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Peralta DM, Túnez JI, Rodríguez Cruz UE, Ceballos SG. A rapid approach for sex assignment by RAD-seq using a reference genome. PLoS One 2024; 19:e0297987. [PMID: 38578816 PMCID: PMC10997085 DOI: 10.1371/journal.pone.0297987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/14/2024] [Indexed: 04/07/2024] Open
Abstract
Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of two ad hoc indexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.
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Affiliation(s)
- Diego M. Peralta
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu-CIC), Luján, Argentina
- Departamento de Ecología de la Diversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Juan I. Túnez
- Grupo de Investigación en Ecología Molecular, Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu-CIC), Luján, Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Ulises E. Rodríguez Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Santiago G. Ceballos
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina
- Centro Austral de Investigaciones Científicas (CADIC-CONICET), Ushuaia, Argentina
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2
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Uno Y, Matsubara K. Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:230-241. [PMID: 38155517 DOI: 10.1002/jez.2776] [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: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
Sex determination systems have greatly diversified between amphibians and reptiles, with such as the different sex chromosome compositions within a single species and transition between temperature-dependent sex determination (TSD) and genetic sex determination (GSD). In most sex chromosome studies on amphibians and reptiles, the whole-genome sequence of Xenopous tropicalis and chicken have been used as references to compare the chromosome homology of sex chromosomes among each of these taxonomic groups, respectively. In the present study, we reviewed existing reports on sex chromosomes, including karyotypes, in amphibians and reptiles. Furthermore, we compared the identified genetic linkages of sex chromosomes in amphibians and reptiles with the chicken genome as a reference, which is believed to resemble the ancestral tetrapod karyotype. Our findings revealed that sex chromosomes in amphibians are derived from genetic linkages homologous to various chicken chromosomes, even among several frogs within single families, such as Ranidae and Pipidae. In contrast, sex chromosomes in reptiles exhibit conserved genetic linkages with chicken chromosomes, not only across most species within a single family, but also within closely related families. The diversity of sex chromosomes in amphibians and reptiles may be attributed to the flexibility of their sex determination systems, including the ease of sex reversal in these animals.
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Affiliation(s)
- Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazumi Matsubara
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
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3
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Zhu J, Wang Y, Chen C, Ji L, Hong X, Liu X, Chen H, Wei C, Zhu X, Li W. Identification of Sex-Specific Markers and Candidate Genes Using WGS Sequencing Reveals a ZW-Type Sex-Determination System in the Chinese Soft-Shell Turtle ( Pelodiscus sinensis). Int J Mol Sci 2024; 25:819. [PMID: 38255893 PMCID: PMC10815769 DOI: 10.3390/ijms25020819] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Male and female Chinese soft-shelled turtles (Pelodiscus sinensis) have sex-dimorphic growth patterns, and males have higher commercial value because of their larger size and thicker calipash. Thus, developing sex-specific markers is beneficial to studies on all-male breeding in P. sinensis. Here, we developed an accurate and efficient workflow for the screening of sex-specific sequences with ZW or XY sex determination systems. Based on this workflow, female and male P. sinensis reference genomes of 2.23 Gb and 2.26 Gb were obtained using de novo assembly. After aligning and filtering, 4.01 Mb female-specific sequences were finally identified. Subsequently, the seven developed sex-specific primer pairs were 100% accurate in preliminary, population, and embryonic validation. The presence and absence of bands for the primers of P44, P45, P66, P67, P68, and P69, as well as two and one bands for the PB1 primer, indicate that the embryos are genetically female and male, respectively. NR and functional annotations identified several sex-determining candidate genes and related pathways, including Ran, Eif4et, and Crkl genes, and the insulin signaling pathway and the cAMP signaling pathway, respectively. Collectively, our results reveal that a ZW-type sex-determination system is present in P. sinensis and provide novel insights for the screening of sex-specific markers, sex-control breeding, and the studies of the sex determination mechanism of P. sinensis.
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Affiliation(s)
- Junxian Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Yongchang Wang
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Chen Chen
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Liqin Ji
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xiaoyou Hong
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xiaoli 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Haigang Chen
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Chengqing Wei
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xinping Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Wei Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- 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; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
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Panthum T, Ariyaraphong N, Wongloet W, Wattanadilokchatkun P, Laopichienpong N, Rasoarahona R, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Fukuda Y, Banks S, Temsiripong Y, Ezaz T, Srikulnath K. Preserving Pure Siamese Crocodile Populations: A Comprehensive Approach Using Multi-Genetic Tools. BIOLOGY 2023; 12:1428. [PMID: 37998027 PMCID: PMC10669835 DOI: 10.3390/biology12111428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00-26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs.
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Affiliation(s)
- Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Department of Botany, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Yusuke Fukuda
- Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, NT 0830, Australia;
| | - Sam Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, NT 0909, Australia;
| | | | - Tariq Ezaz
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617, Australia;
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
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Rasoarahona R, Wattanadilokchatkun P, Panthum T, Jaisamut K, Lisachov A, Thong T, Singchat W, Ahmad SF, Han K, Kraichak E, Muangmai N, Koga A, Duengkae P, Antunes A, Srikulnath K. MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes. Chromosome Res 2023; 31:29. [PMID: 37775555 DOI: 10.1007/s10577-023-09738-4] [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: 08/11/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.
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Affiliation(s)
- Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kitipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixes, Av. General Norton de Matos, S/N, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, S/N, 4169-007, Porto, Portugal
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok, 10900, Thailand.
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand.
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6
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Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species. Commun Biol 2022; 5:1126. [PMID: 36284162 PMCID: PMC9596491 DOI: 10.1038/s42003-022-04074-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/06/2022] [Indexed: 12/12/2022] Open
Abstract
Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei. A highly-complete chromosome-scale genome assembly of the brown anole, Anolis sagrei, provides insight into the evolution of sex chromosomes and is a crucial resource for this model lizard species.
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Zhang K, Yang J, Qin Z, Lu T, Lou D, Ran Q, Huang H, Cheng S, Zellmer L, Ma H, Liao DJ. Establishment of New Genetic Markers and Methods for Sex Determination of Mouse and Human Cells using Polymerase Chain Reactions and Crude DNA Samples. Curr Genomics 2022; 23:275-288. [PMID: 36777874 PMCID: PMC9875541 DOI: 10.2174/1389202923666220610121344] [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: 02/11/2022] [Revised: 03/20/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The currently available methods for sexing human or mouse cells have weaknesses. Therefore, it is necessary to establish new methods. Methods: We used bioinformatics approach to identify genes that have alleles on both the X and Y chromosomes of mouse and human genomes and have a region showing a significant difference between the X and Y alleles. We then used polymerase chain reactions (PCR) followed by visualization of the PCR amplicons in agarose gels to establish these genomic regions as genetic sex markers. Results: Our bioinformatics analyses identified eight mouse sex markers and 56 human sex markers that are new, i.e. are previously unreported. Six of the eight mouse markers and 14 of the 56 human markers were verified using PCR and ensuing visualization of the PCR amplicons in agarose gels. Most of the tested and untested sex markers possess significant differences in the molecular weight between the X- and Y-derived PCR amplicons and are thus much better than most, if not all, previously-reported genetic sex markers. We also established several simple and essentially cost-free methods for extraction of crude genomic DNA from cultured cells, blood samples, and tissues that could be used as template for PCR amplification. Conclusion: We have established new sex genetic markers and methods for extracting genomic DNA and for sexing human and mouse cells. Our work may also lend some methodological strategies to the identification of new genetic sex markers for other organismal species.
