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Boyette JL, Bell RC, Fujita MK, Thomas KN, Streicher JW, Gower DJ, Schott RK. Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs. Mol Biol Evol 2024; 41:msae090. [PMID: 38736374 PMCID: PMC11181710 DOI: 10.1093/molbev/msae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024] Open
Abstract
Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.
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Affiliation(s)
- John L Boyette
- Department of Biological Sciences, The Pennsylvania State University, State College, PA, USA
- Department of Biology, Berry College, Rome, GA, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Kate N Thomas
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
- Natural History Museum, London, UK
| | | | | | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Biology & Centre for Vision Research, York University, Toronto, ON, Canada
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Hussain A, Mehmood A, Raza W, Faheem M, Saleem A, Kashif Majeed M, Iqbal R, Aziz MA. Highly Stretchable Polyurethane Porous Membranes with Adjustable Morphology for Advanced Lithium Metal Batteries. Chem Asian J 2024:e202400245. [PMID: 38634677 DOI: 10.1002/asia.202400245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 04/19/2024]
Abstract
A highly flexible, tunable morphology membrane with excellent thermal stability and ionic conductivity can endow lithium metal batteries with high power density and reduced dendrite growth. Herein, a porous Polyurethane (PU) membrane with an adjustable morphology was prepared by a simple nonsolvent-induced phase separation technique. The precise control of the final morphology of PU membranes can be achieved through appropriate selection of a nonsolvent, resulting a range of pore structures that vary from finger-like voids to sponge-like pores. The implementation of combinatorial DFT and experimental analysis has revealed that spongy PU porous membranes, especially PU-EtOH, show superior electrolyte wettability (472%), high porosity (75%), good mechanical flexibility, robust thermal dimensional stability (above 170 °C), and elevated ionic conductivity (1.38 mS cm-1) in comparison to the polypropylene (PP) separator. The use of PU-EtOH in Li//Li symmetric cell results in a prolonged lifespan of 800 h, surpasing the longevity of PU or PP cells. Moreover, when subjected to a high rate of 5 C, the LiFePO4/Li half-cell with a PU-EtOH porous membrane displayed better cycling performance (115.4 mAh g-1) compared to the PP separator (104.4 mAh g-1). Finally, the prepared PU porous membrane exhibits significant potential for improving the efficiency and safety of LMBs.
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Affiliation(s)
- Arshad Hussain
- Interdisciplinary Research Center for Hydrogen Technologies and Carbon Management (IRC-HTCM), King Fahd University of Petroleum & Minerals, KFUPM Box, 5040, Dhahran, 31261, Saudi Arabia
| | - Andleeb Mehmood
- Institute of Carbon Neutrality, Zhejiang Wanli University, Ningbo, 315100, China
| | - Waseem Raza
- Institute for Advanced Study, Shenzhen University, Guangdong, 518060, China
| | - Muhammad Faheem
- Interdisciplinary Research Center for Hydrogen Technologies and Carbon Management (IRC-HTCM), King Fahd University of Petroleum & Minerals, KFUPM Box, 5040, Dhahran, 31261, Saudi Arabia
| | - Adil Saleem
- College of Mechatronics and Control Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Muhammad Kashif Majeed
- Department of Chemistry, School of Natural Sciences, National University of science and technology, 44000, Islamabad, Pakistan
| | - Rashid Iqbal
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, China
| | - Md Abdul Aziz
- Interdisciplinary Research Center for Hydrogen Technologies and Carbon Management (IRC-HTCM), King Fahd University of Petroleum & Minerals, KFUPM Box, 5040, Dhahran, 31261, Saudi Arabia
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3
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Wu J, Duan C, Lan L, Chen W, Mao X. Sex Differences in Cochlear Transcriptomes in Horseshoe Bats. Animals (Basel) 2024; 14:1177. [PMID: 38672325 PMCID: PMC11047584 DOI: 10.3390/ani14081177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Sexual dimorphism of calls is common in animals, whereas studies on the molecular basis underlying this phenotypic variation are still scarce. In this study, we used comparative transcriptomics of cochlea to investigate the sex-related difference in gene expression and alternative splicing in four Rhinolophus taxa. Based on 31 cochlear transcriptomes, we performed differential gene expression (DGE) and alternative splicing (AS) analyses between the sexes in each taxon. Consistent with the degree of difference in the echolocation pulse frequency between the sexes across the four taxa, we identified the largest number of differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) in R. sinicus. However, we also detected multiple DEGs and ASGs in taxa without sexual differences in echolocation pulse frequency, suggesting that these genes might be related to other parameters of echolocation pulse rather than the frequency component. Some DEGs and ASGs are related to hearing loss or deafness genes in human or mice and they can be considered to be candidates associated with the sexual differences of echolocation pulse in bats. We also detected more than the expected overlap of DEGs and ASGs in two taxa. Overall, our current study supports the important roles of both DGE and AS in generating or maintaining sexual differences in animals.
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Affiliation(s)
| | | | | | | | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; (J.W.); (C.D.); (L.L.); (W.C.)
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Lv Y, Chen C, Yan C, Liao W. The paddy frog genome provides insight into the molecular adaptations and regulation of hibernation in ectotherms. iScience 2024; 27:108844. [PMID: 38261954 PMCID: PMC10797549 DOI: 10.1016/j.isci.2024.108844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/22/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Amphibians, like the paddy frog (Fejervarya multistriata), have played a critical role in the transition from water to land. Hibernation is a vital survival adaptation in cold environments with limited food resources. We decoded the paddy frog genome to reveal the molecular adaptations linked to hibernation in ectotherms. The genome contained 13 chromosomes, with a significant proportion of repetitive sequences. We identified the key genes encoding the proteins of AANAT, TRPM8, EGLN1, and VEGFA essential for circadian rhythms, thermosensation, and hypoxia during hibernation by comparing the hibernator and non-hibernator genomes. Examining organ changes during hibernation revealed the central regulatory role of the brain. We identified 21 factors contributing to hibernation, involving hormone biosynthesis, protein digestion, DNA replication, and the cell cycle. These findings provide deeper insight into the complex mechanisms of ectothermic hibernation and contribute to our understanding of the broader significance of this evolutionary adaptation.
