Article
Microbiology
Zhaobin Deng, Jun Wang, Wenjie Zhang, Yi Geng, Mingde Zhao, Congwei Gu, Lu Fu, Manli He, Qihai Xiao, Wudian Xiao, Lvqin He, Qian Yang, Jianhong Han, Xuefeng Yan, Zehui Yu
Summary: In this study, 23 Iridoviridae core genes were re-determined by re-annotation, core-pan analysis, and local BLASTN search. The phylogenetic tree and amino acid sequences were consistent with previous reports. Information from synteny analysis and codon usage preference also supports the phylogenetic relationship, contributing to understanding the genera demarcation within the Iridoviridae family.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Yahui Xuan, Sheng Wang, Siwei Li, Jianglian Yuan, Qiming Zhou, Ningjia He
Summary: This study used cGISH and self-GISH methods to investigate the chromosome constitution and genetic relationships of 40 mulberry accessions. Multiple homozygous and heterozygous signal patterns were discovered, and five mulberry sections and their genetic relationships were defined. These findings are important for guiding hybrid breeding of perennial crops like mulberry.
Article
Biochemistry & Molecular Biology
Ping Lin, Hengfu Yin, Kailiang Wang, Haidong Gao, Lei Liu, Xiaohua Yao
Summary: In this study, the chloroplast genome sequences of nine Camellia species were determined using Illumina sequencing technology. Comparative analysis revealed high sequence polymorphism and identified specific sequence markers for species identification and phylogenetic analysis. Additionally, regional constraints were found to strongly influence the sequence evolution of the chloroplast genomes.
Article
Biotechnology & Applied Microbiology
Jiaxin Yang, Guoxiong Hu, Guangwan Hu
Summary: This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.
Article
Plant Sciences
Ying-Xia Lei, Xing Fan, Li-Na Sha, Yi Wang, Hou-Yang Kang, Yong-Hong Zhou, Hai-Qin Zhang
Summary: By sequencing nuclear and chloroplast DNA regions, the delimitation and phylogenetic relationships of the Roegneria genus were investigated. The results showed that all Roegneria species were included in the St and Y genome clades, and the Y genome was closely related to the V and Xp genomes. Additionally, Roegneria species were grouped with Pseudoroegneria species, particularly those from the Middle East and Central Asia.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Microbiology
Fenghua Tian, Changtian Li, Yu Li
Summary: The study sequenced and assembled the genome of the important edible and medicinal mushroom Sarcomyxa edulis using single-molecule real-time sequencing technology, identifying genes encoding enzymes involved in metabolites related to pharmacodynamic activities. The annotated whole-genome sequence of S. edulis can serve as a reference for further investigations of bioactive compounds and the development of superior varieties.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Ali Rahnavard, Tyson Dawson, Rebecca Clement, Nathaniel Stearrett, Marcos Perez-Losada, Keith A. Crandall
Summary: The study identified that the nonstructural protein 3 (nsp3) and Spike protein (S) of SARS-CoV-2 have the highest variation in the genome, and are most correlated with the viral whole-genome variation. The country of origin and time since the start of the pandemic were found to be the most influential metadata associated with genomic variation.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Lei Shi, Ke Wang, Lipu Du, Yuxia Song, Huihui Li, Xingguo Ye
Summary: The WOX family is a group of plant-specific transcription factors that regulate plant growth and development. In Triticeae species, WOX genes are conserved and play a role in tissue-specific expression, with TaWOX9 potentially being closely related to the regulation of the regeneration process in wheat. This study provides a foundation for the evolution, functional investigation, and practical application of WOX family genes in Triticeae species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Nicole M. Foley, Victor C. Mason, Andrew J. Harris, Kevin R. Bredemeyer, Joana Damas, Harris A. Lewin, Eduardo Eizirik, John Gatesy, Elinor K. Karlsson, Kerstin Lindblad-Toh, Zoonomia Consortium Zoonomia Consortium, Mark S. Springer, William J. Murphy
Summary: We conducted a comprehensive analysis of 241 placental mammal genome assemblies, providing a deeper understanding of the speciation events and evolution patterns of these mammals. Our analysis revealed low rates of conflict in interordinal relationships across different datasets and methods, while conflicts between X-chromosomes and autosomes characterized multiple independent clades that emerged during the Cenozoic era. Furthermore, our genomic time trees suggest that important speciation events occurred before and after the Cretaceous-Paleogene boundary, indicating the significance of continental vicariance and the K-Pg extinction event in the placental radiation.
