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Lichman V, Ozerov M, López ME, Noreikiene K, Kahar S, Pukk L, Burimski O, Gross R, Vasemägi A. Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38897597 DOI: 10.1111/jfb.15821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole-genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000-100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome-wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data-mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes.
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Affiliation(s)
- Vitalii Lichman
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Mikhail Ozerov
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
- Department of Biology, University of Turku, Turku, Finland
| | - María-Eugenia López
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - Kristina Noreikiene
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Botany and Genetics, Vilnius University, Vilnius, Lithuania
| | - Siim Kahar
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Lilian Pukk
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Oksana Burimski
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Riho Gross
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
| | - Anti Vasemägi
- Institute of Veterinary Medicine and Animal Sciences, Chair of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden
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Ozerov MY, Noreikiene K, Kahar S, Flajšhans M, Gross R, Vasemägi A. Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis). Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110941. [PMID: 38218377 DOI: 10.1016/j.cbpb.2024.110941] [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: 10/09/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multi-tissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.
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Affiliation(s)
- M Y Ozerov
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893 Drottningholm, Sweden; Biodiversity Unit, University of Turku, 20014 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland
| | - K Noreikiene
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia; Department of Botany and Genetics, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania. https://twitter.com/snaudale
| | - S Kahar
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - M Flajšhans
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, 38925 Vodňany, Czech Republic
| | - R Gross
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - A Vasemägi
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893 Drottningholm, Sweden; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia.
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Liu M, Song Y, Zhang S, Yu L, Yuan Z, Yang H, Zhang M, Zhou Z, Seim I, Liu S, Fan G, Yang H. A chromosome-level genome of electric catfish ( Malapterurus electricus) provided new insights into order Siluriformes evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:1-14. [PMID: 38433969 PMCID: PMC10901758 DOI: 10.1007/s42995-023-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 03/05/2024]
Abstract
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
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Affiliation(s)
- Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Hengjia Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zhuocheng Zhou
- Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, 100125 China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Shanshan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
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Zheng S, Tao W, Tao H, Yang H, Wu L, Shao F, Wang Z, Jin L, Peng Z, Wang D, Zhang Y. Characterization of the male-specific region containing the candidate sex-determining gene in Amur catfish (Silurus asotus) using third-generation- and pool-sequencing data. Int J Biol Macromol 2023; 248:125908. [PMID: 37482150 DOI: 10.1016/j.ijbiomac.2023.125908] [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: 04/18/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Amur catfish (Silurus asotus) is an ecologically and economically important fish species in Asia. Here, we assembled the female and male Amur catfish genomes, with genome sizes of 757.15 and 755.44 Mb, respectively, at the chromosome level using nanopore and Hi-C technologies. Consistent with the known diploid chromosome count, both genomes contained 29 chromosome-size scaffolds covering 98.80 and 98.73 % of the complete haplotypic assembly with scaffold N50 of 28.87 and 27.29 Mb, respectively. The female (n = 40) and male (n = 40) pools were re-sequenced. Comparative analysis of sequencing and re-sequencing data from both sexes confirmed the presence of an XX/XY sex determination system in Amur catfish and revealed Chr5 as the sex chromosome containing an approximately 400 kb Y-specific region (MSY). Gene annotation revealed a male-specific duplicate of amhr2, namely amhr2y, in MSY, which is male-specific in different wild populations and expressed only in the testes. Amur catfish shared partially syntenic MSY and amhr2y genes with the southern catfish (S. meridionalis, Chr24), which were located on different chromosomes. High sequence divergence between amhr2y and amhr2 and high sequence similarity with amhr2y were observed in both species. These results indicate the common origin of the sex-determining (SD) gene and transition of amhr2y in the two Silurus species. Accumulation of repetitive elements in the MSY of both species may be the main driver of the transition of amhr2y. Overall, our study provides valuable catfish genomic resources. Moreover, determination of amhr2y as the candidate SD gene in Amur catfish provides another example of amhr2 as the SD gene in fish.