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Affiliation(s)
- Yunyun Lv
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan 637009, China
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China
| | - Chuan Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan 637009, China
| | - Chengzhi Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan 637009, China
| | - Wenbo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan 637009, China
- College of Panda, China West Normal Univetsity, Nanchong, Sichuan 637009, China
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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Ferreira JS, Bruschi DP. Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species. J Mol Evol 2023; 91:793-805. [PMID: 37906255 DOI: 10.1007/s00239-023-10135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Olfaction is a crucial capability for most vertebrates and is realized through olfactory receptors in the nasal cavity. The enormous diversity of olfactory receptors has been created by gene duplication, following a birth-and-death model of evolution. The olfactory receptor genes of the amphibians have received relatively little attention up to now, although recent studies have increased the number of species for which data are available. This study analyzed the diversity and chromosomal distribution of the OR genes of three anuran species (Engystomops pustulosus, Bufo bufo and Hymenochirus boettgeri). The OR genes were identified through searches for homologies, and sequence filtering and alignment using bioinformatic tools and scripts. A high diversity of OR genes was found in all three species, ranging from 917 in B. bufo to 1194 in H. boettgeri, and a total of 2076 OR genes in E. pustulosus. Six OR groups were recognized using an evolutionary gene tree analysis. While E. pustulosus has one of the highest numbers of genes of the gamma group (which detect airborne odorants) yet recorded in an anuran, B. bufo presented the smallest number of pseudogene sequences ever identified, with no pseudogenes in either the beta or epsilon groups. Although H. boettgeri shares many morphological adaptations for an aquatic lifestyle with Xenopus, and presented a similar number of genes related to the detection of water-soluble odorants, it had comparatively far fewer genes related to the detection of airborne odorants. This study is the first to describe the complete OR repertoire of the three study species and represents an important contribution to the understanding of the evolution and function of the sense of smell in vertebrates.
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Affiliation(s)
- Johnny Sousa Ferreira
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil.
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Azadeh H. Association between disease-modifying antirheumatic drugs and bone turnover biomarkers. Int J Rheum Dis 2023; 26:437-445. [PMID: 36573666 DOI: 10.1111/1756-185x.14550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/24/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
Rheumatoid arthritis (RA) has been linked to an increased risk of osteoporosis as well as fractures. Patients diagnosed with RA had a 25% increased risk of osteoporotic fracture, according to a recent population-based cohort study that compared them to people without RA. Several studies have found a correlation between osteoporosis and the presence of pro-inflammatory cytokines, such as tumor necrosis factor (TNF)-α, interleukin (IL)-1, and 6. These cytokines play a crucial part in the process of bone resorption by boosting osteoclast activation and encouraging osteoclast differentiation. Based on the correlation between RA, osteoporosis, and inflammation, it is possible that systemic immunosuppression with disease-modifying antirheumatic drugs (DMARDs) can help individuals with RA have a lower chance of developing osteoporosis and osteoporotic fractures. There is little information on how different DMARDs, biologic or non-biologic, affect RA patients' bone metabolism. In this study, we present an overview of the influence that targeted therapies, such as biologics, non-biologics, and small molecule inhibitors, have on bone homeostasis in RA patients.
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Affiliation(s)
- Hossein Azadeh
- Department of Internal Medicine, Rheumatology Division, Orthopedic Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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Chen W, Chen H, Liao J, Tang M, Qin H, Zhao Z, Liu X, Wu Y, Jiang L, Zhang L, Fang B, Feng X, Zhang B, Reid K, Merilä J. Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation. Front Zool 2023; 20:1. [PMID: 36604706 PMCID: PMC9817415 DOI: 10.1186/s12983-022-00482-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation. RESULTS The R. kukunoris genome was assembled to a size of 4.83 Gb and the contig N50 was 1.80 Mb. The 6555 contigs were clustered and ordered into 12 pseudo-chromosomes covering ~ 93.07% of the assembled genome. In total, 32,304 genes were functionally annotated. Synteny analysis between the genomes of R. kukunoris and a low latitude species Rana temporaria showed a high degree of chromosome level synteny with one fusion event between chr11 and chr13 forming pseudo-chromosome 11 in R. kukunoris. Characterization of features of the R. kukunoris genome identified that 61.5% consisted of transposable elements and expansions of gene families related to cell nucleus structure and taste sense were identified. Ninety-five single-copy orthologous genes were identified as being under positive selection and had functions associated with the positive regulation of proteins in the catabolic process and negative regulation of developmental growth. These gene family expansions and positively selected genes indicate regions for further interrogation to understand adaptation to high altitude. CONCLUSIONS Here, we reported a high-quality chromosome-level genome assembly of a high-altitude amphibian species using a combination of Illumina, PacBio and Hi-C sequencing technologies. This genome assembly provides a valuable resource for subsequent research on R. kukunoris genomics and amphibian genome evolution in general.