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Affiliation(s)
- Keyin Zhang
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China
| | - Jianglin Yang
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P. R. China;,Center for Clinical Laboratories, Guizhou Medical University Hospital, 4 Beijing Rd, Guiyang 550004, Guizhou Province, P.R. China
| | - Zhenwei Qin
- Forensic Science Section, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang 550025, Guizhou Province, P.R. China
| | - Tianzu Lu
- Department of Stomatology, School of Stomatology, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China
| | - Didong Lou
- Forensic Science Section, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang 550025, Guizhou Province, P.R. China
| | - Qianchuan Ran
- Forensic Science Section, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang 550025, Guizhou Province, P.R. China
| | - Hai Huang
- Center for Clinical Laboratories, Guizhou Medical University Hospital, 4 Beijing Rd, Guiyang 550004, Guizhou Province, P.R. China
| | - Shuqiang Cheng
- Center for Clinical Laboratories, Guizhou Medical University Hospital, 4 Beijing Rd, Guiyang 550004, Guizhou Province, P.R. China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center, 730 South 8th St., Minneapolis, MN 5415
| | - Hong Ma
- Department of Stomatology, School of Stomatology, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Address correspondence to these authors at the Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-85186752814; E-mail: and Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University 9 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-851-88512238; E-mail:
| | - Dezhong J. Liao
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P. R. China;,Address correspondence to these authors at the Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-85186752814; E-mail: and Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University 9 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-851-88512238; E-mail:
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8
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Teal CN, Coykendall DK, Campbell MR, Eardley DL, Delomas TA, Shira JT, Schill DJ, Bonar SA, Culver M. Sex-specific markers undetected in green sunfish Lepomis cyanellus using restriction-site associated DNA sequencing. JOURNAL OF FISH BIOLOGY 2022; 100:1528-1540. [PMID: 35439326 DOI: 10.1111/jfb.15063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
We used restriction-site associated DNA sequencing for SNP discovery and genotyping of known-sex green sunfish Lepomis cyanellus DNA samples to search for sex-diagnostic single nucleotide polymorphisms (SNPs) and restriction-site associated sequences present in one sex and absent in the other. The bioinformatic analyses discovered candidate SNPs and sex-specific restriction-site associated sequences that fit patterns of male or female heterogametic sex determination systems. However, when primers were developed and tested, no candidates reliably identified phenotypic sex. The top performing SNP candidate (ZW_218) correlated with phenotypic sex 63.0% of the time and the presence-absence loci universally amplified in both sexes. We recommend further investigations that interrogate a larger fraction of the L. cyanellus genome. Additionally, studies on the effect of temperature and rearing density on sex determination, as well as breeding of sex-reversed individuals, could provide more insights into the sex determination system of L. cyanellus.
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Affiliation(s)
- Chad N Teal
- Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, Tucson, Arizona, USA
| | - D Katharine Coykendall
- Pacific States Marine Fisheries Commission, Eagle Fish Genetics Lab, Eagle, Idaho, USA
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - Matthew R Campbell
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - Daniel L Eardley
- Pacific States Marine Fisheries Commission, Eagle Fish Genetics Lab, Eagle, Idaho, USA
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - Thomas A Delomas
- Pacific States Marine Fisheries Commission, Eagle Fish Genetics Lab, Eagle, Idaho, USA
- Idaho Department of Fish and Game, Eagle Fish Genetics Lab, Eagle, Idaho, USA
| | - James T Shira
- University of Arizona Genetics Core, Tucson, Arizona, USA
| | | | - Scott A Bonar
- US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, University of Arizona, ENR2, Tucson, Arizona, USA
| | - Melanie Culver
- US Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, School of Natural Resources and the Environment, University of Arizona, ENR2, Tucson, Arizona, USA
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9
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Keating SE, Fenelon JC, Pyne M, Pinto BJ, Guzmán-Méndez IA, Johnston SD, Renfree MB, Gamble T. Research Article Genetic sex test for the short-beaked echidna (Tachyglossus aculeatus). CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01258-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Using Sex-Linked Markers via Genotyping-by-Sequencing to Identify XX/XY Sex Chromosomes in the Spiny Frog (Quasipaa boulengeri). Genes (Basel) 2022; 13:genes13040575. [PMID: 35456381 PMCID: PMC9027009 DOI: 10.3390/genes13040575] [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: 01/29/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022] Open
Abstract
We used genotyping-by-sequencing (GBS) to identify sex-linked markers in 43 wild-collected spiny frog (Quasipaa boulengeri) adults from a single site. We identified a total of 1049 putatively sex-linked GBS-tags, 98% of which indicated an XX/XY system, and finally confirmed 574 XY-type sex-linked loci. The sex specificity of five markers was further validated by PCR amplification using a large number of additional individuals from 26 populations of this species. A total of 27 sex linkage markers matched with the Dmrt1 gene, showing a conserved role in sex determination and differentiation in different organisms from flies and nematodes to mammals. Chromosome 1, which harbors Dmrt1, was considered as the most likely candidate sex chromosome in anurans. Five sex-linked SNP makers indicated sex reversals, which are sparsely present in wild amphibian populations, in three out of the one-hundred and thirty-three explored individuals. The variety of sex-linked markers identified could be used in population genetics analyses requiring information on individual sex or in investigations aimed at drawing inferences about sex determination and sex chromosome evolution.
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11
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Hansen CCR, Westfall KM, Pálsson S. Evaluation of four methods to identify the homozygotic sex chromosome in small populations. BMC Genomics 2022; 23:160. [PMID: 35209843 PMCID: PMC8867824 DOI: 10.1186/s12864-022-08393-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types differ in effective population size and can have highly disparate evolutionary histories, it is imperative to take this information into account when analysing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome in a small population using two whole genome sequences (WGS) and 133 RAD sequences of white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold in a male and a female, ii) heterozygosity per scaffold in a male and a female, iii) mapping to the reference genome of a related species (chicken) with annotated sex chromosomes, and iv) analysis of SNP-loadings from a principal components analysis (PCA), based on the low-depth RADseq data. RESULTS The best performing approach was the reference mapping (method iii), which identified 98.12% of the expected homogametic sex chromosome (Z). Read depth per scaffold (method i) identified 86.41% of the homogametic sex chromosome with few false positives. SNP-loading scores (method iv) identified 78.6% of the Z-chromosome and had a false positive discovery rate of more than 10%. Heterozygosity per scaffold (method ii) did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W). The evaluation of these methods also revealed 10 Mb of putative PAR and gametologous regions. CONCLUSION Identification of the homogametic sex chromosome in a small population is best accomplished by reference mapping or examining differences in read depth between sexes.
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Affiliation(s)
| | - Kristen M Westfall
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland.,Current: Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC, Canada
| | - Snæbjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
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12
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Zhang X, Wagner S, Holleley CE, Deakin JE, Matsubara K, Deveson IW, O'Meally D, Patel HR, Ezaz T, Li Z, Wang C, Edwards M, Graves JAM, Georges A. Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation. Proc Natl Acad Sci U S A 2022; 119:e2116475119. [PMID: 35074916 PMCID: PMC8795496 DOI: 10.1073/pnas.2116475119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Pogona vitticeps has female heterogamety (ZZ/ZW), but the master sex-determining gene is unknown, as it is for all reptiles. We show that nr5a1 (Nuclear Receptor Subfamily 5 Group A Member 1), a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-nr5a1 and W-nr5a1), which are both expressed and can recombine. Three transcript isoforms of Z-nr5a1 were detected in gonads of adult ZZ males, two of which encode a functional protein. However, ZW females produced 16 isoforms, most of which contained premature stop codons. The array of transcripts produced by the W-borne allele (W-nr5a1) is likely to produce truncated polypeptides that contain a structurally normal DNA-binding domain and could act as a competitive inhibitor to the full-length intact protein. We hypothesize that an altered configuration of the W chromosome affects the conformation of the primary transcript generating inhibitory W-borne isoforms that suppress testis determination. Under this hypothesis, the genetic sex determination (GSD) system of P. vitticeps is a W-borne dominant female-determining gene that may be controlled epigenetically.
