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
Biochemistry & Molecular Biology
Alexandre Pedro Selvatti, Filipe Romero Rebello Moreira, Daniel Cardoso Carvalho, Francisco Prosdocimi, Claudia Augusta de Moraes Russo, Ana Carolina Martins Junqueira
Summary: This study used mitochondrial genomes and nuclear orthologs to investigate the divergence time of turtles. The findings suggest that the split of Testudines occurred in the Early Jurassic, associated with the fragmentation of Pangaea and the formation of saltwater barriers. The divergence of Pleurodira coincided with Late Jurassic and Early Cretaceous geologic events, while Cryptodira remained in Laurasia and diversified during the Cenozoic. The study also provides a detailed hypothesis of Cryptodira evolution in the Southern Hemisphere correlated with landmass contacts derived from Gondwana and Laurasia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(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
Biology
Nicolas Mongiardino Koch, Jeffrey R. Thompson, Avery S. Hiley, Marina F. McCowin, A. Frances Armstrong, Simon E. Coppard, Felipe Aguilera, Omri Bronstein, Andreas Kroh, Rich Mooi, Greg W. Rouse
Summary: Echinoids, including sand dollars, are crucial components of modern marine ecosystems. However, their early history and the origin of sand dollars have remained uncertain. In this study, we generated genomic data from 18 species of echinoids and used them to reconstruct the phylogeny and divergence times of echinoids. We also introduced a new concept called chronospace to explore different methodological decisions in calibrating phylogenies. Our results revealed that crown group echinoids originated in the Permian and diversified rapidly in the Triassic. We also clarified the relationships between sand dollars and their relatives and confidently dated their origin to the Cretaceous.
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
Biotechnology & Applied Microbiology
Abdul Latif Khan, Sajjad Asaf, Lubna, Ahmed Al-Rawahi, Ahmed Al-Harrasi
Summary: Salvadora persica, a species with economic and medicinal importance, has been sequenced for its complete chloroplast genome for the first time. Comparison with other related species revealed unique features in terms of genome size and encoded genes.
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
Biotechnology & Applied Microbiology
Guangpeng Ren, Yanyou Jiang, Ao Li, Mou Yin, Minjie Li, Wenjie Mu, Ying Wu, Jianquan Liu
Summary: The chromosome-level genome of Achnatherum splendens was determined through a combination of technologies, revealing a significant whole-genome duplication event in the species' evolutionary history that contributed to its strong resistance to salt stress and widespread arid adaptation.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Plant Sciences
Ao Li, Ai Liu, Shuang Wu, Kunjing Qu, Hongyin Hu, Jinli Yang, Nawal Shrestha, Jianquan Liu, Guangpeng Ren
Summary: This study presents the genomic landscape of structural variants (SVs) between two model legume ecotypes, providing valuable genomic resources for future research on legume biology. The study identifies SVs that may contribute to phenotypic differences and discovers extensive SVs within a specific gene family.
Article
Plant Sciences
Yi Wang, Guo-Qian Hao, Xin-Yi Guo, Dan Zhang, Quan-Jun Hu, Jian-Quan Liu
Summary: Both geographic isolation and polyploidization play important roles in species diversification of the genus Eutrema. Phylogenomic analyses based on genome re-sequencing data revealed the backbone relationships of the genus and identified conflicts in interspecific relationships, suggesting hybridization and incomplete lineage sorting.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Review
Plant Sciences
Shengdan Wu, Yi Wang, Zefu Wang, Nawal Shrestha, Jianquan Liu
Summary: The Qinghai-Tibet Plateau is a region with rich species diversity, where geographic isolation, natural selection, and hybridization have played important roles in promoting species divergence and diversification. It is important to identify and functionally analyze the major genes involved in speciation, and to investigate parallel adaptive divergence causing reproductive isolation among different lineages within specific habitats in this region.
Article
Multidisciplinary Sciences
Ziming Wang, Andy Berbille, Yawei Feng, Site Li, Laipan Zhu, Wei Tang, Zhong Lin Wang
Summary: Research has shown that electrons transferred through contact-electrification can be used for catalyzing reactions without conventional catalysts. This new catalytic principle, termed contact-electro-catalysis, has been proven effective for various dielectric materials, such as Teflon, Nylon-6,6, and rubber. This expands the range of catalytic materials and offers a new approach for catalytic processes through mechano-induced contact-electrification.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Mingjia Zhu, Zhenyue Wang, Yongzhi Yang, Zefu Wang, Wenjie Mu, Jianquan Liu
Summary: This study investigated the genomic, transcriptomic, and metabolomic analyses of dimorphic flowers in Sinoswertia tetraptera. The results showed that recent whole-genome duplication and differentially expressed genes may contribute to the origin and maintenance of this innovative trait.
Article
Biodiversity Conservation
Yingbo Yang, Zhenghan Bian, Guangpeng Ren, Jianquan Liu, Nawal Shrestha
Summary: The increase in species number from poles to the equator is a fundamental pattern in ecology. In the case of Medicago genus, Quaternary climate change and environmental energy are important explanatory variables for richness patterns at global, continental, and biome scales. However, the effects of environmental energy differ between temperate and tropical regions, with richness increasing with energy in the temperate and decreasing in the tropics. Medicago species also exhibit strong affinity to their ancestral Mediterranean climatic niche.