Article
Multidisciplinary Sciences
Zefu Wang, Minghui Kang, Jialiang Li, Zhiyang Zhang, Yufei Wang, Chunlin Chen, Yongzhi Yang, Jianquan Liu
Summary: This study reveals the likelihood of homoploid hybrid speciation (HHS) between Carpinus and Ostrya during their early divergence, resulting in the origin of Carpinus sect. Distegocarpus. The findings highlight the importance of considering HHS in understanding species diversification, especially between ancestors of different genera.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Rong Wang, Kuan Liu, Xue-Jie Zhang, Wen-Li Chen, Xiao-Jian Qu, Shou-Jin Fan
Summary: This study investigated the plastomes of Cleistogenes and related genera, revealing similarities in structure and gene content, as well as identifying sequence divergence among taxa. The phylogenetic analysis indicated the evolutionary relationships within Cleistogenes and suggested a rapid divergence within the genus.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Ning Chen, Li-Na Sha, Yi-Ling Wang, Ling-Juan Yin, Yue Zhang, Yi Wang, Dan-Dan Wu, Hou-Yang Kang, Hai-Qin Zhang, Yong-Hong Zhou, Gen-Lou Sun, Xing Fan
Summary: The study comprehensively analyzed chloroplast genome variation in 34 monogenomic Triticeae plants, identifying factors such as indels, gene loss, and size variation in different genera. Results suggest that the size and evolution of chloroplast genomes in Triticeae are highly variable and likely influenced by adaptive processes. Additionally, unique genetic information in specific intergenic regions can serve as important tools for identifying maternal relationships among Triticeae species.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Forestry
Kuo Sun, Qiao-Yun Liu, Ao Wang, Yong-Wei Gao, Liang-Cheng Zhao, Wen-Bin Guan
Summary: This study investigated plastome variations in eight species representing four genera of the Amyridoideae subfamily and Melicope, demonstrating structural variations at the borders of the plastomes in these genera and potential genetic markers. Phylogenomic analyses identified Phellodendron, Tetradium, Toddalia, and Zanthoxylum as close relatives grouped as 'proto-Rutaceae', with specific relationships between the genera and further insights into the evolutionary history provided by plastomes data.
Article
Multidisciplinary Sciences
Alejandra Marcela Ortiz, Laura Chalup, Maria Celeste Silvestri, Guillermo Seijo, Graciela Ines Lavia
Summary: In this study, the genomic affinity between rhizoma peanut and potential diploid donors of related sections was evaluated using genomic in situ hybridization (GISH). The results showed that species from Erectoides and Procumbentes sections had the highest genomic affinity with rhizoma peanut. Double GISH experiments and DNA sequence similarity analysis identified three species as the most probable ancestors of rhizoma peanut, supporting its autopolyploid origin. These findings have important implications for the understanding of the genomic constitution and evolutionary history of rhizoma peanut.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2023)
Article
Multidisciplinary Sciences
Felix L. Wascher, Nancy Stralis-Pavese, J. Mitchell McGrath, Britta Schulz, Heinz Himmelbauer, Juliane C. Dohm
Summary: The phylogeny of wild and cultivated beets is clarified using genomic analysis and it is found that Greece is the domestication site of sugar beet. This study provides comprehensive insights into the evolutionary relationships of beets.
NATURE COMMUNICATIONS
(2022)