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Affiliation(s)
- Xiuwen Zhang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Susan Wagner
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Clare E Holleley
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
- Australian National Wildlife Collection, Commonwealth Scientific and Industrial Research Organisation, Crace, ACT 2911, Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Kazumi Matsubara
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Hardip R Patel
- Genome Sciences Department, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Zhao Li
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Chexu Wang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Melanie Edwards
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
- School of Life Sciences, La Trobe University, Bundoora, VIC 3186, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
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13
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Sex Chromosomes and Master Sex-Determining Genes in Turtles and Other Reptiles. Genes (Basel) 2021; 12:genes12111822. [PMID: 34828428 PMCID: PMC8622242 DOI: 10.3390/genes12111822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022] Open
Abstract
Among tetrapods, the well differentiated heteromorphic sex chromosomes of birds and mammals have been highly investigated and their master sex-determining (MSD) gene, Dmrt1 and SRY, respectively, have been identified. The homomorphic sex chromosomes of reptiles have been the least studied, but the gap with birds and mammals has begun to fill. This review describes our current knowledge of reptilian sex chromosomes at the cytogenetic and molecular level. Most of it arose recently from various studies comparing male to female gene content. This includes restriction site-associated DNA sequencing (RAD-Seq) experiments in several male and female samples, RNA sequencing and identification of Z- or X-linked genes by male/female comparative transcriptome coverage, and male/female transcriptomic or transcriptome/genome substraction approaches allowing the identification of Y- or W-linked transcripts. A few putative master sex-determining (MSD) genes have been proposed, but none has been demonstrated yet. Lastly, future directions in the field of reptilian sex chromosomes and their MSD gene studies are considered.
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14
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Jin L, Liao WB, Merilä J. Genomic evidence for adaptive differentiation among
Microhyla fissipes
populations: Implications for conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme Faculty of Biological and Environmental Sciences FI‐00014 University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity School Biological Sciences The University of Hong KongHong Kong SAR
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15
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The Snakeskin Gourami (Trichopodus pectoralis) Tends to Exhibit XX/XY Sex Determination. FISHES 2021. [DOI: 10.3390/fishes6040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species.
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16
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Xu Y, DU Z, Liu J, Su H, Ning F, Cui S, Wang L, Liu J, Ren C, DI S, Bai X. Male heterogametic sex determination in Rana dybowskii based on sex-linked molecular markers. Integr Zool 2021; 17:105-114. [PMID: 34254736 PMCID: PMC9290989 DOI: 10.1111/1749-4877.12577] [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] [Indexed: 11/28/2022]
Abstract
Identifying the mechanism for sex determination in amphibians is challenging. Very little is known about sex determination mechanisms of Rana dybowskii, a species of importance to evolutionary and conservation biology. We screened for sex‐linked molecular markers in R. dybowskii in China using target region amplification polymorphism with 2 fixed primers against the sequences of Dmrt1. We found 2 male‐linked molecular markers in R. dybowskii, which were 222 bp and 261 bp long. The detection rates of 222 bp marker in males form Xinglong, Huadian, and Dandong were 93.79%, 69.64%, and 13.64%, respectively, while the rate in females from Huadian was 27.50%. Besides, the detection rates of 261 bp marker in the above 3 regions were only observed in males at the rate of 93.79%, 87.50%, and 32.73%, respectively. The inheritance patterns of sex‐linked molecular markers showed that the 2 sex‐linked molecular markers were heterozygous. Compared to the XY‐male parent, progeny from XX‐pseudo‐male parent possessed lower sex reversal ratio at the same rearing temperature, and the proportion of female froglets from an XX‐pseudo‐male parent was more than 95% at low rearing temperature (15°C). Our findings suggest that R. dybowskii displays male heterogamety, and the 2 sex‐linked molecular markers may have a guiding significance for the protection and utilization of R. dybowskii.
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Affiliation(s)
- Yuan Xu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Zhiheng DU
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiayu Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Hang Su
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Fangyong Ning
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Shiquan Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Lijuan Wang
- College of Agricultural, Eastern Liaoning University, Dandong, China
| | - Jianming Liu
- Yili Animal Science Research Institute, Yining, China
| | - Chuanshuai Ren
- Animal Husbandry Administration of Huadian, Huadian, China
| | - Shengwei DI
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiujuan Bai
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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17
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Xing TF, Li YL, Liu JX. Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius). BMC Genomics 2021; 22:495. [PMID: 34215185 PMCID: PMC8254354 DOI: 10.1186/s12864-021-07830-9] [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: 03/30/2021] [Accepted: 06/16/2021] [Indexed: 01/29/2023] Open
Abstract
Background The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification method based on sex specific genetic markers has hindered study on sex determination mechanisms and breeding applications. Results Female-specific genomic regions were discovered by comparing whole genome re-sequencing data of both males and females. Two female-specific genomic regions larger than 50 bp were identified, and one (598 bp) contained a putative FOXI gene, which was paralogous to another FOXI gene with sex-associated SNPs. The two FOXI sequences displayed significant length difference with nine deletions of total length of 230 bp. This deletion-type structural variation could be easily and efficiently detected by traditional PCR and agarose gel electrophoresis with one 569 bp band for males and two bands (569 and 339 bp) for females, which were validated in 50 females and 40 males with known phenotypic sexes. Conclusions The results provided structural genomic evidence for the ZZ/ZW sex determination system in P. hyalocranius discovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07830-9.
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Affiliation(s)
- Teng-Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China. .,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China.
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China
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18
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Whiteley SL, Castelli MA, Dissanayake DSB, Holleley CE, Georges A. Temperature-Induced Sex Reversal in Reptiles: Prevalence, Discovery, and Evolutionary Implications. Sex Dev 2021; 15:148-156. [PMID: 34111872 DOI: 10.1159/000515687] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Sex reversal is the process by which an individual develops a phenotypic sex that is discordant with its chromosomal or genotypic sex. It occurs in many lineages of ectothermic vertebrates, such as fish, amphibians, and at least one agamid and one scincid reptile species. Sex reversal is usually triggered by an environmental cue that alters the genetically determined process of sexual differentiation, but it can also be caused by exposure to exogenous chemicals, hormones, or pollutants. Despite the occurrence of both temperature-dependent sex determination (TSD) and genetic sex determination (GSD) broadly among reptiles, only 2 species of squamates have thus far been demonstrated to possess sex reversal in nature (GSD with overriding thermal influence). The lack of species with unambiguously identified sex reversal is not necessarily a reflection of a low incidence of this trait among reptiles. Indeed, sex reversal may be relatively common in reptiles, but little is known of its prevalence, the mechanisms by which it occurs, or the consequences of sex reversal for species in the wild under a changing climate. In this review, we present a roadmap to the discovery of sex reversal in reptiles, outlining the various techniques that allow new occurrences of sex reversal to be identified, the molecular mechanisms that may be involved in sex reversal and how to identify them, and approaches for assessing the impacts of sex reversal in wild populations. We discuss the evolutionary implications of sex reversal and use the central bearded dragon (Pogona vitticeps) and the eastern three-lined skink (Bassiana duperreyi) as examples of how species with opposing patterns of sex reversal may be impacted differently by our rapidly changing climate. Ultimately, this review serves to highlight the importance of understanding sex reversal both in the laboratory and in wild populations and proposes practical solutions to foster future research.
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Affiliation(s)
- Sarah L Whiteley
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Meghan A Castelli
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Duminda S B Dissanayake
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Clare E Holleley
- Australian National Wildlife Collection, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
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19
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Klobucar SL, Rick JA, Mandeville EG, Wagner CE, Budy P. Investigating the morphological and genetic divergence of arctic char ( Salvelinus alpinus) populations in lakes of arctic Alaska. Ecol Evol 2021; 11:3040-3057. [PMID: 33841765 PMCID: PMC8019052 DOI: 10.1002/ece3.7211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 12/03/2022] Open
Abstract
Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char (Salvelinus sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus was likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using model-based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping by sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha-1), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food-limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation.