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Affiliation(s)
- Wei Chen
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China ,Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi, 247230 China ,grid.252245.60000 0001 0085 4987Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, 230601 China
| | - Hongzhou Chen
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Jiahong Liao
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Min Tang
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Haifen Qin
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Zhenkun Zhao
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Xueyan Liu
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Yanfang Wu
- grid.252245.60000 0001 0085 4987School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 China
| | - Lichun Jiang
- grid.464385.80000 0004 1804 2321School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000 Sichuan China
| | - Lixia Zhang
- grid.462338.80000 0004 0605 6769Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Bohao Fang
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA USA
| | - Xueyun Feng
- grid.7737.40000 0004 0410 2071Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Baowei Zhang
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China
| | - Kerry Reid
- grid.194645.b0000000121742757Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- grid.7737.40000 0004 0410 2071Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland ,grid.194645.b0000000121742757Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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Andrade P, Lyra ML, Zina J, Bastos DFO, Brunetti AE, Baêta D, Afonso S, Brunes TO, Taucce PPG, Carneiro M, Haddad CFB, Sequeira F. Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana. G3 (BETHESDA, MD.) 2022; 12:jkac270. [PMID: 36205610 PMCID: PMC9713437 DOI: 10.1093/g3journal/jkac270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 12/05/2022]
Abstract
Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Mariana L Lyra
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Juliana Zina
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, Brazil
| | - Deivson F O Bastos
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, Brazil
| | - Andrés E Brunetti
- Laboratory of Evolutionary Genetics, Institute of Subtropical Biology, National University of Misiones (UNaM-CONICET) Posadas N3300LQH, Misiones, Argentina
| | - Délio Baêta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Tuliana O Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Pedro P G Taucce
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
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10
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Malcher A, Stokowy T, Berman A, Olszewska M, Jedrzejczak P, Sielski D, Nowakowski A, Rozwadowska N, Yatsenko AN, Kurpisz MK. Whole-genome sequencing identifies new candidate genes for nonobstructive azoospermia. Andrology 2022; 10:1605-1624. [PMID: 36017582 PMCID: PMC9826517 DOI: 10.1111/andr.13269] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/21/2022] [Accepted: 08/17/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Genetic causes that lead to spermatogenetic failure in patients with nonobstructive azoospermia (NOA) have not been yet completely established. OBJECTIVE To identify low-frequency NOA-associated single nucleotide variants (SNVs) using whole-genome sequencing (WGS). MATERIALS AND METHODS Men with various types of NOA (n = 39), including samples that had been previously tested with whole-exome sequencing (WES; n = 6) and did not result in diagnostic conclusions. Variants were annotated using the Ensembl Variant Effect Predictor, utilizing frequencies from GnomAD and other databases to provide clinically relevant information (ClinVar), conservation scores (phyloP), and effect predictions (i.e., MutationTaster). Structural protein modeling was also performed. RESULTS Using WGS, we revealed potential NOA-associated SNVs, such as: TKTL1, IGSF1, ZFPM2, VCX3A (novel disease causing variants), ESX1, TEX13A, TEX14, DNAH1, FANCM, QRICH2, FSIP2, USP9Y, PMFBP1, MEI1, PIWIL1, WDR66, ZFX, KCND1, KIAA1210, DHRSX, ZMYM3, FAM47C, FANCB, FAM50B (genes previously known to be associated with infertility) and ALG13, BEND2, BRWD3, DDX53, TAF4, FAM47B, FAM9B, FAM9C, MAGEB6, MAP3K15, RBMXL3, SSX3 and FMR1NB genes, which may be involved in spermatogenesis. DISCUSSION AND CONCLUSION In this study, we identified novel potential candidate NOA-associated genes in 29 individuals out of 39 azoospermic males. Note that in 5 out of 6 patients subjected previously to WES analysis, which did not disclose potentially causative variants, the WGS analysis was successful with NOA-associated gene findings.
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Affiliation(s)
| | - Tomasz Stokowy
- Scientific Computing GroupIT DivisionUniversity of BergenNorway
| | - Andrea Berman
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marta Olszewska
- Institute of Human GeneticsPolish Academy of SciencesPoznanPoland
| | - Piotr Jedrzejczak
- Division of Infertility and Reproductive EndocrinologyDepartment of GynecologyObstetrics and Gynecological OncologyPoznan University of Medical SciencesPoznanPoland
| | | | - Adam Nowakowski
- Department of Urology and Urologic Oncology in St. Families HospitalPoznanPoland
| | | | - Alexander N. Yatsenko
- Department of OB/GYN and Reproductive SciencesSchool of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
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11
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Shukla A, Maiti P. Nanomedicine and versatile therapies for cancer treatment. MedComm (Beijing) 2022; 3:e163. [PMID: 35992969 PMCID: PMC9386439 DOI: 10.1002/mco2.163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 12/19/2022] Open
Abstract
The higher prevalence of cancer is related to high rates of mortality and morbidity worldwide. By virtue of the properties of matter at the nanoscale, nanomedicine is proven to be a powerful tool to develop innovative drug carriers with greater efficacies and fewer side effects than conventional therapies. In this review, different nanocarriers for controlled drug release and their routes of administration have been discussed in detail, especially for cancer treatment. Special emphasis has been given on the design of drug delivery vehicles for sustained release and specific application methods for targeted delivery to the affected areas. Different polymeric vehicles designed for the delivery of chemotherapeutics have been discussed, including graft copolymers, liposomes, hydrogels, dendrimers, micelles, and nanoparticles. Furthermore, the effect of dimensional properties on chemotherapy is vividly described. Another integral section of the review focuses on the modes of administration of nanomedicines and emerging therapies, such as photothermal, photodynamic, immunotherapy, chemodynamic, and gas therapy, for cancer treatment. The properties, therapeutic value, advantages, and limitations of these nanomedicines are highlighted, with a focus on their increased performance versus conventional molecular anticancer therapies.
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Affiliation(s)
- Aparna Shukla
- School of Materials Science and Technology Indian Institute of Technology (Banaras Hindu University) Varanasi India
| | - Pralay Maiti
- School of Materials Science and Technology Indian Institute of Technology (Banaras Hindu University) Varanasi India
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12
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Gatto KP, Timoshevskaya N, Smith JJ, Lourenço LB. Sequencing of laser captured Z and W chromosomes of the tocantins paradoxical frog (Pseudis tocantins) provides insights on repeatome and chromosomal homology. J Evol Biol 2022; 35:1659-1674. [PMID: 35642451 DOI: 10.1111/jeb.14027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/06/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022]
Abstract
Pseudis tocantins is the only frog species of the hylid genus Pseudis that possesses highly heteromorphic sex chromosomes. Z and W chromosomes of Ps. tocantins differ in size, morphology, position of the nucleolar organizer region (NOR) and the amount and distribution of heterochromatin. A chromosomal inversion and heterochromatin amplification on the W chromosome were previously inferred to be involved in the evolution of this sex chromosome pair. Despite these findings, knowledge related to the molecular composition of the large heterochromatic band of this W chromosome is restricted to the PcP190 satellite DNA, and no data are available regarding the gene content of either the W or the Z chromosome of Ps. tocantins. Here, we sequenced microdissected Z and W chromosomes of this species to further resolve their molecular composition. Comparative genomic analysis suggests that Ps. tocantins sex chromosomes are likely homologous to chromosomes 4 and 10 of Xenopus tropicalis. Analyses of the repetitive DNA landscape in the Z and W assemblies allowed for the identification of several transposable elements and putative satellite DNA sequences. Finally, some transposable elements from the W assembly were found to be highly diverse and divergent from elements found elsewhere in the genome, suggesting a rapid amplification of these elements on the W chromosome.
