Article
Multidisciplinary Sciences
Anthony K. Redmond, Dearbhaile Casey, Manu Kumar Gundappa, Daniel J. Macqueen, Aoife McLysaght
Summary: Whole genome duplication (WGD) is an important event in evolution, generating new genes and potentially promoting survival during mass extinctions. Paddlefish and sturgeon, sister lineages, show genomic evidence of ancient WGD. Although the duplications appear to be independent, they actually stem from a shared WGD event over 200 million years ago, prior to the Permian-Triassic extinction. The shared WGD is masked by lineage divergence before the completion of rediploidization.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Zhong-Shuai Zhang, Qing-Yin Zeng, Yan-Jing Liu
Summary: The variation of chromosome number and genome size within the Salicaceae family demonstrates frequent ploidy changes and widespread sharing of the salicoid whole genome duplication event among relatives of Populus and Salix. Genome size reduction after whole genome duplication suggests substantial loss of genomic components. The phylogenetic asymmetry in the clade of Populus, Salix, and their close relatives indicates a delayed subsequent radiation post the salicoid whole genome duplication event.
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
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Endocrinology & Metabolism
Daniel Ocampo Daza, Christina A. Bergqvist, Dan Larhammar
Summary: This study provides a parsimonious explanation for the origin of the OTR/VTR gene family, based on phylogenetic and chromosomal conserved synteny analyses. The findings suggest a chromosome quadruplication event associated with whole-genome duplications early in vertebrate evolution, prior to the radiation of jawed vertebrates. The evolution of the OTR/VTR gene family can be explained by two whole-genome duplications followed by differential gene losses of VTR2 genes in different lineages.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Plant Sciences
Natalia Tkach, Marcin Nobis, Julia Schneider, Hannes Becher, Grit Winterfeld, Surrey W. L. Jacobs, Martin Roser
Summary: The Australian grass genus Austrostipa, with approximately 64 species, represents an evolutionary radiation. Molecular phylogenetic and SEM analyses were conducted to study diversification and morphological variation within the genus, with focus on lemma epidermal pattern. The study revealed low plastid DNA variation, two main subgenera clades, and the presence of two distinct Acc1 clades in polyploid Austrostipa and Anemanthele.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Lei Yang, Gavin J. P. Naylor, Richard L. Mayden
Summary: Despite the rarity of polyploidy in animals, the subfamily Cyprininae fishes present a complex and interesting pattern of reticulate evolution. Thirteen independent polyploidization events are hypothesized to have occurred during the evolution of Cyprininae, leading to a complicated post-polyploidization dynamics. The evolutionary history of Cyprinine can be divided into three stages, with the second stage witnessing all tetraploidization events and the last stage hosting hexaploidization events as well as species-specific polyploidization events.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Sarah Farhat, Maria Vittoria Modica, Nicolas Puillandre
Summary: The diversity of venomous organisms and the toxins they produce have been increasingly investigated, but taxonomic bias remains important. Neogastropods, a group of marine predators representing almost 22% of the known gastropod diversity, evolved a wide range of feeding strategies, including the production of toxins to subdue their preys. However, whether the diversity of these compounds is at the origin of the hyperdiversification of the group and how genome evolution may correlate with both the compounds and species diversities remain understudied.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Shu-Lei Jia, Mei Zhang, Guang-Lei Liu, Zhen-Ming Chi, Zhe Chi
Summary: The high-quality chromosome-level reference genome assemblies of A. melanogenum TN3-1 and A. melanogenum P16 were constructed using PacBio sequencing and Hi-C technologies, revealing structural variations and gene mutations. The TN3-1 strain was identified as a recent hybrid/fusion with metabolic processes related to harsh environmental adaptability, leading to high pullulan production from glucose.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Plant Sciences
Luis Diaz-Garcia, Luis Fernando Garcia-Ortega, Maria Gonzalez-Rodriguez, Luis Delaye, Massimo Iorizzo, Juan Zalapa
Summary: The American cranberry is an important fruit crop model due to its unique fruit composition, recent domestication, and various reproductive modes. This study presents the first chromosome-scale genome assembly of cranberry, providing insights into its genetic history and evolutionary relationships with other plant species. Phylogenetic analysis also identified potential regulators of anthocyanin biosynthesis in cranberry fruit.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Jessie A. Pelosi, Emily H. Kim, W. Brad Barbazuk, Emily B. Sessa
Summary: In this study, we assembled the largest nuclear dataset for ferns and investigated the fern phylogeny, whole genome duplications (WGDs), and gene retention patterns following WGDs. Our results revealed high levels of gene tree-species tree conflict in the fern phylogeny and identified multiple WGDs events. We also found that functions of retained genes following WGDs were largely convergent.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer
Summary: This study introduces a genome alignment method called AnchorWave, which shows significant improvement when applied to species with complex genomes. It can accurately identify multikilobase indels and improve the recall rate of transcription factor-binding sites.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Bing Xie, Daniel Dashevsky, Darin Rokyta, Parviz Ghezellou, Behzad Fathinia, Qiong Shi, Michael K. Richardson, Bryan G. Fry
Summary: The evolution of snake toxins shows novel convergences in both structural and functional aspects, providing insights for future studies on predator-prey evolutionary arms races, clinical pathologies, and biodiscovery for drug design.