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Affiliation(s)
- Stephen L. Klobucar
- Department of Watershed Sciences and the Ecology CenterUtah State UniversityLoganUTUSA
- Present address:
Institute of Arctic BiologyUniversity of Alaska FairbanksFairbanksAKUSA
| | - Jessica A. Rick
- Department of BotanyUniversity of WyomingLaramieWYUSA
- Program in EcologyUniversity of WyomingLaramieWYUSA
| | - Elizabeth G. Mandeville
- Department of BotanyUniversity of WyomingLaramieWYUSA
- Wyoming Cooperative Fish and Wildlife Research UnitDepartment of Zoology and PhysiologyUniversity of WyomingLaramieWYUSA
- Present address:
Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Catherine E. Wagner
- Department of BotanyUniversity of WyomingLaramieWYUSA
- Program in EcologyUniversity of WyomingLaramieWYUSA
| | - Phaedra Budy
- Department of Watershed Sciences and the Ecology CenterUtah State UniversityLoganUTUSA
- U.S. Geological SurveyUtah Cooperative Fish and Wildlife Research UnitLoganUTUSA
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20
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Feron R, Pan Q, Wen M, Imarazene B, Jouanno E, Anderson J, Herpin A, Journot L, Parrinello H, Klopp C, Kottler VA, Roco AS, Du K, Kneitz S, Adolfi M, Wilson CA, McCluskey B, Amores A, Desvignes T, Goetz FW, Takanashi A, Kawaguchi M, Detrich HW, Oliveira MA, Nóbrega RH, Sakamoto T, Nakamoto M, Wargelius A, Karlsen Ø, Wang Z, Stöck M, Waterhouse RM, Braasch I, Postlethwait JH, Schartl M, Guiguen Y. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data. Mol Ecol Resour 2021; 21:1715-1731. [PMID: 33590960 DOI: 10.1111/1755-0998.13360] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
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Affiliation(s)
- Romain Feron
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Qiaowei Pan
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ming Wen
- INRAE, LPGP, Rennes, France.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Jennifer Anderson
- INRAE, LPGP, Rennes, France.,Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Christophe Klopp
- SIGENAE, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
| | - Verena A Kottler
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Alvaro S Roco
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Kang Du
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mateus Adolfi
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | | | | | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Frederick W Goetz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Ato Takanashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Harry William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, MA, USA
| | - Marcos A Oliveira
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Rafael H Nóbrega
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Takashi Sakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Masatoshi Nakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | | | - Zhongwei Wang
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ingo Braasch
- Department of Integrative Biology, Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | | | - Manfred Schartl
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
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21
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Koomgun T, Laopichienpong N, Singchat W, Panthum T, Phatcharakullawarawat R, Kraichak E, Sillapaprayoon S, Ahmad SF, Muangmai N, Peyachoknagul S, Duengkae P, Ezaz T, Srikulnath K. Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana ( Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes. Front Genet 2020; 11:556267. [PMID: 33193634 PMCID: PMC7606854 DOI: 10.3389/fgene.2020.556267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/24/2020] [Indexed: 12/27/2022] Open
Abstract
The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseqTM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.
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Affiliation(s)
- Tassika Koomgun
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | | | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University, Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology, Bangkok, Thailand.,Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok, Thailand
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22
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Dissanayake DSB, Holleley CE, Hill LK, O'Meally D, Deakin JE, Georges A. Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction. BMC Genomics 2020; 21:667. [PMID: 32993477 PMCID: PMC7526180 DOI: 10.1186/s12864-020-07071-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
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Affiliation(s)
- Duminda Sampath Bandara Dissanayake
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Clare Ellen Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Laura Kate Hill
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Present Address: Centre for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Janine Eileen Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
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23
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Wen M, Feron R, Pan Q, Guguin J, Jouanno E, Herpin A, Klopp C, Cabau C, Zahm M, Parrinello H, Journot L, Burgess SM, Omori Y, Postlethwait JH, Schartl M, Guiguen Y. Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758). BMC Genomics 2020; 21:552. [PMID: 32781981 PMCID: PMC7430817 DOI: 10.1186/s12864-020-06959-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/29/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. Here we used sequencing approaches to better characterize sex determination and sex-chromosomes in an experimental strain of goldfish. RESULTS Our results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18 °C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (~ 11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the coding DNA sequence of the goldfish amh gene. CONCLUSIONS These results show that our goldfish strain has a relatively large sex locus on LG22, which is likely the Y chromosome of this experimental population. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers, which will be important tools for future research on sex determination in our experimental goldfish population. However, additional work would be needed to explore whether this sex locus is conserved in other populations of goldfish.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
- INRAE, LPGP, 35000, Rennes, France
| | - Romain Feron
- INRAE, LPGP, 35000, Rennes, France
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Qiaowei Pan
- INRAE, LPGP, 35000, Rennes, France
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | | | | | | | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Cedric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Margot Zahm
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Laurent Journot
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Yoshihiro Omori
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, Japan
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | | | - Manfred Schartl
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
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24
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Keating SE, Griffing AH, Nielsen SV, Scantlebury DP, Gamble T. Conserved ZZ/ZW sex chromosomes in Caribbean croaking geckos (
Aristelliger
: Sphaerodactylidae). J Evol Biol 2020; 33:1316-1326. [DOI: 10.1111/jeb.13682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 01/04/2023]
Affiliation(s)
| | - Aaron H. Griffing
- Department of Biological Sciences Marquette University Milwaukee WI USA
| | - Stuart V. Nielsen
- Department of Biological Sciences Marquette University Milwaukee WI USA
- Florida Museum of Natural HistoryUniversity of Florida Gainesville FL USA
| | | | - Tony Gamble
- Department of Biological Sciences Marquette University Milwaukee WI USA
- Milwaukee Public Museum Milwaukee WI USA
- Bell Museum of Natural HistoryUniversity of Minnesota Saint Paul MN USA
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25
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Trenkel VM, Boudry P, Verrez-Bagnis V, Lorance P. Methods for identifying and interpreting sex-linked SNP markers and carrying out sex assignment: application to thornback ray (Raja clavata). Mol Ecol Resour 2020; 20:1610-1619. [PMID: 32657500 DOI: 10.1111/1755-0998.13225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 11/28/2022]
Abstract
Sex-determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex-linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex-determination systems and corresponding statistical methods for identifying sex-linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex-linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) FST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays (Raja clavata). Using method (a), nineteen putative sex-linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex-determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).
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Affiliation(s)
| | - Pierre Boudry
- CNRS, IRD, LEMAR, Ifremer, Univ Brest, Plouzané, France
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26
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Restriction site-associated DNA sequencing (RAD-seq) analysis in Pacific oyster Crassostrea gigas based on observation of individual sex changes. Sci Rep 2020; 10:9873. [PMID: 32555506 PMCID: PMC7303127 DOI: 10.1038/s41598-020-67007-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/03/2020] [Indexed: 11/25/2022] Open
Abstract
The diverse modes of sexual reproduction in Bivalvia make it an excellent clade to understand the evolution of sex and sex determination. The cosmopolitan Pacific oyster Crassostrea gigas is an ideal model for bivalve sex determination studies because of its complicated sexuality, including dioecy, sex change and rare hermaphroditism. A major barrier to C. gigas sex determination study has been the lack of information on the type of sex determination. To identify its sex-determining system, sex observation by following the same individual in two consecutive years was conducted on 760 oysters from distinct populations. Stable sexuality and sex reversal in both directions were observed, which provides a case against the protandry of C. gigas. Restriction site-associated DNA sequencing (RAD-seq) based on 26 samples with unchanged and converted sexualities was carried out for identifying sex-linked marker. One SNP Cgsl-40 was proved to be sex-related, but sex-biased heterozygosity varied between populations for RAD-seq and validation, showing no evidence for sex chromosomes or single-locus models for C. gigas primary sex determination. Information obtained in our study provides novel insight into sex determination mechanism in C. gigas.