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Affiliation(s)
- Kaleb Pretto Gatto
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil.,Laboratory of Herpetology and Aquaculture Center, Department of Zoology, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
| | - Nataliya Timoshevskaya
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Jeramiah J Smith
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Luciana Bolsoni Lourenço
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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13
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Velsankar K, Parvathy G, Mohandoss S, Sudhahar S. Effect of green synthesized ZnO nanoparticles using Paspalum scrobiculatum grains extract in biological applications. Microsc Res Tech 2022; 85:3069-3094. [PMID: 35611771 DOI: 10.1002/jemt.24167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/02/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022]
Abstract
In this report, ZnO nanoparticles were biosynthesized using Paspalum scrobiculatum grains extract for the first time. GC-MS analysis explicated that diethyl phthalate was the major phytocompound with 94.09% in aqueous extract. ZnO nanoparticles formation was confirmed by various physicochemical analyses. HR-TEM images showed the hexagonal, rectangular shaped nanoparticles in 15-30 nm size. The antioxidant, anti-inflammatory, and anti-diabetic analyses showed the effective bioactivity of ZnO nanoparticles in 80 μg/ml concentration with 95.36%, 94.08%, and 91.96%, respectively. The morphological and tissue changes witnessed in larvicidal and insecticidal activities against Culex tritaeniorhynchus and Tribolium castaneum revealed the efficient nature of ZnO nanoparticles in 100 ppm at 48 h and 100 μg/kg at 72 h, respectively. The morphological changes in antibacterial activity demonstrated the bactericidal nature of ZnO nanoparticles against Salmonella typhi and Staphylococcus aureus in 150 μg/ml concentration. The morphological observations in anticancer activity against HepG2 liver cancer cells showed the potent drug features of ZnO nanoparticles in 100 μg/ml concentration with 97.18% of cytotoxicity. The ZnO nanoparticles showed no toxicity against HDF normal cells in lower concentrations and it explicated the biocompatible features of nanoparticles. The Vigna radiata plant growth was efficiently promoted by low (60 ppm) concentration of nanoparticles. The ZnO nanoparticles divulged effective degradation of IPA, EDTA, BQ, and DPBF in 75%, 45%, 55%, and 80% through ROS formation, respectively. Thus, the synthesized ZnO nanoparticles are biocompatible and inexpensive material compared to the traditional one and can be utilized as an efficient material in biological fields.
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Affiliation(s)
- K Velsankar
- Department of Physics, Alagappa University, Karikudi, India
| | - G Parvathy
- Department of Physics, Alagappa University, Karikudi, India
| | - S Mohandoss
- School of Chemical Engineering, Yeungnam University, Gyeongsan, Republic of Korea
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14
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Abstract
SignificanceTo adapt to arboreal lifestyles, treefrogs have evolved a suite of complex traits that support vertical movement and gliding, thus presenting a unique case for studying the genetic basis for traits causally linked to vertical niche expansion. Here, based on two de novo-assembled Asian treefrog genomes, we determined that genes involved in limb development and keratin cytoskeleton likely played a role in the evolution of their climbing systems. Behavioral and morphological evaluation and time-ordered gene coexpression network analysis revealed the developmental patterns and regulatory pathways of the webbed feet used for gliding in Rhacophorus kio.
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15
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Schott RK, Perez L, Kwiatkowski MA, Imhoff V, Gumm JM. Evolutionary analyses of visual opsin genes in frogs and toads: Diversity, duplication, and positive selection. Ecol Evol 2022; 12:e8595. [PMID: 35154658 PMCID: PMC8820127 DOI: 10.1002/ece3.8595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 01/12/2023] Open
Abstract
Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found that anurans consistently express four visual opsin genes (RH1, LWS, SWS1, and SWS2, but not RH2) even though reported photoreceptor complements vary widely among species. The proteins encoded by these genes showed considerable sequence variation among species, including at sites known to shift the spectral sensitivity of visual pigments in other vertebrates and had conserved substitutions that may be related to dim-light adaptation. Using molecular evolutionary analyses of selection (dN/dS) we found significant evidence for positive selection at a subset of sites in the dim-light rod opsin gene RH1 and the long wavelength sensitive cone opsin LWS. The function of sites inferred to be under positive selection are largely unknown, but a few are likely to affect spectral sensitivity and other visual pigment functions based on proximity to previously identified sites in other vertebrates. We also found the first evidence of visual opsin duplication in an amphibian with the duplication of the LWS gene in the African bullfrog, which had distinct LWS copies on the sex chromosomes suggesting the possibility of sex-specific visual adaptation. Taken together, our results indicate that ecological factors, such as habitat and life history, as well as behavior, may be driving changes to anuran visual systems.
