian-Ni Liu, Xiong-Feng Ma, Zhong-Hu Li
Summary: Novel structural variations were identified in cotton chloroplast tRNAs, and gene loss events were more prominent than duplications in chloroplast tRNAs. Analysis of 27 Gossypium species' chloroplast tRNAs revealed new tRNA structural variations in cotton plants.
Article
Plant Sciences
Shuaibin Wang, Junping Gao, Haoyu Chao, Zhaowu Li, Wenxuan Pu, Yaofu Wang, Ming Chen
Summary: In this study, the chloroplast genomes of Nicotiana species were compared, revealing new insights into the genetic variation and phylogenetic relationships in Nicotiana, and providing genetic resources for future speciation and biodiversity research.
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
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
Forestry
Huijuan Zhou, Xiaoxiao Gao, Keith Woeste, Peng Zhao, Shuoxin Zhang
Summary: Chloroplast (cp) DNA genomes of Castanea species show similar genomic structures with differences in gene loss and pseudogenization in certain genes. These findings contribute to a better understanding of the evolutionary history and phylogenetic relationships of chestnut species.
Article
Biotechnology & Applied Microbiology
Chaochen Huang, Pengbo Li, Junfeng Cao, Zishou Zheng, Jinquan Huang, Xiufang Zhang, Xiaoxia Shangguan, Lingjian Wang, Zhiwen Chen
Summary: In this study, a systematic analysis was performed on the CRY gene family in cotton species, revealing the structures, classification, synteny, and cis-elements of the genes. The potential biological functions of the genes in different tissues and in response to abiotic stress were predicted.
Article
Biochemistry & Molecular Biology
Joel Sharbrough, Justin L. Conover, Matheus Fernandes Gyorfy, Corrinne E. Grover, Emma R. Miller, Jonathan F. Wendel, Daniel B. Sloan
Summary: Whole-genome duplications (WGDs) are important for diversification in eukaryotes. The interaction between nuclear and cytoplasmic genomes plays a central role in eukaryotic function and adaptation. Our study on allopolyploids suggests that mismatches between paternal homoeologs and cytoplasmic genomes may lead to accelerated evolution in the paternal homoeologs.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Xuhu Guo, Jianguo Zhao, Zhiwen Chen, Jun Qiao, Yongfang Zhang, Hong Shen, Zhongli Hu
Summary: This study generated SlCMT4 mutants in tomato plants using the CRISPR-Cas9 gene editing system and found that the mutants exhibited severe developmental defects and altered fruit characteristics. The expression of genes related to hormone levels and pollen development was affected in the mutants. Whole-genome bisulfite sequencing revealed a reduction in DNA methylation in the mutants. These findings shed light on the function of SlCMT4 and the molecular regulatory mechanism of tomato plant development and fruit ripening.
HORTICULTURE RESEARCH
(2022)
Article
Plant Sciences
Yating Dong, Guanjing Hu, Corrinne E. Grover, Emma R. Miller, Shuijin Zhu, Jonathan F. Wendel
Summary: Polyploidy provides an opportunity for species diversification and evolutionary innovation, especially under stressful conditions. This study investigates the regulatory mechanisms underlying salt resistance diversity in Gossypium species. The results show that salt responsiveness varies across different cotton species, with differences in gene expression patterns and functional implications. Allopolyploid cottons have acquired a wide range of stress response flexibility relative to their diploid ancestors, which is likely mediated by duplicated genes and regulatory factors.
Article
Biochemistry & Molecular Biology
Wenrui Cui, Zhiwen Chen, Xiaoxia Shangguan, Taotao Li, Lingjian Wang, Xueyi Xue, Junfeng Cao
Summary: In this study, the researchers investigated the role of the second intron of the TRY gene in the spatial distribution of trichomes in Arabidopsis. They found that the expression of TRY increased with stem node number and peaked in the inflorescence, while the distribution of trichomes decreased. Further analysis revealed that flowering-related genes, such as SPL9, could directly bind to cis-elements in the TRY intron2 sequence, contributing to the spatial expression of TRY. They also found similar cis-elements in the intron2 of cotton TRY genes, suggesting a general regulatory mechanism across different plants.
Article
Genetics & Heredity
Corrinne E. Grover, Evan S. Forsythe, Joel Sharbrough, Emma R. Miller, Justin L. Conover, Rachael A. DeTar, Carolina Chavarro, Mark A. Arick, Daniel G. Peterson, Soraya C. M. Leal-Bertioli, Daniel B. Sloan, Jonathan F. Wendel
Summary: Cytonuclear coevolution, important in plant evolution, coordinates gene expression between the nucleus and organelles but can lead to incompatibilities in hybrid taxa. Allopolyploidy, common in plants, can result in cytonuclear conflicts, which may be resolved by nuclear redundancy created during polyploidy. Evaluating expression changes in organelle-targeted nuclear genes across multiple allopolyploid lineages revealed subtlety and variability in cytonuclear evolution, reflecting diverse mechanisms to resolve incompatibilities.