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27
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Lange A, Paris JR, Gharbi K, Cézard T, Miyagawa S, Iguchi T, Studholme DJ, Tyler CR. A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus). Mol Ecol Resour 2020; 20:1007-1022. [PMID: 32293100 DOI: 10.1111/1755-0998.13166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/19/2020] [Accepted: 04/08/2020] [Indexed: 01/14/2023]
Abstract
Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to confirm whether intersex fish in the wild arise from genetic males or females, or whether sex reversal occurs in the wild, as this condition can be induced experimentally in controlled exposures to WwTW effluents and a steroidal oestrogen. Using restriction site-associated DNA sequencing (RAD-seq), we identified a candidate for a genetic sex marker and validated this marker as a sex probe through PCR analyses of samples from wild roach populations from nonpolluted rivers. We also applied the sex marker to samples from roach exposed experimentally to oestrogen and oestrogenic effluents to confirm suspected phenotypic sex reversal from males to females in some treatments, and also that sex-reversed males are able to breed as females. We then show, unequivocally, that intersex in wild roach populations results from feminisation of males, but find no strong evidence for complete sex reversal in wild roach at river sites contaminated with oestrogens. The discovered marker has utility for studies in roach on chemical effects, wild stock assessments, and reducing the number of fish used where only one sex is required for experimentation. Furthermore, we show that the marker can be applied nondestructively using a fin clip or skin swab, with animal welfare benefits.
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Affiliation(s)
- Anke Lange
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Josephine R Paris
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Timothée Cézard
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Shinichi Miyagawa
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - David J Studholme
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
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28
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Shi C, Wu X, Su L, Shang C, Li X, Wang Y, Li G. A ZZ/ZW Sex Chromosome System in Cephalochordate Amphioxus. Genetics 2020; 214:617-622. [PMID: 31980449 PMCID: PMC7054019 DOI: 10.1534/genetics.120.303051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/20/2020] [Indexed: 01/14/2023] Open
Abstract
Sex determination is remarkably variable among animals with examples of environmental sex determination, male heterogametic (XX/XY) and female heterogametic (ZZ/ZW) chromosomal sex determination, and other genetic mechanisms. The cephalochordate amphioxus occupies a key phylogenetic position as a basal chordate and outgroup to vertebrates, but its sex determination mechanism is unknown. During the course of generating Nodal mutants with transcription activator-like effector nucleases (TALENs) in amphioxus Branchiostoma floridae, serendipitously, we generated three mutant strains that reveal the sex determination mechanism of this animal. In one mutant strain, all heterozygous mutant offspring over three generations were female and all wild-type descendants were male. This pattern suggests the Nodal allele targeted is on a female-specific W chromosome. A second mutant showed the same W-linked inheritance pattern, with a female heterozygote passing the mutation only to daughters. In a third mutant strain, both male and female offspring could be heterozygous, but a female heterozygote passed the mutation only to sons. This pattern is consistent with the targeted allele being on a Z chromosome. We found an indel polymorphism linked to a Nodal allele present in most females, but no males in our cultured population. Together, these results indicate that Nodal is sex chromosome-linked in B. floridae, and that B. floridae has a ZZ/ZW sex chromosome system.
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Affiliation(s)
- Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaotong Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Liuru Su
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Chaoqi Shang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xuewen Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yiquan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
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29
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Choo A, Nguyen TNM, Ward CM, Chen IY, Sved J, Shearman D, Gilchrist AS, Crisp P, Baxter SW. Identification of Y-chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species. INSECT MOLECULAR BIOLOGY 2019; 28:873-886. [PMID: 31150140 DOI: 10.1111/imb.12602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bactrocera tryoni (Queensland fruit fly) are polyphagous horticultural pests of eastern Australia. Heterogametic males contain a sex-determining Y-chromosome thought to be gene poor and repetitive. Here, we report 39 Y-chromosome scaffolds (~700 kb) from B. tryoni identified using genotype-by-sequencing data and whole-genome resequencing. Male diagnostic PCR assays validated eight Y-scaffolds, and one (Btry4096) contained a novel gene with five exons that encode a predicted 575 amino acid protein. The Y-gene, referred to as typo-gyf, is a truncated Y-chromosome paralogue of X-chromosome gene gyf (1773 aa). The Y-chromosome contained ~41 copies of typo-gyf, and expression occurred in male flies and embryos. Analysis of 13 tephritid transcriptomes confirmed typo-gyf expression in six additional Bactrocera species, including Bactrocera latifrons, Bactrocera dorsalis and Bactrocera zonata. Molecular dating estimated typo-gyf evolved within the past 8.02 million years (95% highest posterior density 10.56-5.52 million years), after the split with Bactrocera oleae. Phylogenetic analysis also highlighted complex evolutionary histories among several Bactrocera species, as discordant nuclear (116 genes) and mitochondrial (13 genes) topologies were observed. B. tryoni Y-sequences may provide useful sites for future transgene insertions, and typo-gyf could act as a Y-chromosome diagnostic marker for many Bactrocera species, although its function is unknown.
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Affiliation(s)
- Amanda Choo
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Thu N M Nguyen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christopher M Ward
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Isabel Y Chen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - John Sved
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Deborah Shearman
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthony S Gilchrist
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter Crisp
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - Simon W Baxter
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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30
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Scharmann M, Grafe TU, Metali F, Widmer A. Sex is determined by XY chromosomes across the radiation of dioecious Nepenthes pitcher plants. Evol Lett 2019; 3:586-597. [PMID: 31867120 PMCID: PMC6906984 DOI: 10.1002/evl3.142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 08/23/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
Species with separate sexes (dioecy) are a minority among flowering plants, but dioecy has evolved multiple times independently in their history. The sex-determination system and sex-linked genomic regions are currently identified in a limited number of dioecious plants only. Here, we study the sex-determination system in a genus of dioecious plants that lack heteromorphic sex chromosomes and are not amenable to controlled breeding: Nepenthes pitcher plants. We genotyped wild populations of flowering males and females of three Nepenthes taxa using ddRAD-seq and sequenced a male inflorescence transcriptome. We developed a statistical tool (privacy rarefaction) to distinguish true sex specificity from stochastic noise in read coverage of sequencing data from wild populations and identified male-specific loci and XY-patterned single nucleotide polymorphsims (SNPs) in all three Nepenthes taxa, suggesting the presence of homomorphic XY sex chromosomes. The male-specific region of the Y chromosome showed little conservation among the three taxa, except for the essential pollen development gene DYT1 that was confirmed as male specific by PCR in additional Nepenthes taxa. Hence, dioecy and part of the male-specific region of the Nepenthes Y-chromosomes likely have a single evolutionary origin.
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Affiliation(s)
- Mathias Scharmann
- Institute of Integrative BiologyETH ZurichZürich8092Switzerland
- Department of Ecology and EvolutionUniversity of LausanneLausanne1015Switzerland
| | - T. Ulmar Grafe
- Faculty of ScienceUniversiti Brunei DarussalamGadongBE 1410Brunei Darussalam
| | - Faizah Metali
- Faculty of ScienceUniversiti Brunei DarussalamGadongBE 1410Brunei Darussalam
| | - Alex Widmer
- Institute of Integrative BiologyETH ZurichZürich8092Switzerland
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31
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Cytogenetic Analysis Did Not Reveal Differentiated Sex Chromosomes in Ten Species of Boas and Pythons (Reptilia: Serpentes). Genes (Basel) 2019; 10:genes10110934. [PMID: 31731798 PMCID: PMC6896069 DOI: 10.3390/genes10110934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 01/16/2023] Open
Abstract
Homologous and differentiated ZZ/ZW sex chromosomes (or derived multiple neo-sex chromosomes) were often described in caenophidian snakes, but sex chromosomes were unknown until recently in non-caenophidian snakes. Previous studies revealed that two species of boas (Boa imperator, B. constrictor) and one species of python (Python bivittatus) independently evolved XX/XY sex chromosomes. In addition, heteromorphic ZZ/ZW sex chromosomes were recently revealed in the Madagascar boa (Acrantophis sp. cf. dumerili) and putatively also in the blind snake Myriopholis macrorhyncha. Since the evolution of sex chromosomes in non-caenophidian snakes seems to be more complex than previously thought, we examined ten species of pythons and boas representing the families Boidae, Calabariidae, Candoiidae, Charinidae, Pythonidae, and Sanziniidae by conventional and molecular cytogenetic methods, aiming to reveal their sex chromosomes. Our results show that all examined species do not possess sex-specific differences in their genomes detectable by the applied cytogenetic methods, indicating the presence of poorly differentiated sex chromosomes or even the absence of sex chromosomes. Interestingly, fluorescence in situ hybridization with telomeric repeats revealed extensive distribution of interstitial telomeric repeats in eight species, which are likely a consequence of intra-chromosomal rearrangements.
