Article
Biotechnology & Applied Microbiology
Jun Chen, Yu Zang, Shuo Liang, Song Xue, Shuai Shang, Meiling Zhu, Ying Wang, Xuexi Tang
Summary: This study sequenced and compared the mitochondrial genomes of Zostera japonica and Phyllospadix iwatensis, providing new evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. It found a large number of repeat sequences and extensive loss of ribosomal protein genes in seagrass species. Additionally, it identified positive selection genes associated with seagrass adaptation to the marine environment.
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
Yan Cheng, Xiaoxue He, S. V. G. N. Priyadarshani, Yu Wang, Li Ye, Chao Shi, Kangzhuo Ye, Qiao Zhou, Ziqiang Luo, Fang Deng, Ling Cao, Ping Zheng, Mohammad Aslam, Yuan Qin
Summary: In this study, the mitochondrial genome of a halophytic model plant S. glauca was assembled and annotated, providing insights into the genome characteristics and variation of mt genomes in plants. The subsequent analysis revealed the importance of protein-coding genes in the mt genomes and their negative selections.
Article
Plant Sciences
Yichao Wang, Shuya Liu, Jing Wang, Yanxin Yao, Yang Chen, Qing Xu, Zengxia Zhao, Nansheng Chen
Summary: Mitochondrial genomes can be used as super barcodes to distinguish diatom species with higher resolution compared to common molecular markers. Comparative analysis of mitochondrial genomes revealed extensive genome rearrangement events and showed their value in evolutionary studies.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Yonggang Qiao, Xinrui Zhang, Zheng Li, Yun Song, Zhe Sun
Summary: In this study, the mitochondrial genome of Bupleurum chinense was assembled and annotated. The results provide extensive information about the characteristics of the mitochondrial genome and lay the foundation for future studies on genetic variations, phylogeny, and breeding in B. chinense.
Article
Biochemistry & Molecular Biology
Weidong Huang, Changhua Zhang, Tingzhen Zhang, Ye Xu, Shiwen Xu, Li Tian, Hu Li, Wanzhi Cai, Fan Song
Summary: This study investigates the characteristics and evolution of the control region (CR) in Tortricidae, a type of moth. Through mitochondrial genome analysis, the researchers found that the CR sequences in Tortricidae exhibit high structural diversity, indicating the plasticity of the mitochondrial DNA molecule in this insect group.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Xinghao Li, Nan Song, Heng Zhang
Summary: The research sequenced complete or nearly complete mitogenomes of seven species in the tribe Coccinellini and found that they all share the same gene content and order as the putative ancestral insect mitogenome. Through comparative analysis of over 30 coccinellid species, the study confirmed the monophyletic nature of the Coccinellidae family.
Article
Genetics & Heredity
Xiao Huang, Wei Tan, Feng Li, Ruyu Liao, Zhongren Guo, Ting Shi, Zhihong Gao
Summary: The study reported the complete chloroplast genome sequence of Prunus zhengheensis, revealing subtle divergences with other Prunus plants and a close relationship with Prunus mume. The research provides important genomic information for the molecular phylogeny of Prunus zhengheensis.
Article
Genetics & Heredity
Nripendra Vikram Singh, Prakash Goudappa Patil, Roopa P. Sowjanya, Shilpa Parashuram, Purushothaman Natarajan, Karuppannan Dhinesh Babu, Ram Krishna Pal, Jyotsana Sharma, Umesh K. Reddy
Summary: Comprehensive chloroplast genome analysis of 16 pomegranate genotypes revealed variability in genome size and conservation in gene content, with distinct differences among genotypes and clear divergence from other taxa. The study also identified varietal-specific SNP/indel markers and provided valuable genomic resources for future genetic, taxonomical, and phylogenetic research in pomegranate.
FRONTIERS IN GENETICS
(2021)
Article
Entomology
Xian Zhou, Yuejie Lei, Christopher H. Dietrich, Min Huang
Summary: Typhlocybinae is the second-largest subfamily in the leafhopper family Cicadellidae, consisting of approximately 6000 species. The subfamily has been divided into six tribes, with Typhlocybini and Zyginellini being distinguished based on hind wing venation. However, there is a lack of mitogenome sequences representative of major lineages of Typhlocybini for phylogenetic analysis. In this study, complete mitogenome sequencing and functional annotations were performed for 19 Typhlocybinae species, and the results confirm the synonymy of Zyginellini with Typhlocybini while revealing the correspondence between certain generic groups and monophyletic lineages.
Article
Ecology
Can Zhong, Jian Jin, Rongrong Zhou, Hao Liu, Jing Xie, Dan Wan, Shengen Xiao, Shuihan Zhang
Summary: Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, the complete mitochondrial genome of Ophiocordyceps xuefengensis was sequenced, assembled, and annotated, followed by comparison with three other complete cordyceps mitogenomes. The comparative analysis revealed both commonalities and differences in the structure and conserved genes among these mitochondrial genomes.
ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Qi Chen, Lu Chen, Cheng-Qing Liao, Xing Wang, Min Wang, Guo-Hua Huang
Summary: This study integrated 794 mitogenomes from 26 lepidopteran superfamilies for comparative genomic and phylogenetic analysis, revealing gene codon differences and unique base overlaps in primitive taxon, as well as uncovering the main phylogenetic relationships within Lepidoptera.
Article
Agriculture, Dairy & Animal Science
Yuan Gao, Zhonghuai Zhang, Chunren Wang, Kai Zhao
Summary: The study reported the complete mitochondrial genome of C. elongatus, confirming its placement in Cylicocyclus, and highlighted the utility of mt genome as a gene marker to address taxonomy controversies.
Article
Microbiology
Peng Wu, Tian Yao, Yuanhang Ren, Jinghua Ye, Yuan Qing, Qiang Li, Mingying Gui
Summary: This study sequenced and compared the mitochondrial genomes of two Pisolithus species, revealing certain characteristics and differences. The research on Pisolithus mitochondrial genomes contributes to a better understanding of the evolutionary history of these fungal species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shi-Jie Ke, Ding-Kun Liu, Xiong-De Tu, Xin He, Meng-Meng Zhang, Meng-Jia Zhu, Di-Yang Zhang, Cui-Li Zhang, Si-Ren Lan, Zhong-Jian Liu
Summary: In this study, the complete mitochondrial genome of Apostasia shenzhenica was sequenced and assembled, revealing its genetic diversity and phylogenetic relationships among monocotyledons. The mitochondrial genome was 672,872 bp in length and contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis showed the presence of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high conservation of the mitogenome in related species. RNA editing identified 416 sites in the protein-coding region. Additionally, 44 chloroplast genomic DNA fragments were transferred to the mitogenome, with five plastid-derived genes remaining intact. Phylogenetic analysis showed well-determined evolution and classification of most monocots. These findings contribute to the genetic resources of orchids and provide valuable insights into the taxonomy and molecular evolution of monocots.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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)