Article
Physiology
Cheng Xue, Kang Xu, Yiting Jin, Chao Bian, Shengming Sun
Summary: This study utilized RNA sequencing to analyze the transcriptomes of gill and hepatopancreas tissues of Macrobrachium nipponense under salinity stress, revealing the molecular mechanisms underlying salinity adaptation. Important salinity adaptation-related genes and signaling pathways, such as ion transport, oxidative phosphorylation, and glycometabolism, were found to be enriched.
FRONTIERS IN PHYSIOLOGY
(2022)
Review
Genetics & Heredity
Yu Huang, Jia Li, Chao Bian, Ruihan Li, Xinxin You, Qiong Shi
Summary: Melatonin, an important hormone, plays a role in endocrine regulation in vertebrates. Fish have the most diverse aanat genes compared to other vertebrates, potentially contributing to seasonal migration, amphibious aerial vision, and adaptation to cave or deep-sea environments. Advances in genetic sequencing will enhance our understanding of AANAT function in various fish species.
FRONTIERS IN GENETICS
(2022)
Article
Environmental Sciences
Jinxing Fu, Yanbin He, Chao Peng, Tianle Tang, Aihua Jin, Yanling Liao, Qiong Shi, Bingmiao Gao
Summary: Sea anemone venom is a valuable marine drug resource library that contains diverse and complex peptide neurotoxins. This study identified a large number of protein and peptide toxin sequences from different developmental stages of Exaiptasia diaphana, a type of sea anemone. The proteins were classified into known superfamilies based on predicted functions, and the 3D structure and pharmacological activity of the peptide neurotoxins were predicted. These findings provide a valuable high-throughput method for obtaining sea anemone proteins and peptides, and lay the foundation for targeted studies on the diversity and pharmacological effects of sea anemone peptide neurotoxins.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Yishan Lu, Ruihan Li, Liqun Xia, Jun Cheng, Hongli Xia, Qiuyao Zhan, Dapeng Yu, Xinxin You, Ruobo Gu, Junmin Xu, Qiong Shi, Chao Bian
Summary: In this study, we sequenced the genome of the jade perch, a highly profitable freshwater bass species endemic to Australia, to identify the genes involved in the biosynthesis of omega-3 polyunsaturated fatty acids (PUFAs) and to deduce the ancestor genome karyotypes of bass. We constructed a chromosome-level genome assembly and identified repetitive elements and protein-coding genes. We also characterized key genes in the PUFA biosynthesis pathway and performed comparative genomic analyses among different bass species, resulting in sequences of a deductive bass ancestor genome.
Editorial Material
Endocrinology & Metabolism
Shubo Jin, Chao Bian, Jie Ma, Pengchao Wang, Pao Xu, Hongtuo Fu
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Genetics & Heredity
Jonny Andres Yepes-Blandon, Chao Bian, Maria Jose Benitez-Galeano, Jorge Luis Aristizabal-Regino, Ana Lucia Estrada-Posada, Daiana Mir, Gersson Vasquez-Machado, Victor Julio Atencio-Garcia, Qiong Shi, Nelida Rodriguez-Osorio
Summary: We present the first draft genome assembly of Prochilodus magdalenae in Colombia, which is a leading representative species in the Prochilodontidae family. This genome assembly, with a 1.2-Gb size, 42.0% GC content, and 31.0% repetitive content, shows similarities with other characid species genomes. Annotation identified 34,725 nuclear genes, and the completeness value was 94.9% according to BUSCO analysis. The genomic analysis revealed similar traits to other characid species and confirmed the taxonomic classification of P. magdalenae through mitochondrial genome sequencing. Phylogenomic analysis using nuclear single-copy orthologous genes further supported the evolutionary position of the species. This genome assembly provides valuable genetic resources for sustainable management of P. magdalenae in Colombia and contributes to fish genomics research in South America.