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32
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Palmer DH, Rogers TF, Dean R, Wright AE. How to identify sex chromosomes and their turnover. Mol Ecol 2019; 28:4709-4724. [PMID: 31538682 PMCID: PMC6900093 DOI: 10.1111/mec.15245] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non-model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.
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Affiliation(s)
- Daniela H. Palmer
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Thea F. Rogers
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Rebecca Dean
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Alison E. Wright
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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33
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Nielsen SV, Guzmán-Méndez IA, Gamble T, Blumer M, Pinto BJ, Kratochvíl L, Rovatsos M. Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata). Biol Lett 2019; 15:20190498. [PMID: 31594492 DOI: 10.1098/rsbl.2019.0498] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Most pleurodont lizard families (anoles, iguanas and their relatives), with the exception of the basilisks and casquehead lizards (family Corytophanidae), share homologous XX/XY sex chromosomes, syntenic with chicken chromosome 15. Here, we used a suite of methods (i.e. RADseq, RNAseq and qPCR) to identify corytophanid sex chromosomes for the first time. We reveal that all examined corytophanid species have partially degenerated XX/XY sex chromosomes, syntenic with chicken chromosome 17. Transcriptomic analyses showed that the expression of X-linked genes in the corytophanid, Basiliscus vittatus, is not balanced between the sexes, which is rather exceptional under male heterogamety, and unlike the dosage-balanced sex chromosomes in other well-studied XX/XY systems, including the green anole, Anolis carolinensis. Corytophanid sex chromosomes may represent a rare example of a turnover away from stable, differentiated sex chromosomes. However, because of poor phylogenetic resolution among pleurodont families, we cannot reject the alternative hypothesis that corytophanid sex chromosomes evolved independently from an unknown ancestral system.
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Affiliation(s)
- Stuart V Nielsen
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | | | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Madison Blumer
- Keck Science Department, Scripps College, Claremont, CA 91711, USA
| | - Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic
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Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes. G3-GENES GENOMES GENETICS 2019; 9:3467-3476. [PMID: 31439718 PMCID: PMC6778777 DOI: 10.1534/g3.119.400556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.
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35
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Pan Q, Feron R, Yano A, Guyomard R, Jouanno E, Vigouroux E, Wen M, Busnel JM, Bobe J, Concordet JP, Parrinello H, Journot L, Klopp C, Lluch J, Roques C, Postlethwait J, Schartl M, Herpin A, Guiguen Y. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLoS Genet 2019; 15:e1008013. [PMID: 31437150 PMCID: PMC6726246 DOI: 10.1371/journal.pgen.1008013] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 09/04/2019] [Accepted: 07/26/2019] [Indexed: 01/17/2023] Open
Abstract
Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade. In stark contrast to mammals and birds, a high proportion of teleosts have homomorphic sex chromosomes and display a high diversity of sex determining genes. Yet, population level knowledge of both the sex chromosome and the master sex determining gene is only available for the Japanese medaka, a model species. Here we identified and provided functional proofs of an old duplicate of anti-Müllerian hormone (Amh), a member of the Tgf- β family, as the male master sex determining gene in the Northern pike, Esox lucius. We found that this duplicate, named amhby (Y-chromosome-specific anti-Müllerian hormone paralog b), was translocated to the sub-telomeric region of the new sex chromosome, and now amhby shows strong sequence divergence as well as substantial expression pattern differences from its autosomal paralog, amha. We assembled a male genome sequence using Nanopore long reads and identified a restricted region of differentiation within the sex chromosome pair in a wild population. Our results provide insight on the conserved players in sex determination pathways, the mechanisms of sex chromosome turnover, and the diversity of levels of differentiation between homomorphic sex chromosomes in teleosts.
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Affiliation(s)
- Qiaowei Pan
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
- Department of Ecology and Evolution, University of Lausanne,1015, Lausanne, Switzerland
| | - Romain Feron
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
- Department of Ecology and Evolution, University of Lausanne,1015, Lausanne, Switzerland
| | - Ayaka Yano
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - René Guyomard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | - Ming Wen
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - Jean-Mickaël Busnel
- Fédération d’Ille-et-Vilaine pour la pêche et la protection du milieu aquatique (FDPPMA35), CS 26713, Rennes, France
| | - Julien Bobe
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, MNHN, Muséum National d'Histoire Naturelle, France
| | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet Tolosan, France
- SIGENAE, GenPhySE, Université de Toulouse, INRA, ENVT, Castanet Tolosan, France
| | - Jérôme Lluch
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Céline Roques
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Manfred Schartl
- University of Wuerzburg, Physiological Chemistry, Biocenter, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Hospital, Würzburg, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Amaury Herpin
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - Yann Guiguen
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
- * E-mail:
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Wilson CA, Titus T, Batzel P, Postlethwait JH, Raman R. A Search for Sex-Linked Loci in the Agamid Lizard, Calotes versicolor. Sex Dev 2019; 13:143-150. [PMID: 31247625 DOI: 10.1159/000500465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2019] [Indexed: 11/19/2022] Open
Abstract
The Indian garden lizard, Calotes versicolor, lacks cytologically recognizable sex chromosomes, and its mechanism of sex determination is unclear. We evaluated genotype-to-sex-phenotype association using RAD-seq in wild-caught males and females, 30 of each sex. Of 210,736 unique, 96-nt long RAD-tags, 48% contained polymorphisms, 23% of which were present in at least 40 of 60 individuals. Twenty one RAD-tags neared, but none achieved, the inclusion criteria for sex enrichment, as expected if C. versicolor lacks highly differentiated sex chromosomes. Three RAD-tags with alleles most strongly associated with sex tended to be heterozygous in females and to lack male-specific alleles, suggesting a ZW female/ZZ male system. Putative female alleles, however, were present in some males and lacking from some females, suggesting either recombination between these markers and the sex locus or sex reversal due to environmental or genetic factors. Paired-end, 250-nt reads from 1 male provided a fragmented draft genome assembly. Four sex-associated RAD-tags were identical to portions of 4 unique C. versicolor genomic contigs rather than linked to a single putative sex-linked region. The lack of strongly sex-linked loci coupled with weak evidence for temperature-associated sex determination intensifies the need for further investigation of the puzzling sex determination mechanism in C. versicolor.
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Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus. BMC Genomics 2019; 20:415. [PMID: 31122206 PMCID: PMC6533744 DOI: 10.1186/s12864-019-5771-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/03/2019] [Indexed: 11/15/2022] Open
Abstract
Background Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex determination were unclear which hinder the improvement of the artificial breeding. Detection of a sex specific marker provides an effective approach to identify genetic sex and investigate the sex determination mechanism. Results We used restriction-site-associated DNA (RAD) sequencing to isolate a sex-specific genetic marker in A. davidianus to expand knowledge of the sex determination mechanism. Four male and four female specimens were subjected to RAD sequencing, which generated 934,072,989 reads containing approximately 134.4 Gb of sequences. The first round of comparison of the assembled sequence against the opposite sex raw reads revealed 19,097 female and 17,994 male unmatched sequences. Subsequently, 19,097 female sequences were subjected to a BLAST search against male genomic data, which revealed 308 sequences unmapped to the male genome. One hundred of these were randomly selected and validated by PCR in five male and five female specimens, and four putative sex-specific sequences were produced. Further validation was performed by PCR in another 24 females and 24 males, and all female individuals exhibited the expected specific bands, while the males did not. To apply the sex-specific marker, three specimens reversed from genetic female to physiological male were found in a group exposed to elevated temperature, and 13 individuals reversed from genetic male to physiological female were obtained in a 17β-estradiol exposed group. Conclusion This is the first report of a sex-specific marker in A. davidianus and may have potential for elucidation of its sex determination mechanism and, hence, its conservation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5771-5) contains supplementary material, which is available to authorized users.