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Affiliation(s)
- Ryan K. Schott
- Department of BiologyYork UniversityTorontoOntarioCanada
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Leah Perez
- Department of BiologyStephen F. Austin State UniversityNacogdochesTexasUSA
| | | | - Vance Imhoff
- Southern Nevada Fish and Wildlife OfficeUS Fish and Wildlife ServiceLas VegasNevadaUSA
| | - Jennifer M. Gumm
- Department of BiologyStephen F. Austin State UniversityNacogdochesTexasUSA
- Ash Meadows Fish Conservation FacilityUS Fish and Wildlife ServiceAmargosa ValleyNevadaUSA
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16
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Fu C, Ai Q, Cai L, Qiu F, Yao L, Wu H. Genetic Diversity and Population Dynamics of Leptobrachium leishanense (Anura: Megophryidae) as Determined by Tetranucleotide Microsatellite Markers Developed from Its Genome. Animals (Basel) 2021; 11:3560. [PMID: 34944336 PMCID: PMC8698065 DOI: 10.3390/ani11123560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Persisting declination of amphibians around the world has resulted in the public attaching importance to the conservation of their biodiversity. Genetic data can be greatly helpful in conservation planning and management, especially in species that are small in size and hard to observe. It is essential to perform genetic assessments for the conservation of Leptobrachium leishanense, an endangered toad and receiving secondary protection on the list of state-protected wildlife in China. However, current molecular markers with low reliability and efficiency hinder studies. Here, we sampled 120 adult toes from the population in the Leishan Mountain, 23 of which were used to develop tetranucleotide microsatellite markers based on one reference L. leishanense genome. After primer optimization, stability detection, and polymorphism detection, we obtained 12 satisfactory microsatellite loci. Then, we used these loci to evaluate the genetic diversity and population dynamics of the 120 individuals. Our results show that there is a low degree of inbreeding in the population, and it has a high genetic diversity. Recently, the population has not experienced population bottlenecks, and the estimated effective population size was 424.3. Accordingly, stabilizing genetic diversity will be key to population sustainability. Recovering its habitat and avoiding intentional human use will be useful for conservation of this species.
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Affiliation(s)
| | | | | | | | | | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (C.F.); (Q.A.); (L.C.); (F.Q.); (L.Y.)
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17
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Nürnberger B, Baird SJE, Čížková D, Bryjová A, Mudd AB, Blaxter ML, Szymura JM. A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombina and Bombina variegata). G3 (BETHESDA, MD.) 2021; 11:6353606. [PMID: 34849761 PMCID: PMC8664441 DOI: 10.1093/g3journal/jkab286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022]
Abstract
Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7–10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.
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Affiliation(s)
- Beate Nürnberger
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Stuart J E Baird
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Dagmar Čížková
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Anna Bryjová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Austin B Mudd
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, 94720 CA, USA
| | - Mark L Blaxter
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jacek M Szymura
- Department of Comparative Anatomy, Jagiellonian University, 30-387 Kraków, Poland
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18
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Shaheen J, Mudd AB, Diekwisch TGH, Abramyan J. Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae). Integr Comp Biol 2021; 61:1933-1945. [PMID: 33905504 PMCID: PMC8699095 DOI: 10.1093/icb/icab039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary time line of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In this study, we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86-93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison with functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46-60 million years ago in the lineage leading to modern true toads, a time line that coincides with the rise of the family Bufonidae.
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Affiliation(s)
- John Shaheen
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI 48128, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Thomas G H Diekwisch
- Center for Craniofacial Research and Diagnosis, Texas A&M University, Dallas, TX 75246, USA
| | - John Abramyan
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI 48128, USA
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19
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Mu Q, Zhang Y, Gu L, Gerner ST, Qiu X, Tao Q, Pang J, Dipritu G, Zhang L, Yin S, Jiang Y, Peng J. Transcriptomic Profiling Reveals the Antiapoptosis and Antioxidant Stress Effects of Fos in Ischemic Stroke. Front Neurol 2021; 12:728984. [PMID: 34744970 PMCID: PMC8566985 DOI: 10.3389/fneur.2021.728984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/09/2021] [Indexed: 12/02/2022] Open
Abstract
Arterial hypertension is considered the most prevalent risk factor for stroke. Both pathophysiologic and clinical data previously acquired suggest a strong correlation between the hemodynamic nature of arterial hypertension and an increase in the risk of ischemic insult to tissues. However, the knowledge of specific molecular interactions between hypertension and ischemic stroke (IS) is limited. In this study, we performed systematic bioinformatics analysis of stroke-prone spontaneous hypertensive brain tissue samples of rats (GSE41452), middle cerebral artery occlusion of brain tissue samples of rats (GSE97537), and peripheral blood array data of IS patients (GSE22255). We identified that Fos, an immediate-early gene (IEG) that responds to alterations in arterial blood pressure, has a strong correlation with the occurrence and prognosis of IS. To further evaluate the potential function of Fos, the oxygen–glucose deprivation model and RNA sequencing of HT22 neuronal cells were performed. Consistent with the sequencing results, real-time quantitative PCR and Western blot indicate that Fos was elevated at 3 h and returned to normal levels at 6 h after oxygen–glucose deprivation. Knock-down of Fos by lentivirus significantly increased the oxidative stress level, neuronal apoptosis, and inhibited the mitochondrial function. In conclusion, Fos acts as an important link between hypertension and IS. Furthermore, Fos can be used as a potential biomarker for target therapy in the prevention of stroke among hypertensive patients and also potential treatment targeting apoptosis and oxidative stress after its onset.