FRONTIERS IN GENETICS
(2023)
Article
Environmental Sciences
Yanling Liao, Chao Peng, Yabing Zhu, Jinxing Fu, Zhiqiang Ruan, Qiong Shi, Bingmiao Gao
Summary: The study constructed and sequenced a transcriptome library of different organs from the piscivorous Conus striatus, identifying a large number of conotoxin precursor peptides with significant diversity between NGS and TGS data. Additionally, point mutations were found in the signal peptide sequences of some conotoxins, challenging traditional views on conotoxin conservation and variability. The integrated NGS and TGS technologies provide insights into mining diverse conotoxins in Conus species for potential drug development.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Environmental Sciences
Ruihan Li, Yu Huang, Chao Peng, Zijian Gao, Jie Liu, Xiaoting Yin, Bingmiao Gao, Tatiana V. Ovchinnikova, Limei Qiu, Chao Bian, Qiong Shi
Summary: This study systematically characterized the antimicrobial peptide (AMP) repertoire in the representative Chinese tubular cone snail (C. betulinus) using genomic, transcriptomic, and peptidomic data. A total of 466 putative AMP-derived genes were identified from the genome, primarily annotated as histones. Only 77 of these genes were confirmed at the mRNA level. Additionally, 30 AMPs were validated by peptidomic data. In vitro analysis showed that eight of the synthesized peptides exhibited good antifungal activity. This research provides a valuable genetic resource for in-depth therapeutic applications and drug development.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Marine & Freshwater Biology
Yuting Huang, Qiong Shi
Summary: In this study, the tps, tpp, and tre genes from various crustacean species were analyzed. The tps and tpp genes were found to be fused in crustaceans with multiple gene copies, potentially due to whole-genome duplication or segmental duplications. The phylogenetic subgroups of enzymes in the same species were attributed to differences in domain lengths and distribution positions. The trehalase (TRE) enzymes in crustaceans were found to have an alpha-helix-rich structure with a barrel core, and can be membrane-bound, cytoplasmic, or secreted. The expression profiles and co-expression networks suggest that TPS (including TPP) and TRE play important roles in the physiological activities of development and environmental adaptation in crustaceans. Multiple copies of the tre gene may enhance copepods' survival ability in diverse and harsh environments, and certain crustaceans may adopt acid TRE as a supplementary strategy in response to stress.
JOURNAL OF CRUSTACEAN BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tianle Tang, Yu Huang, Chao Peng, Yanling Liao, Yunyun Lv, Qiong Shi, Bingmiao Gao
Summary: This study successfully constructed a genome assembly for the reef stonefish and conducted comparative analysis of its toxin genes. It was found that sntx genes had higher transcription levels, especially those clustered on chromosome 2. Furthermore, comparative genomic analysis revealed independent duplication events of toxin genes in Scorpaenoidei species, marking the origin of authentic toxic stonustoxins.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Chao Bian, Chenglong Liu, Guiying Zhang, Ming Tao, Danqiong Huang, Chaogang Wang, Sulin Lou, Hui Li, Qiong Shi, Zhangli Hu
Summary: This study sequenced the genome of the green microalga Haematococcus pluvialis and constructed a chromosome-level assembly. The results provide valuable genetic information for further research on this alga and commercial production of astaxanthin.
Article
Multidisciplinary Sciences
Kai Zhang, Yu Huang, Yuxuan Zhang, Rishen Liang, Qingqing Li, Ruihan Li, Xiaomeng Zhao, Chao Bian, Yongnan Chen, Jinhui Wu, Qiong Shi, Li Lin
Summary: Due to potential threats and elusive habitats, moray eels have not been extensively studied as apex predators in coral reefs worldwide. In this study, a haplotype genome assembly for the Reeve's moray eel was constructed, with 97.87% of sequences anchored into 21 chromosomes. The genome assembly contains repetitive sequences (56.34%) and 23,812 protein-coding genes, with 96.77% of them functionally annotated. This genome sequencing provides valuable genetic resources for studying the Reeve's moray eel and comparing eel genomes.
Article
Biotechnology & Applied Microbiology
Zhaoqun Liu, Yuting Huang, Hao Chen, Chang Liu, Minxiao Wang, Chao Bian, Lingling Wang, Linsheng Song
Summary: In this study, a chromosome-level genome of the deep-sea snail Phymorhynchus buccinoides was constructed, providing a comprehensive genomic basis for understanding its adaptation strategy to the extreme environment at the deep-sea cold seeps. The snail species has expanded glutamate regulative and related genes for acclimation to hypoxia and coldness, evolved a highly developed and sensitive olfactory organ for orientation and predation, and developed a sulfite-tolerance mechanism through H2S detoxification.