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Development and Validation of Sex-Specific Markers in Pelodiscus Sinensis Using Restriction Site-Associated DNA Sequencing. Genes (Basel) 2019; 10:genes10040302. [PMID: 30991756 PMCID: PMC6523797 DOI: 10.3390/genes10040302] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 11/17/2022] Open
Abstract
The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, Pelodiscus sinensis, is an economically important aquatic species that shows significant male sexual dimorphism, with a large body size, faster growth, a thick and wide calipash, and lower body fat. In this study, ten male and ten female turtles were subjected to restriction site-associated DNA sequencing (RAD-seq) using the Hi-Seq 4000 sequencing platform to isolate female-specific DNA fragments. We identified 5967 bp and 6532 bp fragments using genome walking. Three female-specific markers designed from these two fragments were confirmed to separate the sexes of Pelodiscus sinensis perfectly. One of the female-specific markers showed dosage association in female and male individuals. Individuals from different populations (n = 296) were used to validate that the female-specific markers could identify the genetic sex of Pelodiscus sinensis with 100% accuracy. The results of the present study demonstrated that RAD-seq was useful to develop sex-related markers in animals, and verified that the sex determination system of Pelodiscus sinensis belonged to the ZZ/ZW heterogametic system. Importantly, the developed markers could lead to a method for sex-controlled breeding in the Chinese soft-shelled turtle.
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Shi X, Waiho K, Li X, Ikhwanuddin M, Miao G, Lin F, Zhang Y, Li S, Zheng H, Liu W, Aweya JJ, Azmie G, Baylon JC, Quinitio ET, Ma H. Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification. BMC Genomics 2018; 19:981. [PMID: 30594128 PMCID: PMC6311006 DOI: 10.1186/s12864-018-5380-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals. RESULTS Restriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively. CONCLUSIONS Sex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.
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Affiliation(s)
- Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
| | - Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
| | - Xincang Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090 China
| | - Mhd Ikhwanuddin
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Malaysia
| | - Guidong Miao
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Fan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Jude Juventus Aweya
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Ghazali Azmie
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Malaysia
| | - Juliana C. Baylon
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines, Visayas, 5023 Miagao, Philippines
| | - Emilia T. Quinitio
- Aquaculture Department, Southeast Asian Fisheries Development Center, 5021 Tigbauan, Philippines
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
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Hoey JA, Pinsky ML. Genomic signatures of environmental selection despite near-panmixia in summer flounder. Evol Appl 2018; 11:1732-1747. [PMID: 30344639 PMCID: PMC6183468 DOI: 10.1111/eva.12676] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 06/13/2018] [Accepted: 06/16/2018] [Indexed: 01/01/2023] Open
Abstract
Rapid environmental change is altering the selective pressures experienced by marine species. While adaptation to local environmental conditions depends on a balance between dispersal and natural selection across the seascape, the spatial scale of adaptation and the relative importance of mechanisms maintaining adaptation in the ocean are not well understood. Here, using population assignment tests, Approximate Bayesian Computation (ABC), and genome scans with double-digest restriction-site associated DNA sequencing data, we evaluated population structure and locus-environment associations in a commercially important species, summer flounder (Paralichthys dentatus), along the U.S. east coast. Based on 1,137 single nucleotide polymorphisms across 232 individuals spanning nearly 1,900 km, we found no indication of population structure across Cape Hatteras, North Carolina (F ST = 0.0014) or of isolation by distance along the coast using individual relatedness. ABC estimated the probability of dispersal across the biogeographic break at Cape Hatteras to be high (95% credible interval: 7%-50% migration). However, we found 15 loci whose allele frequencies were associated with at least one of four environmental variables. Of those, 11 were correlated with bottom temperature. For summer flounder, our results suggest continued fisheries management as a single population and identify likely response mechanisms to climate change. Broadly speaking, our findings suggest that spatial balancing selection can manifest in adaptive divergence on regional scales in marine fish despite high dispersal, and that these conditions likely result in the widespread distribution of adaptive alleles and a high potential for future genetic adaptation in response to changing environmental conditions. In the context of a rapidly changing world, a landscape genomics perspective offers a useful approach for understanding the causes and consequences of genetic differentiation.
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Affiliation(s)
- Jennifer A. Hoey
- Department of Ecology, Evolution, & Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
| | - Malin L. Pinsky
- Department of Ecology, Evolution, & Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
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41
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Liu H, Pang M, Yu X, Zhou Y, Tong J, Fu B. Sex-specific markers developed by next-generation sequencing confirmed an XX/XY sex determination system in bighead carp (Hypophthalmichehys nobilis) and silver carp (Hypophthalmichthys molitrix). DNA Res 2018; 25:4791395. [PMID: 29315393 PMCID: PMC6014435 DOI: 10.1093/dnares/dsx054] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
Sex-specific markers are powerful tools for identifying sex-determination system in various animals. Bighead carp (Hypophthalmichehys nobilis) and silver carp (Hypophthalmichthys molitrix) are two of the most important edible fish in Asia, which have a long juvenility period that can lasts for 4-5 years. In this study, we found one sex-specific marker by next-generation sequencing together with bioinformatics analysis in bighead carp. The male-specific markers were used to perform molecular sexing in the progenies of artificial gynogenetic diploids and found all progenies (n = 160) were females. Meanwhile, around 1 : 1 sex ratio was observed in a total of 579 juvenile offspring from three other families. To further extend the male-specific region, we performed genome walking and got a male-specific sequence of 8,661 bp. Five pairs of primers were designed and could be used to efficiently distinguish males from females in bighead carp and silver carp. The development of these male-specific markers and results of their molecular sexing in different populations provide strong evidence for a sex determination system of female homogametry or male heterogametry (XX/XY) in bighead carp and silver carp. To the best of our knowledge, this is the first report of effective sex-specific markers in these two large carp species.
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Affiliation(s)
- Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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42
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Marin R, Cortez D, Lamanna F, Pradeepa MM, Leushkin E, Julien P, Liechti A, Halbert J, Brüning T, Mössinger K, Trefzer T, Conrad C, Kerver HN, Wade J, Tschopp P, Kaessmann H. Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage. Genome Res 2017; 27:1974-1987. [PMID: 29133310 PMCID: PMC5741051 DOI: 10.1101/gr.223727.117] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
Abstract
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.
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Affiliation(s)
- Ray Marin
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Diego Cortez
- Center for Genomic Sciences, UNAM, CP62210 Cuernavaca, Mexico
| | - Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Madapura M Pradeepa
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Philippe Julien
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Angélica Liechti
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Katharina Mössinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Timo Trefzer
- Department of Theoretical Bioinformatics, German Cancer Research Center/BioQuant, D-69120 Heidelberg, Germany
| | - Christian Conrad
- Department of Theoretical Bioinformatics, German Cancer Research Center/BioQuant, D-69120 Heidelberg, Germany
| | - Halie N Kerver
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Juli Wade
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA.,Department of Psychology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Patrick Tschopp
- Institute of Zoology, University of Basel, 4051 Basel, Switzerland
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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43
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Evolution and conservation of Characidium sex chromosomes. Heredity (Edinb) 2017; 119:237-244. [PMID: 28745717 DOI: 10.1038/hdy.2017.43] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 01/02/2023] Open
Abstract
Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9863 single-nucleotide polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation. With this data set, we identified 26 female-specific RAD loci, putatively located on the W chromosome, as well as 148 sex-associated SNPs showing significant differentiation (average FST=0.144) between males and females, and therefore in regions of more recent divergence between the Z and W chromosomes. In addition, we detected 25 RAD loci showing extreme heterozygote deficiency in females but which were in Hardy-Weinberg equilibrium in males, consistent with degeneration of the W chromosome and therefore female hemizygosity. We validated seven female-specific and two sex-associated markers in a larger sample of C. gomesi, of which three localised to the W chromosome, thereby providing useful markers for sexing wild samples. Validated markers were evaluated in other populations and species of the genus Characidium, this exploration suggesting a rapid turnover of W-specific repetitive elements. Together, our analyses point to a complex origin for the sex chromosome of C. gomesi and highlight the utility of RAD-seq for studying the composition and evolution of sex chromosomes systems in wild populations.
