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Kaus A, Michalski S, Hänfling B, Karthe D, Borchardt D, Durka W. Fish conservation in the land of steppe and sky: Evolutionarily significant units of threatened salmonid species in Mongolia mirror major river basins. Ecol Evol 2019; 9:3416-3433. [PMID: 30962902 PMCID: PMC6434579 DOI: 10.1002/ece3.4974] [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: 08/02/2017] [Revised: 12/12/2018] [Accepted: 12/31/2018] [Indexed: 11/21/2022] Open
Abstract
Mongolia's salmonids are suffering extensive population declines; thus, more comprehensive fisheries management and conservation strategies are required. To assist with their development, a better understanding of the genetic structure and diversity of these threatened species would allow a more targeted approach for preserving genetic variation and ultimately improve long-term species recoveries. It is hypothesized that the unfragmented river basins that have persisted across Mongolia provide unobstructed connectivity for resident salmonid species. Thus, genetic structure is expected to be primarily segregated between major river basins. We tested this hypothesis by investigating the population structure for three salmonid genera (Hucho, Brachymystax and Thymallus) using different genetic markers to identify evolutionarily significant units (ESUs) and priority rivers to focus conservation efforts. Fish were assigned to separate ESUs when the combined evidence of mitochondrial and nuclear data indicated genetic isolation. Hucho taimen exhibited a dichotomous population structure forming two ESUs, with five priority rivers. Within the Brachymystax genus, there were three B. lenokESUs and one B. tumensisESU, along with six priority rivers. While B. tumensiswas confirmed to display divergent mtDNA haplotypes, haplotype sharing between these two congeneric species was also identified. For T. baicalensis,only a single ESU was assigned, with five priority rivers identified plus Lake Hovsgol. Additionally, we confirmed that T. nigrescens from Lake Hovsgol is a synonym of T. baicalensis. Across all species, the most prominent pattern was strong differentiation among major river basins with low differentiation and weak patterns of isolation by distance within river basins, which corroborated our hypothesis of high within-basin connectivity across Mongolia. This new genetic information provides authorities the opportunity to distribute resources for management between ESUs while assigning additional protection for the more genetically valuable salmonid rivers so that the greatest adaptive potential within each species can be preserved.
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Affiliation(s)
- Andrew Kaus
- Department of Aquatic Ecosystem Analysis and ManagementHelmholtz Centre for Environmental Research – UFZMagdeburgGermany
- Department of Agriculture and FisheriesBribie Island Research CentreWoorimAustralia
| | - Stefan Michalski
- Department of Community EcologyHelmholtz Centre for Environmental Research – UFZHalleGermany
| | - Bernd Hänfling
- School of Environmental SciencesUniversity of HullHullUK
| | - Daniel Karthe
- Department of Aquatic Ecosystem Analysis and ManagementHelmholtz Centre for Environmental Research – UFZMagdeburgGermany
- Environmental Engineering SectionGerman Mongolian Institute for Resources and TechnologyNalaikhMongolia
| | - Dietrich Borchardt
- Department of Aquatic Ecosystem Analysis and ManagementHelmholtz Centre for Environmental Research – UFZMagdeburgGermany
| | - Walter Durka
- Department of Community EcologyHelmholtz Centre for Environmental Research – UFZHalleGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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Patnaik BB, Wang TH, Kang SW, Hwang HJ, Park SY, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JS, Han YS, Park HS, Lee YS. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery. PLoS One 2016; 11:e0148622. [PMID: 26872384 PMCID: PMC4752248 DOI: 10.1371/journal.pone.0148622] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction. RESULTS The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats. CONCLUSIONS This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata.
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Affiliation(s)
- Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar- 751024, Odisha, India
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Changmu Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Soonok Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Republic of Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-gu, Gwangju, 500-757, Republic of Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- * E-mail:
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