Article
Genetics & Heredity
Sylvia Hofmann, Chitra Bahadur Baniya, Matthias Stoeck, Lars Podsiadlowski
Summary: The study presented annotated transcriptome data of the Ladakh Ground skink and identified positive selection for some genes in this species. Although the results are limited by the use of a single animal, the transcriptome resource could be valuable for further research on squamate reptile evolution in the Himalayas.
Article
Biology
Weiming Li, Juan Du, Lingyun Yang, Qiqi Liang, Mengyuan Yang, Xuming Zhou, Weiguo Du
Summary: This study investigated the genetic adaptation of lizards to high-altitude environments using comparative genomics analysis. It identified unique adaptive genes in populations endemic to high altitudes and revealed the molecular mechanism of high-altitude adaptation in ectothermic animals. A high-quality lizard genomic resource for future research was also provided.
Article
Biochemistry & Molecular Biology
Adam H. Freedman, Michele Clamp, Timothy B. Sackton
Summary: De novo transcriptome assembly is a powerful tool for evolutionary inferences, but it often faces bias and noise issues in data analysis, leading to underestimation of diversity and gene expression estimates. Researchers should look for ways to minimize the impact of bias in transcriptome assemblies.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Zhijun Zhang, Jiahui Zhang, Qizhang Chen, Jianyun He, Xiaowei Li, Yunsheng Wang, Yaobin Lu
Summary: In this study, a complete genome assembly of Wolbachia strain wFI in Thysanopteran insects was successfully obtained using Nanopore long reads and Illumina short reads. The assembled genome consisted of 1838 protein-coding genes and various other functional genes. The research revealed the nutritional mutualism between Wolbachia and flower thrips and provided a valuable resource for further studies on the interactions between Wolbachia and its host.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Xiaojuan Wang, Hua Rao, Jianxiang Ma, Xiaodan Chen, Guanglin Li, Guifang Zhao
Summary: By resequencing the whole genomes of natural populations of Eutrema salsugineum across its Asian and North American distributions, selection signals for genes involved in salt and other abiotic tolerance were detected at the species level. Additionally, local adaptation in North America-NE Russia and northern China led to selection signals in cold-induced and defense genes. These variations provide valuable insights for understanding the genetic mechanisms underlying stress tolerance and local adaptations in this model species.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Chunmei Cai, Yingzhong Yang, Qin Ga, Guocai Xu, Rili Ge, Feng Tang
Summary: This study revealed the genetic adaptations of Tibetan Mastiff and Canis Lupus to high altitude, including the expansion of gene families related to DNA repair and damage response, contraction related to ATPase activity, and positive selection for fatty-acid oxidation and DNA repair genes.
Article
Biotechnology & Applied Microbiology
Wirulda Pootakham, Chaiwat Naktang, Wasitthee Kongkachana, Chutima Sonthirod, Thippawan Yoocha, Duangjai Sangsrakru, Nukoon Jomchai, Sonicha U-Thoomporn, Kanokwan Romyanon, Theerayut Toojinda, Sithichoke Tangphatsornruang
Summary: Centella asiatica, a herbaceous perennial species with medicinal properties, had its genome assembly obtained using advanced technologies. This assembly serves as a valuable reference for future studies and breeding efforts in C. asiatica.
Article
Multidisciplinary Sciences
Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong Won Kim, Yibing Zeng, Christine H. O'Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia Krasileva, John L. Portwood, Ethalinda K. S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe
Summary: The study reports de novo genome assemblies, transcriptomes, annotations, and methylomes for 26 maize inbreds, with over 103,000 pangenes identified. It shows that the ancient tetraploid character of maize continues to degrade by fractionation, and reveals variation in DNA methylation levels across genotypes.
Article
Zoology
Xuejuan Li, Xiaoyang Wang, Chao Yang, Liliang Lin, Hao Yuan, Fumin Lei, Yuan Huang
Summary: By analyzing the genomics and population genetics of the Tibetan Partridge, researchers have discovered unique adaptation mechanisms, including positively selected genes and immunity pathways, that differ from other endangered bird species in high-altitude environments.