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44
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 28405374 DOI: 10.5061/dryad.rs7bm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A Haguenauer
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - S Chenesseau
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - K Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - G Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - E Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - M Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - S Rialle
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - D Aurelle
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - P Pontarotti
- Aix Marseille Univ , CNRS, Centrale Marseille, I2M , Marseille , France
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45
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). ROYAL SOCIETY OPEN SCIENCE 2017; 4:160880. [PMID: 28405374 PMCID: PMC5383831 DOI: 10.1098/rsos.160880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/01/2017] [Indexed: 05/29/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M. Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A. Haguenauer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - S. Chenesseau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - K. Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - G. Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - E. Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - M. Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - S. Rialle
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - D. Aurelle
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - P. Pontarotti
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
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46
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Rovatsos M, Kratochvíl L. Molecular sexing applicable in 4000 species of lizards and snakes? From dream to real possibility. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12714] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology Faculty of Science Charles University in Prague Viničná 7 12844 Prague Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology Faculty of Science Charles University in Prague Viničná 7 12844 Prague Czech Republic
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Lambert MR, Skelly DK, Ezaz T. Sex-linked markers in the North American green frog (Rana clamitans) developed using DArTseq provide early insight into sex chromosome evolution. BMC Genomics 2016; 17:844. [PMID: 27793086 PMCID: PMC5084323 DOI: 10.1186/s12864-016-3209-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extent to which sex reversal is associated with transitions in sex determining systems (XX-XY, ZZ-ZW, etc.) or abnormal sexual differentiation is predominantly unexplored in amphibians. This is in large part because most amphibian taxa have homomorphic sex chromosomes, which has traditionally made it challenging to identify discordance between phenotypic and genetic sex in amphibians, despite all amphibians having a genetic component to sex determination. Recent advances in molecular techniques such as genome complexity reduction and high throughput sequencing present a valuable avenue for furthering our understanding of sex determination in amphibians and other taxa with homomorphic sex chromosomes like many fish and reptiles. RESULTS We use DArTseq as a novel approach to identify sex-linked markers in the North American green frog (Rana clamitans melanota) using lab-reared tadpoles as well as wild-caught adults from seven ponds either in undeveloped, forested habitats or suburban ponds known to be subject to contamination by anthropogenic chemicals. The DArTseq methodology identified 13 sex-linked SNP loci and eight presence-absence loci associated with males, indicating an XX-XY system. Both alleles from a single locus show partial high sequence homology to Dmrt1, a gene linked to sex determination and differentiation throughout Metazoa. Two other loci have sequence similarities to regions of the chimpanzee and human X-chromosome as well as the chicken Z-chromosome. Several loci also show geographic variation in sex-linkage, possibly indicating sex chromosome recombination. While all loci are statistically sex-linked, they show varying degrees of female heterozygosity and male homozygosity, providing further evidence that some markers are on regions of the sex chromosomes undergoing higher rates of recombination and therefore further apart from the putative sex determining locus. CONCLUSION The ease of the DArTseq platform provides a useful avenue for future research on sex reversal and sex chromosome evolution in vertebrates, particularly for non-model species with homomorphic or cryptic or nascent sex chromosomes.
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Affiliation(s)
- Max R Lambert
- School of Forestry and Environmental Studies, Yale University, Greeley Memorial Lab, 370 Prospect St, New Haven, CT, 06511, USA.
| | - David K Skelly
- School of Forestry and Environmental Studies, Yale University, Greeley Memorial Lab, 370 Prospect St, New Haven, CT, 06511, USA
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
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Chandler JC, Aizen J, Elizur A, Battaglene SC, Ventura T. Male Sexual Development and the Androgenic Gland: Novel Insights through the de novo Assembled Transcriptome of the Eastern Spiny Lobster, Sagmariasus verreauxi. Sex Dev 2016; 9:338-54. [PMID: 26927314 DOI: 10.1159/000443943] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2015] [Indexed: 11/19/2022] Open
Abstract
The Eastern spiny lobster, Sagmariasus verreauxi, is commercially important in fisheries, with growing aquaculture potential, driving an interest to better understand male sexual differentiation. Amongst the Decapoda, the androgenic gland (AG) and the insulin-like androgenic gland hormone (IAG) have a well-defined function in male sexual differentiation. However, IAG is not a sex determinant and therefore must be considered as part of a broader, integrated pathway. This work uses a transcriptomic, multi-tissue approach to provide an integrated description of male-biased expression as mediated through the AG. Transcriptomic analyses demonstrate that IAG expression is stage- and eyestalk-regulated (low in immature, high in mature and 6-times higher in hypertrophied glands), with IAG being the predominant AG-specific factor. The low expression of this key factor in immature males suggests the involvement of other tissues in male sexual differentiation. Across tissues, the gonad (87.8%) and antennal gland (73.5%) show the highest male-biased differential expression of transcripts and also express 4 sex-determination regulators, known as Dmrts, with broader expression of Sv-Sxl and Sv-TRA-2. In order to better understand male sexual differentiation, tissues other than the AG must also be considered. This research highlights the gonad and antennal gland as showing significant male-biased expression patterns, including the Sv-Dmrts.
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Affiliation(s)
- Jennifer C Chandler
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast (USC), Maroochydore, Qld., Australia
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49
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Brelsford A, Dufresnes C, Perrin N. High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex. Heredity (Edinb) 2015; 116:177-81. [PMID: 26374238 DOI: 10.1038/hdy.2015.83] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/12/2015] [Accepted: 07/29/2015] [Indexed: 01/16/2023] Open
Abstract
Identifying homology between sex chromosomes of different species is essential to understanding the evolution of sex determination. Here, we show that the identity of a homomorphic sex chromosome pair can be established using a linkage map, without information on offspring sex. By comparing sex-specific maps of the European tree frog Hyla arborea, we find that the sex chromosome (linkage group 1) shows a threefold difference in marker number between the male and female maps. In contrast, the number of markers on each autosome is similar between the two maps. We also find strongly conserved synteny between H. arborea and Xenopus tropicalis across 200 million years of evolution, suggesting that the rate of chromosomal rearrangement in anurans is low. Finally, we show that recombination in males is greatly reduced at the centers of large chromosomes, consistent with previous cytogenetic findings. Our research shows the importance of high-density linkage maps for studies of recombination, chromosomal rearrangement and the genetic architecture of ecologically or economically important traits.
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Affiliation(s)
- A Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - C Dufresnes
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - N Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Zhang N, Zhang L, Tao Y, Guo L, Sun J, Li X, Zhao N, Peng J, Li X, Zeng L, Chen J, Yang G. Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus. BMC Genomics 2015; 16:189. [PMID: 25887315 PMCID: PMC4369078 DOI: 10.1186/s12864-015-1371-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. RESULTS We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. CONCLUSIONS A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.
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Affiliation(s)
- Ning Zhang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Linan Zhang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Ye Tao
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Li Guo
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Juan Sun
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xia Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Nan Zhao
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Jie Peng
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Liang Zeng
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Jinsa Chen
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Guanpin Yang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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