Article
Multidisciplinary Sciences
Rachel L. Moran, Emilie J. Richards, Claudia Patricia Ornelas-Garcia, Joshua B. Gross, Alexandra Donny, Jonathan Wiese, Alex C. Keene, Johanna E. Kowalko, Nicolas Rohner, Suzanne E. McGaugh
Summary: Laboratory studies have shown that a single phenotype can be produced by many different genotypes, but in natural systems, phenotypic convergence is often due to parallel genetic changes. This study used whole genome resequencing in Mexican tetra to investigate how selection has shaped the repeated evolution of trait loss and enhancement in cavefish. The results suggest that both standing genetic variation and de novo mutations contribute to repeated adaptation, and that genes with larger mutational targets are more likely to be involved in repeated evolution.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Qingyuan Zhao, Feng Shao, Yanping Li, Soojin Yi, Zuogang Peng
Summary: Cavefishes around the world exhibit similar phenotypic traits and share some common features in their genomes, including lower mutation rates, relaxation of purifying selection, and increased mutational load. However, there is no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes is not caused by positive selection of the same genes. Genes related to lipid metabolism show relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes.
Article
Genetics & Heredity
Masato Mikami, Toshinao Ineno, Andrew W. Thompson, Ingo Braasch, Mikio Ishiyama, Kazuhiko Kawasaki
Summary: The study revealed that Polypteriformes and Lepisosteiformes have more SCPP genes, which may be involved in the formation of ganoid scales, while many genes have been lost in Acipenseriformes and Amiiformes. The common ancestors of extant actinopterygians likely had a large repertoire of SCPP genes, with many genes independently lost in evolution.
Article
Zoology
Yahui Zhao, Zushi Huang, Jinqing Huang, Chunguang Zhang, Fanwei Meng
Summary: The study found that eye-degenerated species in Sinocyclocheilus are polyphyletic, showing varying degrees of photoreceptor defects. While S. anophthalmus is classified as an eye-normal species, it exhibits high levels of eye degeneration and significant differences in eye-related gene expression compared to other eye-normal species.
INTEGRATIVE ZOOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nelson T. Chuang, Eugene J. Gardner, Diane M. Terry, Jonathan Crabtree, Anup A. Mahurkar, Guillermo L. Rivell, Charles C. Hong, James A. Perry, Scott E. Devine
Summary: This study successfully discovered a large number of MEIs in tens of thousands of human genomes and exomes using a newly developed mobile element locator tool. It provides new insights into the mechanisms of MEI mutagenesis and their impact on the human genome.
Article
Multidisciplinary Sciences
Kazuhiko Kawasaki, Joseph N. Keating, Mitsushiro Nakatomi, Monique Welten, Masato Mikami, Ichiro Sasagawa, Mark N. Puttick, Philip C. J. Donoghue, Mikio Ishiyama
Summary: Analyzing matrix protein-encoding SCPP genes and phylogenetic inference of hypermineralized tissues helps resolve the debate over the evolution of vertebrate hypermineralized tissues. The study shows that AMBN and ENAM originated alongside ancestral enamel, SCPP5 evolved in association with ganoin, and AMEL evolved with true enamel. Shifts in gene expression domain and timing explain the evolution of different hypermineralized tissues. The research suggests that hypermineralized tissues in osteichthyans coevolved with matrix SCPP genes.