INTEGRATIVE ZOOLOGY
(2023)
Article
Plant Sciences
Juan Wang, Haifei Hu, Xizhen Liang, Muhammad Tahir ul Qamar, Yunxiang Zhang, Jianguo Zhao, Hongqian Ren, Xingrong Yan, Baopeng Ding, Jinping Guo
Summary: Yellowhorn (Xanthoceras sorbifolia) is a versatile deciduous tree native to Northern and Central China. It is often cultivated for its ornamental value and as a source of edible seeds that contain rich oil and fatty acid contents. This study presents a high-quality genome assembly of yellowhorn, which provides insights into its environmental adaptation and seed oil content variations. The findings suggest that certain gene families and a specific gene, 3-ketoacyl-CoA thiolase (KAT), play important roles in the adaptability and oil synthesis of yellowhorn.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Xiangbin Jia, Shujie Zhang, Senwei Tan, Bing Du, Mei He, Haisong Qin, Jia Chen, Xinyu Duan, Jingsi Luo, Fei Chen, Luping Ouyang, Jian Wang, Guodong Chen, Bin Yu, Ge Zhang, Zimin Zhang, Yongqing Lyu, Yi Huang, Jian Jiao, Jin Yun Helen Chen, Kathryn J. Swoboda, Emanuele Agolini, Antonio Novelli, Chiara Leoni, Giuseppe Zampino, Gerarda Cappuccio, Nicola Brunetti-Pierri, Benedicte Gerard, Emmanuelle Ginglinger, Julie Richer, Hugh McMillan, Alexandre White-Brown, Kendra Hoekzema, Raphael A. Bernier, Evangeline C. Kurtz-Nelson, Rachel K. Earl, Claartje Meddens, Marielle Alders, Meredith Fuchs, Roseline Caumes, Perrine Brunelle, Thomas Smol, Ryan Kuehl, Debra-Lynn Day-Salvatore, Kristin G. Monaghan, Michelle M. Morrow, Evan E. Eichler, Zhengmao Hu, Ling Yuan, Jieqiong Tan, Kun Xia, Yiping Shen, Hui Guo
Summary: This study reports a newly identified neurodevelopmental disorder and suggests the importance of stress granules (SGs) in its pathology. By studying mice and analyzing data from a large number of patients, the researchers found that genetic variants in genes related to SGs were associated with the disorder. These findings provide significant insights into the underlying mechanisms of neurodevelopmental disorders.
Article
Biochemistry & Molecular Biology
Jing-Ge Kuang, Zhi-Tong Han, Ming-Hui Kang, Tsam Ju, Sonam Tso, Xiao-Xiao Chen, Jia-Liang Li, Zhong-Ping Xiong, Tao Ma, Kang-Shan Mao
Summary: In this study, chromosome-level genome assemblies for two oligophagous conifer parasitoid species of Megastigmus were provided, representing the first two chromosome-level genomes of the genus. The expanded genomes of these species were larger than most hymenopterans due to the expansion of transposable elements. The study found differences in sensory-related genes between the two species, reflecting the difference in their hosts. The study also found that these two species have fewer family members but more single-gene duplications in certain gene families compared to polyphagous congeners.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Computer Science, Information Systems
Kimia Behizadi, Nafiseh Jafarzadeh, Ali Iranmanesh
Summary: This paper focuses on the graph-theoretical side of de novo genome assembly algorithms, exploring the construction of various graph data structures and classifying the most significant and recent assemblers based on these structures.
Article
Genetics & Heredity
Jack T. Sumner, Cassidy L. Andrasz, Christine A. Johnson, Sarah Wax, Paul Anderson, Elena L. Keeling, Jean M. Davidson
Summary: This study utilized a hybrid assembly technique to assemble and annotate the genome of the botryllid ascidian, Botrylloides violaceus, and identified 13 protein-coding genes. Comparative genomic analysis with other tunicates revealed patterns of conservation and divergence within orthologous gene families. Characterization of the Wnt gene family, encoding developmental and regenerative signaling ligands, showed conserved patterns of subfamily presence and gene copy number in botryllids, supporting the use of genomic data from nonmodel organisms in biological investigations.
G3-GENES GENOMES GENETICS
(2023)
Article
Evolutionary Biology
Wirulda Pootakham, Chaiwat Naktang, Chutima Sonthirod, Wasitthee Kongkachana, Thippawan Yoocha, Nukoon Jomchai, Chatree Maknual, Pranom Chumriang, Tamanai Pravinvongvuthi, Sithichoke Tangphatsornruang
Summary: In this study, the Upriver orange mangrove genome was assembled using the 10x Genomics linked-read technology, and the resulting chromosome-level assembly provides a valuable genetic resource for studying the physiological and morphological adaptations of mangroves in intertidal zones.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Chun-Lin Chen, Lei Zhang, Jia-Liang Li, Xing-Xing Mao, Lu-Shui Zhang, Quan-Jun Hu, Jian-Quan Liu, Zhen-Xiang Xi
Summary: This study aimed to reconstruct the genome-scale phylogeny and identify major gene duplication events in the subtribe Gentianinae. By sequencing and assembling transcriptomes from 70 samples, including all recognized genera in the subtribe, the study found a high occurrence of duplicated genes likely arising from hybrid polyploidy. Multiple gene tree reconciliation methods identified 10 nodes with large concentrations of duplicated genes in the species tree, shedding light on the evolutionary history of Gentianinae.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Michael D. Nowak, Siri Birkeland, Terezie Mandakova, Rimjhim Roy Choudhury, Xinyi Guo, Anna Lovisa S. Gustafsson, Abel Gizaw, Audun Schroder-Nielsen, Marco Fracassetti, Anne K. Brysting, Loren Rieseberg, Tanja Slotte, Christian Parisod, Martin A. Lysak, Christian Brochmann
Summary: The research team completed the chromosome-scale genome assembly of the plant Draba nivalis adapted to the harsh Arctic environment, revealing expanded gene families associated with drought and cold stress, possibly driven by transposable elements. Tests of positive selection identified candidate genes associated with meiosis, photoperiodism, cold, drought, and oxidative stress responses.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Xinyi Guo, Terezie Mandakova, Karolina Trachtova, Baris Ozudogru, Jianquan Liu, Martin A. Lysak
Summary: This study reveals the complex genomic history of the mustard family tribe Biscutelleae, showing contentious relationships within this plant family. Genome evolution in Biscutelleae was influenced by pervasive hybridizations and subsequent genome duplications, leading to a complex pattern of relationships among the genera.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Wenjie Yang, Lei Zhang, Terezie Mandakova, Li Huang, Ting Li, Jiebei Jiang, Yongzhi Yang, Martin A. Lysak, Jianquan Liu, Quanjun Hu
Summary: The study assembled a high-quality chromosome-scale genome for Megadenia pygmaea, revealing its phylogenetic relationships and chromosomal composition. The genome provided fundamental information for further studies on karyotypic evolution and evolutionary analysis of this genus.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Genetics & Heredity
Landi Feng, Hao Lin, Minghui Kang, Yumeng Ren, Xi Yu, Zhanpeng Xu, Shuo Wang, Ting Li, Wenjie Yang, Quanjun Hu
Summary: This study reveals the mechanisms of chromosomal karyotype evolution and gene family expansion in alpine genus plants adapting to high-altitude environments.