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Affiliation(s)
- Qiancheng Mu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yuxuan Zhang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Long Gu
- Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Stefan T Gerner
- Department of Neurology, University Hospital Erlangen-Nuremberg, Erlangen, Germany
| | - Xiancheng Qiu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qianke Tao
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinwei Pang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China
| | - Ghosh Dipritu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lifang Zhang
- Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shigang Yin
- Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China
| | - Yong Jiang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China
| | - Jianhua Peng
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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20
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Lake J, Reed X, Langston RG, Nalls MA, Gan-Or Z, Cookson MR, Singleton AB, Blauwendraat C, Leonard HL. Coding and Noncoding Variation in LRRK2 and Parkinson's Disease Risk. Mov Disord 2021; 37:95-105. [PMID: 34542912 PMCID: PMC9292230 DOI: 10.1002/mds.28787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 01/31/2023] Open
Abstract
Background The leucine‐rich repeat kinase 2 (LRRK2) gene harbors both rare highly damaging missense variants (eg, p.G2019S) and common noncoding variants (eg, rs76904798) with lower effect sizes that are associated with Parkinson's disease (PD) risk. Objectives This study aimed to investigate in a large meta‐analysis whether the LRRK2 Genome‐Wide Association Study (GWAS) signal represented by rs76904798 is independently associated with PD risk from LRRK2 coding variation and whether complex linkage disequilibrium structures with p.G2019S and the 5′ noncoding haplotype account for the association of LRRK2 coding variants. Methods We performed a meta‐analysis using imputed genotypes from 17,838 patients, 13,404 proxy patients, and 173,639 healthy controls of European ancestry. We excluded carriers of p.G2019S and/or rs76904798 to clarify the role of LRRK2 coding variation in mediating disease risk and excluded carriers of relatively rare LRRK2 coding variants to assess the independence of rs76904798. We also investigated the co‐inheritance of LRRK2 coding variants with p.G2019S, rs76904798, and p.N2081D. Results LRRK2 rs76904798 remained significantly associated with PD after excluding the carriers of relatively rare LRRK2 coding variants. LRRK2 p.R1514Q and p.N2081D were frequently co‐inherited with rs76904798, and the allele distribution of p.S1647T significantly changed among patients after removing rs76904798 carriers. Conclusions These data suggest that the LRRK2 coding variants previously related to PD (p.N551K, p.R1398H, p.M1646T, and p.N2081D) do not drive the 5′ noncoding GWAS signal. These data, however, do not preclude the independent association of the haplotype p.N551K‐p.R1398H and p.M1646T with altered disease risk. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Rebekah G Langston
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA.,Data Tecnica International, Glen Echo, Maryland, USA
| | - Ziv Gan-Or
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada.,Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA.,Data Tecnica International, Glen Echo, Maryland, USA.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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21
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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22
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Luo G, Jiang Y, Xie C, Lu X. Metal‐organic framework‐based biomaterials for biomedical applications. BIOSURFACE AND BIOTRIBOLOGY 2021. [DOI: 10.1049/bsb2.12012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Gang Luo
- Key Laboratory of Advanced Technologies of Materials Ministry of Education School of Materials Science and Engineering Yibin Institute of Southwest Jiaotong University Southwest Jiaotong University Chengdu China
| | - Yanan Jiang
- Key Laboratory of Advanced Technologies of Materials Ministry of Education School of Materials Science and Engineering Yibin Institute of Southwest Jiaotong University Southwest Jiaotong University Chengdu China
| | - Chaoming Xie
- Key Laboratory of Advanced Technologies of Materials Ministry of Education School of Materials Science and Engineering Yibin Institute of Southwest Jiaotong University Southwest Jiaotong University Chengdu China
| | - Xiong Lu
- Key Laboratory of Advanced Technologies of Materials Ministry of Education School of Materials Science and Engineering Yibin Institute of Southwest Jiaotong University Southwest Jiaotong University Chengdu China
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23
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Deng Y, Meng M, Fang J, Jiang H, Sun N, Lv W, Lei Y, Wang C, Bo J, Liu C, Wang Y, Yang L, He S. Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life. Mol Ecol Resour 2021; 21:1922-1935. [PMID: 33893720 DOI: 10.1111/1755-0998.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448.52-Mb genome assembly with contig N50 length of 5.53 Mb by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin map. Demographic history reconstruction of the butterfly hillstream loach reveals that the population dynamics is correlated with the different stages of uplifting of the Tibetan Plateau. Comparative genomic analysis finds evidence of six keratin genes in butterfly hillstream loach evolving under positive selection. Within these genes, two keratin genes exhibit species-specific and divergent amino acid changes, suggesting a role in the formation of the unculi. Additionally, a series of positively selected genes, rapid evolving genes, specific variant genes and expanded gene families are found, including genes related to Hedgehog, Notch and BMP pathways, which may be involved in craniofacial development. These findings may have important implications for understanding the genetic basis of phenotypic adaptation to torrential mountain stream life.
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Affiliation(s)
- Yu Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Minghui Meng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Haifeng Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Lei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Bo
- University of Chinese Academy of Sciences, Beijing, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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24
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Yin X, Martinez AS, Sepúlveda MS, Christie MR. Rapid genetic adaptation to recently colonized environments is driven by genes underlying life history traits. BMC Genomics 2021; 22:269. [PMID: 33853517 PMCID: PMC8048285 DOI: 10.1186/s12864-021-07553-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Uncovering the mechanisms underlying rapid genetic adaptation can provide insight into adaptive evolution and shed light on conservation, invasive species control, and natural resource management. However, it can be difficult to experimentally explore rapid adaptation due to the challenges associated with propagating and maintaining species in captive environments for long periods of time. By contrast, many introduced species have experienced strong selection when colonizing environments that differ substantially from their native range and thus provide a “natural experiment” for studying rapid genetic adaptation. One such example occurred when sea lamprey (Petromyzon marinus), native to the northern Atlantic, naturally migrated into Lake Champlain and expanded their range into the Great Lakes via man-made shipping canals. Results Utilizing 368,886 genome-wide single nucleotide polymorphisms (SNPs), we calculated genome-wide levels of genetic diversity (i.e., heterozygosity and π) for sea lamprey collected from native (Connecticut River), native but recently colonized (Lake Champlain), and invasive (Lake Michigan) populations, assessed genetic differentiation between all populations, and identified candidate genes that responded to selection imposed by the novel environments. We observed a 14 and 24% reduction in genetic diversity in Lake Michigan and Lake Champlain populations, respectively, compared to individuals from the Connecticut River, suggesting that sea lamprey populations underwent a genetic bottleneck during colonization. Additionally, we identified 121 and 43 outlier genes in comparisons between Lake Michigan and Connecticut River and between Lake Champlain and Connecticut River, respectively. Six outlier genes that contained synonymous SNPs in their coding regions and two genes that contained nonsynonymous SNPs may underlie the rapid evolution of growth (i.e., GHR), reproduction (i.e., PGR, TTC25, STARD10), and bioenergetics (i.e., OXCT1, PYGL, DIN4, SLC25A15). Conclusions By identifying the genomic basis of rapid adaptation to novel environments, we demonstrate that populations of invasive species can be a useful study system for understanding adaptive evolution. Furthermore, the reduction in genome-wide levels of genetic diversity associated with colonization coupled with the identification of outlier genes underlying key life history traits known to have changed in invasive sea lamprey populations (e.g., growth, reproduction) illustrate the utility in applying genomic approaches for the successful management of introduced species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07553-x.