Article
Multidisciplinary Sciences
J. Boutin, J. Rosier, D. Cappellen, F. Prat, J. Toutain, P. Pennamen, J. Bouron, C. Rooryck, J. P. Merlio, I. Lamrissi-Garcia, G. Cullot, S. Amintas, V. Guyonnet-Duperat, C. Ged, J. M. Blouin, E. Richard, S. Dabernat, F. Moreau-Gaudry, A. Bedel
Summary: The study reveals the genotoxicity caused by CRISPR-Cas9 leading to loss of heterozygosity changes, while also highlighting the potential safety concerns of this technology for gene therapy.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Nicolas Leurs, Camille Martinand-Mari, Sylvain Marcellini, Melanie Debiais-Thibaud
Summary: A scpp gene present in elasmobranchs (sharks and rays) is remarkably similar to the osteichthyan scpp members, but originated independently. In catsharks, this gene is coexpressed with sparc-L and fam20 degrees C, supporting a single origin for the hypermineralized outer odontode layer.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Corine M. van der Weele, William R. Jeffery
Summary: Dark caves lacking primary productivity expose subterranean animals to hypoxia. Cavefish cope with hypoxia by increasing erythrocyte development and constitutive hif1 gene overexpression.
Article
Biochemistry & Molecular Biology
Morgan O'Gorman, Sunishka Thakur, Gillian Imrie, Rachel L. Moran, Stefan Choy, Itzel Sifuentes-Romero, Helena Bilandzija, Kenneth J. Renner, Erik Duboue, Nicolas Rohner, Suzanne E. McGaugh, Alex C. Keene, Johanna E. Kowalko
Summary: Adaptation to novel environments often leads to the evolution of multiple morphological, physiological, and behavioral traits, such as regression of eyes, loss of pigmentation, and enhancement of non-visual sensory systems in cave animals. The study found that Mexican tetra, Astyanax mexicanus, in caves have evolved traits including reduced pigmentation, eye loss, and alterations to behavior, and that these traits are shared genetic basis between pigmented and albino hybrid fish. Furthermore, mutations in oculocutaneous albinism 2 (oca2) underlie the adaptive evolution of albinism and sleep loss in cavefish and other species.
Article
Biochemistry & Molecular Biology
Guosheng Ma, Xiaojing Zhao, Xinyi Shentu, Liye Zhang
Summary: Gene loss is a common phenomenon affecting genome evolution. Compensatory mutations in homologous genes have been identified as a strategy to rescue defects caused by gene loss. Bioinformatics analysis also suggests that point mutations in homologous genes may serve as an additional mechanism to compensate for gene loss.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Genetics & Heredity
Jaya Krishnan, Chris W. Seidel, Ning Zhang, Narendra Pratap Singh, Jake VanCampen, Robert Peuss, Shaolei Xiong, Alexander Kenzior, Hua Li, Joan W. Conaway, Nicolas Rohner
Summary: Cis-regulatory changes have been found to contribute to the metabolic adaptation in different morphotypes of Astyanax mexicanus, with genetically diverged and differentially regulated elements identified between surface and cave populations. This study sheds light on the molecular mechanisms underlying metabolic adaptations to nutrient-deprived cave environments.
Article
Computer Science, Artificial Intelligence
Wu Deng, Shifan Shang, Xing Cai, Huimin Zhao, Yongquan Zhou, Huayue Chen, Wuquan Deng
Summary: The proposed HMCFQDE combines quantum evolutionary algorithm (QEA) and cooperative coevolution evolutionary algorithm (CCEA) to improve the solution efficiency and search speed. A new hybrid mutation strategy is designed to enhance convergence accuracy and stability in solving high-dimensional complex functions.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Biochemistry & Molecular Biology
Evan Lloyd, Brittnee McDole, Martin Privat, James B. Jaggard, Erik R. Duboue, German Sumbre, Alex C. Keene
Summary: The Mexican cavefish Astyanax mexicanus provides an opportunity to study the evolutionary changes in sensory circuits in response to environmental perturbation. The study shows that the functional connectivity of the optic tectum in cavefish remains largely unchanged except for the loss of negatively correlated activity, indicating the resistance of positively correlated neural activity to the loss of input from the retina. Additionally, the changes in the tectum are found to be genetically distinct from the encoding of eye loss.