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Affiliation(s)
- Shuqing Zheng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongyan Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haowen Yang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Limin Wu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Feng Shao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zhijian Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Li Jin
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zuogang Peng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Yaoguang Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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5
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Apex Predators Enhance Environmental Adaptation but Reduce Community Stability of Bacterioplankton in Crustacean Aquaculture Ponds. Int J Mol Sci 2022; 23:ijms231810785. [PMID: 36142697 PMCID: PMC9506085 DOI: 10.3390/ijms231810785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
Aquaculture environments harbor complex bacterial communities that are critical for the growth and health of culture species. Apex predators are frequently added to aquaculture ponds to improve ecosystem stability. However, limited research has explored the effects of apex predators on the composition and function of bacterioplankton communities, as well as the underlying mechanisms of community assembly. Using 16S ribosomal RNA (rRNA) high-throughput sequencing, we investigated bacterioplankton communities of crustacean aquaculture ponds with and without apex predators (mandarin fish, Siniperca chuatsi) throughout the culture process. In addition to investigating differences in bacterioplankton communities, we also explored variations in environmental adaptation, functional redundancy, and community stability. Significant differences were observed in bacterioplankton composition among different cultural stages; there was an increase in Bacteriobota and fermentation-related bacteria, but a decrease in Firmicutes and pathogens in the middle stages of aquaculture. Apex predators increased the abundance of organic matter degradation bacteria and decreased pathogens. Bacterioplankton communities under apex predator disturbances had a wider environmental breadth, indicating broader environmental adaptation. Moreover, functional prediction and network analyses revealed that communities under apex predator disturbances were less functionally redundant and unstable. Based on the null model, stochastic processes drove community assembly during aquaculture, whereas apex predators elevated the contribution of deterministic processes. Greater changes in nitrate in culture ponds caused by apex predator disturbances were decisive in controlling the balance between stochasticity and determinism in community assembly. Our study provided insight into the mechanisms underlying bacterioplankton community assembly in aquaculture systems in response to apex predator disturbances.
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Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures. Mol Genet Genomics 2022; 297:1627-1642. [PMID: 36006456 PMCID: PMC9596584 DOI: 10.1007/s00438-022-01947-6] [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: 04/10/2022] [Accepted: 08/12/2022] [Indexed: 11/01/2022]
Abstract
The catfish Ancistrus triradiatus belongs to the species-rich family Loricariidae. Loricariids display remarkable traits such as herbivory, a benthic lifestyle, the absence of scales but the presence of dermal bony plates. They are exported as ornamental fish worldwide, with escaped fishes becoming a threat locally. Although genetic and phylogenetic studies are continuously increasing and developmental genetic investigations are underway, no genome assembly has been formally proposed for Loricariidae yet. We report a high-quality genome assembly of Ancistrus triradiatus using long and short reads, and a newly assembled transcriptome. The genome assembly is composed of 9530 scaffolds, including 85.6% of ray-finned fish BUSCOs, and 26,885 predicted protein-coding genes. The genomic GC content is higher than in other catfishes, reflecting the higher metabolism associated with herbivory. The examination of the SCPP gene family indicates that the genes presumably triggering scale loss when absent, are present in the scaleless A. triradiatus, questioning their explanatory role. The analysis of the opsin gene repertoire revealed that gene losses associated to the nocturnal lifestyle of catfishes were not entirely found in A. triradiatus, as the UV-sensitive opsin 5 is present. Finally, most gene family expansions were related to immunity except the gamma crystallin gene family which controls pupil shape and sub-aquatic vision. Thus, the genome of A. triradiatus reveals that fish herbivory may be related to the photic zone habitat, conditions metabolism, photoreception and visual functions. This genome is the first for the catfish suborder Loricarioidei and will serve as backbone for future genetic, developmental and conservation studies.
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Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H, Chang G, Wu N, Ding H, Zhao H, Zhang L, Yu X. Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome. DNA Res 2022; 29:dsac028. [PMID: 35861402 PMCID: PMC9358014 DOI: 10.1093/dnares/dsac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/20/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Zhengjun Pan
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Lei Cheng
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Yanhong Sun
- Wuhan Aquaculture Science Research Institute, Wuhan 430207, China
| | - Hui Wang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Guoliang Chang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Nan Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Huaiyu Ding
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Haitao Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an 223300, China
| | - Lei Zhang
- Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai’an City, Huai’an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences, Huai’an 223002, China
| | - Xiangsheng Yu
- Huai’an Fisheries Technical Guidance Station, Huai’an 223001, China
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Stervander M, Cresko WA. A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae). G3 (BETHESDA, MD.) 2021; 11:jkab306. [PMID: 34849773 PMCID: PMC8664458 DOI: 10.1093/g3journal/jkab306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022]
Abstract
The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons-the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole-genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.
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Affiliation(s)
- Martin Stervander
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
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9
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Zheng S, Shao F, Tao W, Liu Z, Long J, Wang X, Zhang S, Zhao Q, Carleton KL, Kocher TD, Jin L, Wang Z, Peng Z, Wang D, Zhang Y. Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles. Mol Ecol Resour 2021; 21:1575-1592. [PMID: 33503304 DOI: 10.1111/1755-0998.13338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 01/07/2023]
Abstract
The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.
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Affiliation(s)
- Shuqing Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhilong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Juan Long
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Xiaoshuang Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Shuai Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
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