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Affiliation(s)
- Xiaoshen Yin
- Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, Indiana, 47907-2054, USA
| | - Alexander S Martinez
- Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, Indiana, 47907-2054, USA
| | - Maria S Sepúlveda
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, Indiana, 47907-2054, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, 915 W. State St., West Lafayette, Indiana, 47907-2054, USA. .,Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, Indiana, 47907-2054, USA.
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25
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Katsura Y, Ikemura T, Kajitani R, Toyoda A, Itoh T, Ogata M, Miura I, Wada K, Wada Y, Satta Y. Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency. Life Sci Alliance 2021; 4:4/5/e202000905. [PMID: 33712508 PMCID: PMC7994367 DOI: 10.26508/lsa.202000905] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/30/2022] Open
Abstract
Genome sequencing of a unique frog (Glandirana rugosa) having XY/ZW systems within the species and comparative genomics with other six frogs were performed using a batch-learning self-organizing map, which is unsupervised AI for oligonucleotide compositions, to clarify its genome characteristics. The Japanese wrinkled frog (Glandirana rugosa) is unique in having both XX-XY and ZZ-ZW types of sex chromosomes within the species. The genome sequencing and comparative genomics with other frogs should be important to understand mechanisms of turnover of sex chromosomes within one species or during a short period. In this study, we analyzed the newly sequenced genome of G. rugosa using a batch-learning self-organizing map which is unsupervised artificial intelligence for oligonucleotide compositions. To clarify genome characteristics of G. rugosa, we compared its short oligonucleotide compositions in all 1-Mb genomic fragments with those of other six frog species (Pyxicephalus adspersus, Rhinella marina, Spea multiplicata, Leptobrachium leishanense, Xenopus laevis, and Xenopus tropicalis). In G. rugosa, we found an Mb-level large size of repeat sequences having a high identity with the W chromosome of the African bullfrog (P. adspersus). Our study concluded that G. rugosa has unique genome characteristics with a high CG frequency, and its genome is assumed to heterochromatinize a large size of genome via methylataion of CG.
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Affiliation(s)
- Yukako Katsura
- Primate Research Institute, Kyoto University, Inuyama-shi, Japan .,Amphibian Research Center, Hiroshima University, Hiroshima-shi, Japan.,Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University For Advanced Studies (SOKENDAI), Shonankokuraimura, Hayama-machi, Japan
| | - Toshimichi Ikemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Japan
| | - Rei Kajitani
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo-to, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima-shi, Japan
| | - Takehiko Itoh
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo-to, Japan
| | | | - Ikuo Miura
- Amphibian Research Center, Hiroshima University, Hiroshima-shi, Japan
| | - Kennosuke Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Japan
| | - Yoshiko Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University For Advanced Studies (SOKENDAI), Shonankokuraimura, Hayama-machi, Japan
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26
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Lu B, Jiang J, Wu H, Chen X, Song X, Liao W, Fu J. A large genome with chromosome-scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans). Mol Ecol Resour 2021; 21:1256-1273. [PMID: 33426774 DOI: 10.1111/1755-0998.13319] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 01/15/2023]
Abstract
We present a high-quality genome assembly for the Asiatic toad (Bufo gargarizans) and explore the evolution of several large gene families in amphibians. With a large genome assembly size of 4.55 Gb, the chromosome-scale assembly includes 747 scaffolds with an N50 of 539.8 Mb and 1.79% gaps. Long terminal repeats (LTRs) constitute a high proportion of the genome and their expansion is a key contributor to the inflated genome size in this species. This is very different from other small amphibian genomes, but similar to that of the enormous axolotl genome. The genome retains a large number of duplicated genes, with tandem (TD) and proximal duplications (PD) the predominant mode of duplication. A total of 122 gene families have undergone significant expansion and were mainly enriched in sensory perception of smell and bitter taste. The CYP2C subfamily, which plays an important role in metabolic detoxification, specifically expanded via TD and PD in the Asiatic toad and the cane toad (true toads). Most of Na+ /K+ -ATPase genes experienced accelerated evolution along Bufonid lineages and two amino acid sites involving toad-toxin resistance were found to experience positive selection. We also revealed a dynamic evolution of olfactory and vomeronasal receptor gene families which was likely driven by the water-to-land transition. The high-quality genome of the Asiatic toad will provide a solid foundation to understand the genetic basis of its many biological processes.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xiaohong Chen
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Xiaowei Song
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Wenbo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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27
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Abstract
Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.
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Affiliation(s)
- Yan-Bo Sun
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, Yunnan 650091, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Yi Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, Oklahoma 73072, USA
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28
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The rise and fall of globins in the amphibia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100759. [PMID: 33202310 DOI: 10.1016/j.cbd.2020.100759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 12/28/2022]
Abstract
The globin gene repertoire of gnathostome vertebrates is dictated by differential retention and loss of nine paralogous genes: androglobin, neuroglobin, globin X, cytoglobin, globin Y, myoglobin, globin E, and the α- and β-globins. We report the globin gene repertoire of three orders of modern amphibians: Anura, Caudata, and Gymnophiona. Combining phylogenetic and conserved synteny analysis, we show that myoglobin and globin E were lost only in the Batrachia clade, but retained in Gymnophiona. The major amphibian groups also retained different paralogous copies of globin X. None of the amphibian presented αD-globin gene. Nevertheless, two clades of β-globins are present in all amphibians, indicating that the amphibian ancestor possessed two paralogous proto β-globins. We also show that orthologs of the gene coding for the monomeric hemoglobin found in the heart of Rana catesbeiana are present in Neobatrachia and Pelobatoidea species we analyzed. We suggest that these genes might perform myoglobin- and globin E-related functions. We conclude that the repertoire of globin genes in amphibians is dictated by both retention and loss of the paralogous genes cited above and the rise of a new globin gene through co-option of an α-globin, possibly facilitated by a prior event of transposition.