Article
Genetics & Heredity
Katya L. Mack, James B. Jaggard, Jenna L. Persons, Emma Y. Roback, Courtney N. Passow, Bethany A. Stanhope, Estephany Ferrufino, Dai Tsuchiya, Sarah E. Smith, Brian D. Slaughter, Johanna Kowalko, Nicolas Rohner, Alex C. Keene, Suzanne E. McGaugh
Summary: The study shows that moving into an environment without daily cycles has led to predictable disruptions to the biological clock among cavefish populations, but that the disruptions occur through different molecular mechanisms. The changes to the biological clock may also affect aspects of cavefish behavior, such as the sleep-wake cycle. The study provides insight into how evolved changes in the biological clock can contribute to variation in sleep and circadian behavior in cavefish populations.
Article
Biochemistry & Molecular Biology
Chengfei Sun, Jia Li, Junjian Dong, Yongchao Niu, Jie Hu, Jinmin Lian, Wuhui Li, Jiang Li, Yuanyuan Tian, Qiong Shi, Xing Ye
Summary: This study presents a chromosome-level genome assembly of largemouth bass, highlighting its unique 23 chromosomes and a chromosomal fusion event. By comparing transcriptome and genome data, gene families associated with ionic regulation were identified, providing insights into the molecular mechanisms of largemouth bass adaptation to fresh and brackish water. This high-quality genome will serve as a valuable resource for biological and evolutionary studies, germplasm conservation, and genetic breeding of the species.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Cell Biology
Chao Peng, Yu Huang, Chao Bian, Jia Li, Jie Liu, Kai Zhang, Xinxin You, Zhilong Lin, Yanbin He, Jieming Chen, Yunyun Lv, Zhiqiang Ruan, Xinhui Zhang, Yunhai Yi, Yanping Li, Xueqiang Lin, Ruobo Gu, Junmin Xu, Jia'an Yang, Chongxu Fan, Ge Yao, Ji-Sheng Chen, Hui Jiang, Bingmiao Gao, Qiong Shi
Summary: This study sequenced and assembled the first Conus genome, identifying 133 conopeptide genes. By integrating genomics, transcriptomics, and peptidomics data, the researchers established a primary genetic central dogma of diverse conopeptides.
Article
Genetics & Heredity
Pengwei Xu, Chenxi Zhao, Xinxin You, Fan Yang, Jieming Chen, Zhiqiang Ruan, Ruobo Gu, Junmin Xu, Chao Bian, Qiong Shi
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Chao Bian, Ruihan Li, Zhengyong Wen, Wei Ge, Qiong Shi
Summary: Melanin is the most prevalent pigment in animals, and its synthesis involves a series of functional genes. This study conducted a comparative genomic analysis on core genes related to melanin synthesis across 90 representative vertebrate genomes, identifying newly identified nonsense mutations in diverse albino fishes. These mutations may provide molecular guidance for ornamental fish breeding and enhance our understanding of human skin coloration.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Ruihan Li, Xiaoai Wang, Chao Bian, Zijian Gao, Yuanwei Zhang, Wansheng Jiang, Mo Wang, Xinxin You, Le Cheng, Xiaofu Pan, Junxing Yang, Qiong Shi
Summary: This study reported the first genome assembly of Sinocyclocheilus maitianheensis, providing valuable genetic resources for further comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish. Comparative analysis revealed the close relationship between S. maitianheensis and cave-restricted Sinocyclocheilus anophthalmus, as well as a decreased tendency of copy number in important genes related to immunity and apoptosis in cave-restricted species.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Wu Gan, Chenxi Zhao, Xinran Liu, Chao Bian, Qiong Shi, Xinxin You, Wei Song
Summary: The study constructed a genome assembly of spiny head croaker, revealing a closer relationship between C. lucidus and Larimichthys crocea, with some gene families related to calcium signaling pathway and inner ear function significantly expanded. Critical deletions or mutations were identified in some otolith-related genes, suggesting possible molecular mechanisms for well-developed otoliths in the Sciaenidae family.
FRONTIERS IN GENETICS
(2021)
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)
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
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.