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)
Article
Genetics & Heredity
Ting Li, Xi Yu, Yumeng Ren, Minghui Kang, Wenjie Yang, Landi Feng, Quanjun Hu
Summary: In this study, a high-quality chromosome-level genome of Gentiana dahurica was generated, revealing two whole-genome duplication events and identifying genes and factors related to gentiopicroside biosynthesis. It was found that gentiopicrosides were mainly synthesized in the rhizomes. This research is of great importance for evolutionary, ecological, and pharmaceutical studies of the Gentianaceae family.
Article
Plant Sciences
Mert Dogan, Terezie Mandakova, Xinyi Guo, Martin A. Lysak
Summary: The study used cytogenomic and phylogenomic methods to investigate the phylogenetic relationships and genome duplications in Idahoa and Subularia plants. The results revealed diploidized mesotetraploid genome in Idahoa and diploidized mesoctoploid genomes in two Subularia species. Multiple ancient allopolyploidy events were also detected in closely related taxa.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Plant Sciences
Martin A. Lysak, Mark Edginton, Sheng Zuo, Xinyi Guo, Terezie Mandakova, Ihsan A. Al-Shehbaz
Summary: The taxonomic limits of Arabidella, Cuphonotus, and Lemphoria (Brassicaceae, Microlepidieae) have been revised based on a critical evaluation of morphology considering recent cytogenomic and molecular phylogenetic findings. As a result, Lemphoria has been reinstated to include species previously classified under Cuphonotus and Arabidella. A new species, Lemphoria queenslandica, has been described, and new combinations such as L. andraeana, L. eremigena, L. humistrata, and L. procumbens have been proposed. Keys to differentiate Arabidella and Lemphoria species, as well as an expanded generic description of Lemphoria, are provided.
Article
Biochemistry & Molecular Biology
Wenjie Yang, Landi Feng, Pengfei Jiao, Ling Xiang, Luobai Yang, Marina V. V. Olonova, Victor V. V. Chepinoga, Ihsan A. A. Al-Shehbaz, Jianquan Liu, Quanjun Hu
Summary: By sequencing the genomes of Megadenia and analyzing its genetic groups, this study provides evidence for the migration and survival of alpine plants during the Last Glacial Maximum, supporting the out-of-QTP hypothesis.
Correction
Plant Sciences
Mert Dogan, Milan Pouch, Terezie Mandakova, Petra Hlouskova, Xinyi Guo, Pieter Winter, Zuzana Chumova, Adriaan Van Niekerk, Klaus Mummenhoff, Ihsan A. Al-Shehbaz, Ladislav Mucina, Martin A. Lysak
FRONTIERS IN PLANT SCIENCE
(2022)
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
Quanjun Hu, Yazhen Ma, Terezie Mandakova, Sheng Shi, Chunlin Chen, Pengchuan Sun, Lei Zhang, Landi Feng, Yudan Zheng, Xiaoqin Feng, Wenjie Yang, Jiebei Jiang, Ting Li, Pingping Zhou, Qiushi Yu, Dongshi Wan, Martin A. Lysak, Zhenxiang Xi, Eviatar Nevo, Jianquan Liu
Summary: Deserts impose strong selection pressures on plants, but the genomic drivers of ecological adaptation and speciation in desert species are still largely unknown. Through genomic analyses of the psammophytic genus Pugionium, it was discovered that the genus had undergone an allopolyploid event, with genes related to abiotic stress responses and lignin biosynthesis expanding postpolyploidization to facilitate environmental adaptations. Population genomic analyses of both species revealed recent divergence with continuous gene flow, with divergent regions centered on three highly structurally reshuffled chromosomes contributing greatly to interspecific divergence in microhabitat adaptation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)