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29
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Yin J, Jiang L, Wang L, Han X, Guo W, Li C, Zhou Y, Denton M, Zhang P. A high-quality genome of taro (Colocasia esculenta (L.) Schott), one of the world's oldest crops. Mol Ecol Resour 2020; 21:68-77. [PMID: 32790213 DOI: 10.1111/1755-0998.13239] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023]
Abstract
Taro (Colocasia esculenta (L.), Schott), from the Araceae family, is one of the oldest crops with important edible, medicinal, nutritional and economic value. Taro is a highly polymorphic species including diverse genotypes adapted to a broad range of environments, but the taro genome has rarely been investigated. Here, a high-quality chromosome-level genome of C. esculenta was assembled using data sequenced by Illumina, PacBio and Nanopore platforms. The assembled genome size was 2,405 Mb with a contig N50 of 400.0 kb and a scaffold N50 of 159.4 Mb. In total, 2,311 Mb (96.09%) of the contig sequences was anchored onto 14 chromosomes to form pseudomolecules, and 2,126 Mb (88.43%) was annotated as repetitive sequences. Of the 28,695 predicted protein-coding genes, 26,215 genes (91.4%) could be functionally annotated. On the basis of phylogenetic analysis using 769 genes, C. esculenta and Spirodela polyrhiza were placed on one branch of the tree that diverged approximately 73.23 million years ago. The synteny analyses showed that there have been two whole-genome duplication events in C. esculenta separated by a relatively short gap. According to comparative genome analysis, a larger number (1,189) of distinct gene families and long terminal repeats were enriched in C. esculenta. Our high-quality taro genome will provide valuable resources for further genetic, ecological and evolutionary analyses of taro or other species in the Araceae.
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Affiliation(s)
- Jianmei Yin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lu Jiang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Li Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaoyong Han
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenqi Guo
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chunhong Li
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yi Zhou
- School of Agriculture, Food & Wine, The University of Adelaide, Urrbrae, SA, Australia
| | - Matthew Denton
- School of Agriculture, Food & Wine, The University of Adelaide, Urrbrae, SA, Australia
| | - Peitong Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Transcriptional Inhibition of Sp-IAG by Crustacean Female Sex Hormone in the Mud Crab, Scylla paramamosain. Int J Mol Sci 2020; 21:ijms21155300. [PMID: 32722594 PMCID: PMC7432471 DOI: 10.3390/ijms21155300] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/09/2023] Open
Abstract
In crustaceans, the regulation of sex differentiation is mediated by insulin-like androgenic hormone (IAG) and crustacean female sex hormone (CFSH). CFSH is reported to inhibit IAG gene (Sp-IAG) expression in the mud crab Scylla paramamosain, but the regulatory mechanism is not well understood. A 2674 bp 5′ flanking Sp-IAG contains many potential transcription factor binding sites. In this study, analysis of serially deleted 5′ flanking Sp-IAG and site-directed mutation (SDM) of transcription factor binding sites of the same gene showed that the promoter activity of reporter vectors with Sox-5-binding site, signal transducers and activators of transcription (STAT)-binding site and activator protein 1 (AP-1)-binding site were significantly higher than that of vectors without these regions, suggesting that they were involved in transcriptional regulation of Sp-IAG expression. The expression analysis of these transcription factor showed that there was no difference in the level of mRNA in Sox-5 and AP-1 in androgenic gland treated with recombinant CFSH, but expression of Sp-STAT was significantly reduced, suggesting that CFSH regulates the expression of Sp-STAT, inhibiting its function to regulate Sp-IAG. Further experiment revealed that RNAi mediated Sp-STAT gene knockdown reduced the expression of Sp-IAG. These results suggested that Sp-CFSH regulates Sp-IAG by inhibiting STAT. This is a pioneering finding on the transcriptional mechanism of IAG gene in crustaceans.
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Li Q, Guo Q, Zhou Y, Tan H, Bertozzi T, Zhu Y, Li J, Donnellan S, Zhang G. A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae). GIGABYTE 2020; 2020:gigabyte2. [PMID: 36824594 PMCID: PMC9632003 DOI: 10.46471/gigabyte.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/15/2020] [Indexed: 01/09/2023] Open
Abstract
Amphibian genomes are usually challenging to assemble due to their large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.
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Affiliation(s)
- Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yang Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huishuang Tan
- BGI-Shenzhen, Shenzhen 518083, China,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Terry Bertozzi
- South Australian Museum, North Terrace, Adelaide 5000, Australia,School of Biological Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
| | - Yuanzhen Zhu
- BGI-Shenzhen, Shenzhen 518083, China,School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Ji Li
- BGI-Shenzhen, Shenzhen 518083, China,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | | | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark, Corresponding author. E-mail:
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Kuhl H, Li L, Wuertz S, Stöck M, Liang XF, Klopp C. CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes. Gigascience 2020; 9:giaa034. [PMID: 32449778 PMCID: PMC7247394 DOI: 10.1093/gigascience/giaa034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 03/24/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce. RESULT Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads. CONCLUSIONS CSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects.
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Affiliation(s)
- Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
| | - Ling Li
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University; Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, No.1 Shizishan Street, Hongshan District, 430070 Wuhan, Hubei Province, P.R. China
| | - Sven Wuertz
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
| | - Matthias Stöck
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University; Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, No.1 Shizishan Street, Hongshan District, 430070 Wuhan, Hubei Province, P.R. China
| | - Christophe Klopp
- Sigenae, Bioinfo Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAe, 24 Chemin de Borde Rouge, 31320 Auzeville-Tolosane, Castanet Tolosan, France
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