Article
Chemistry, Multidisciplinary
Zhiwen Chen, Jianguo Zhao, Zehui Liu, Xiuli Bai, Weijia Li, Zhifang Guan, Ming Zhou, Hongwei Zhu
Summary: Nanopesticides enhance the effectiveness of insecticides through increased permeability and toxicity, reducing the need for high dosages. Graphene has been found to enhance the insecticidal activity of lambda-cyhalothrin and cyfluthrin against cotton bollworm. Optimal compositions of graphene-delivered insecticides showed the strongest inhibitory effects and highest mortality rates.
Article
Multidisciplinary Sciences
Zehui Liu, Jianguo Zhao, Jinxian Huo, Hongfang Ma, Zhiwen Chen
Summary: The cultivation of yellowhorn plants significantly affected the composition of the rhizosphere microbial communities in fly ash, which is of great significance for the biological remediation of fly ash.
Article
Evolutionary Biology
Corrinne E. Grover, Mark A. Arick, Adam Thrash, Joel Sharbrough, Guanjing Hu, Daojun Yuan, Samantha Snodgrass, Emma R. Miller, Thiruvarangan Ramaraj, Daniel G. Peterson, Joshua A. Udall, Jonathan F. Wendel
Summary: This study provides insights into genome evolution and domestication in cultivated diploid cotton species, Gossypium herbaceum and Gossypium arboreum, showing their independent domestication and variable permeability to introgression among chromosomes. The findings establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between these species.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Junfeng Cao, Chaochen Huang, Jun'e Liu, Chenyi Li, Xia Liu, Zishou Zheng, Lipan Hou, Jinquan Huang, Lingjian Wang, Yugao Zhang, Xiaoxia Shangguan, Zhiwen Chen
Summary: This study investigated the functions of the m(6)A RNA methyltransferase (METTL) gene family in cotton. Through a systematic analysis, the expression and regulatory patterns of several METTL genes in cotton were identified. Overexpression and suppression experiments confirmed the importance of these genes in cotton plant growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Maojun Wang, Jianying Li, Zhengyang Qi, Yuexuan Long, Liuling Pei, Xianhui Huang, Corrinne E. Grover, Xiongming Du, Chunjiao Xia, Pengcheng Wang, Zhenping Liu, Jiaqi You, Xuehan Tian, Yizan Ma, Ruipeng Wang, Xinyuan Chen, Xin He, David D. Fang, Yuqiang Sun, Lili Tu, Shuangxia Jin, Longfu Zhu, Jonathan F. Wendel, Xianlong Zhang
Summary: In this study, we constructed a pan-genome of the Gossypium genus and explored the impact of transposon amplification on genome composition and evolution. We found evolutionary connections between genome size variation, chromatin structure reorganization, and chromatin interactome rewiring, as well as identified regulatory variations underlying fiber length in cotton. Our findings provide insights into the evolution of genome organization and regulation, and can inform cotton improvement strategies.
Article
Genetics & Heredity
Mark A. Arick, Corrinne E. Grover, Chuan-Yu Hsu, Zenaida Magbanua, Olga Pechanova, Emma R. Miller, Adam Thrash, Ramey C. Youngblood, Lauren Ezzell, Md Samsul Alam, John A. H. Benzie, Matthew G. Hamilton, Attila Karsi, Mark L. Lawrence, Daniel G. Peterson
Summary: Labeo rohita (rohu) is an important carp in South Asian aquaculture, and a high-quality de novo genome has been produced for it using next-generation sequencing technologies. The genome consists of 946 Mb and 25 chromosomes, and represents 97.9% of the estimated genome size. Sequencing from 120 individuals was used to study population structure, diversity, and sex determination mechanisms in rohu, showing the potential of the new genome in modernizing rohu genetic improvement programs.
G3-GENES GENOMES GENETICS
(2023)
Article
Genetics & Heredity
Thiruvarangan Ramaraj, Corrinne E. Grover, Azalea C. Mendoza, Mark A. Arick II, Josef J. Jareczek, Alexis G. Leach, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall
Summary: In this study, the genome of G. herbaceum cv. Wagad, representing the first domesticated accession for this species, was sequenced and assembled. The genome of this cultivar was compared to wild G. herbaceum subspecies africanum to investigate changes in the G. herbaceum genome during domestication, and gene expression analysis was performed using RNA-seq. The results demonstrate the importance of studying the G. herbaceum cv. Wagad genome for understanding domestication in diploid species and guiding modern breeding programs.
G3-GENES GENOMES GENETICS
(2023)
Article
Genetics & Heredity
Josef J. Jareczek, Corrinne E. Grover, Guanjing Hu, Xianpeng Xiong, Mark A. A. Arick II, Daniel G. Peterson, Jonathan F. Wendel
Summary: The study reveals that there are differential gene expressions between upland cotton and Pima cotton during fiber development, indicating selection of different genes during domestication. Furthermore, despite the impacts of domestication and speciation on gene expression, both species share similar expression patterns in certain gene modules.
Article
Agriculture, Multidisciplinary
Zhiwen Chen, Jianguo Zhao, Jun Qiao, Weijia Li, Zhifang Guan, Zehui Liu, Xiuli Bai, Baoyan Xing, Jin Zhang, Jingwei Li, Weilun Yin, Hongwei Zhu
Summary: Graphene has been shown to affect the growth of various plant species' root systems, and the molecular mechanisms behind its effects have been uncovered.
ACS AGRICULTURAL SCIENCE & TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)