Article
Evolutionary Biology
Zeyu Zheng, Hongyin Hu, Weixiao Lei, Jin Zhang, Mingjia Zhu, Ying Li, Xu Zhang, Jianchao Ma, Dongshi Wan, Tao Ma, Guangpeng Ren, Dafu Ru
Summary: This study investigates the somatic mutation rates and patterns in Populus alba var. pyramidalis, a clonally propagated species that has been domestically cultivated. The study finds that the mutation rate in this species is higher than in related species, with mutations predominantly occurring near heterozygous regions. The presence of CpG and CHG sites suggests a potential involvement of methylation in blocking DNA repair. Additionally, deleterious mutations are not shared among individuals and occur in heterozygous states, indicating strong selective pressure against harmful mutations.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Shuo Feng, Wei Wan, Yang Li, DongLei Wang, Guangpeng Ren, Tao Ma, Dafu Ru
Summary: This study investigates the adaptive divergence and genetic differentiation between two closely related spruce species. Despite morphological similarities, the two species exhibit genetic differentiation, which can be traced back to the late Quaternary. Analysis of genes associated with environmental variables reveals differences in adaptive responses to temperature and precipitation between the two species. These findings provide insights into the evolutionary dynamics of species adaptation and their demographic histories.
Article
Biochemistry & Molecular Biology
Chunlin Chen, Brad R. Ruhfel, Jialiang Li, Zefu Wang, Lushui Zhang, Lei Zhang, Xingxing Mao, Ji Wang, Dashan He, Yue Luo, Quanjun Hu, Yuanwen Duan, Xiaoting Xu, Zhenxiang Xi, Jianquan Liu
Summary: Establishing phylogenetic relationships among lineages with similar traits is crucial for understanding the origin of biodiversity on Earth. This study focused on the subtribe Swertiinae in the Gentianaceae family, which includes more than 350 species with diverse floral traits. Through phylogenetic analysis using nuclear and plastid genome data, the study revealed extensive conflicts between the trees constructed from the two genomes and the polyphyletic nature of three of the genera. Key floral traits showed random distribution without phylogenetic correlation. Additionally, the study suggested an ancient hybrid origin for a clade comprising 10 genera with diverse floral traits. These findings highlight the complex evolutionary history of the subtribe and provide a foundation for further research on species diversification and floral diversity.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Hong Wu, Zefu Wang, Yuxing Zhang, Laurent Frantz, Christian Roos, David M. Irwin, Chenglin Zhang, Xuefeng Liu, Dongdong Wu, Song Huang, Tongtong Gu, Jianquan Liu, Li Yu
Summary: It is discovered that historical hybridization occurred among a group of snub-nosed monkeys, leading to the origin of a hybrid species. The gray snub-nosed monkey has a stable mixed genomic ancestry derived from the golden snub-nosed monkey, the ancestor of black-white and black snub-nosed monkeys. Genes derived from the parental lineages have been identified, potentially contributing to the mosaic coat coloration of the hybrid and promoting reproductive isolation. This study highlights the underappreciated role of hybridization in generating species and phenotypic diversity in mammals.
Article
Multidisciplinary Sciences
Bao-Lin Zhang, Wu Chen, Zefu Wang, Wei Pang, Meng -Ting Luo, Sheng Wang, Yong Shao, Wen-Qiang He, Yuan Deng, Long Zhou, Jiawei Chen, Min -Min Yang, Yajiang Wu, Lu Wang, Hugo Fernandez-Bellon, Sandra Molloy, Helene Meunler, Fanelie Wanert, Lukas Kuderna, Tomas Marques-Bonet, Christian Roos, Xiao-Guang Qi, Ming Li, Zhiji Liu, Mikkel Heide Schierup, David N. Cooper, Jianquan Liu, Yong-Tang Zheng, Guojie Zhang, Dong-Dong Wu
Summary: Through phylogenomic analysis of 12 macaque species, we discovered that the fascicularis group originated from an ancient hybridization event between the sinica and silenus groups around 3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions showed equal contributions from each parental lineage, suggesting their importance in maintaining hybrid integrity. We also identified reproduction-associated genes and confirmed susceptibility to HIV-1 infection in all extant Western silenus species. Our study provides new insights into macaque evolution and highlights a rare hybrid speciation event in primates.
Article
Plant Sciences
Yile Huang, Xinyi Guo, Kang Zhang, Terezie Mandakova, Feng Cheng, Martin A. Lysak
Summary: The high diversity of the South African Cape flora is not associated with polyploidy. However, the genome assembly of the cruciferous species Heliophila variabilis reveals an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome likely originated through hybridization between two allotetraploids formed by distant hybridization, and its rediploidization was marked by extensive reorganization of subgenomes and genome downsizing.
Article
Plant Sciences
Sheng Zuo, Xinyi Guo, Terezie Mandakova, Mark Edginton, Ihsan A. Al-Shehbaz, Martin A. Lysak
Summary: The different rates of postpolyploid genome diploidization in the Microlepidieae tribe result in intra-tribal cladogenesis and are associated with variation in morphological disparity and plastid-nuclear genome coevolution. Faster genome diploidization is positively correlated with mean morphological disparity and evolution of chloroplast genes, while higher speciation rates are observed in perennial species. The study highlights the potential of Microlepidieae as a subject for analyzing postpolyploid genome diploidization in Brassicaceae.
Article
Multidisciplinary Sciences
Zefu Wang, Yuanzhong Jiang, Xiaoyue Yang, Hao Bi, Jialiang Li, Xingxing Mao, Yazhen Ma, Dafu Ru, Cheng Zhang, Guoqian Hao, Jing Wang, Richard J. Abbott, Jianquan Liu
Summary: Parallel evolution of reproductive isolation was observed in two sister species pairs from different genera, Carpinus and Ostryopsis. The speciation process was driven by divergence in temperature and soil-iron concentration in their respective habitats. Positive selection was detected in genes related to flowering time and iron tolerance, leading to high levels of prezygotic reproductive isolation.