1
|
Guo A, Yuan J, Lian Q, Li M, Gu Z. Isolation and characterization of 20 polymorphic microsatellites loci for Xenocypris davidi based on high-throughput sequencing. Mol Biol Rep 2020; 47:8305-8310. [PMID: 32974841 DOI: 10.1007/s11033-020-05834-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/09/2020] [Indexed: 11/26/2022]
Abstract
Xenocypris davidi is one of the most economically important freshwater fish in China. However, few molecular markers have been reported for this species, impeding in-depth population genetic, dispersal, and gene flow studies. In the present study, a batch of novel polymorphic microsatellites from the genome of X. davidi were isolated and characterized using high-throughput sequencing. A total of 20 microsatellite markers were isolated. Analysis of 33 individuals revealed an average of 7.35 alleles per locus, ranging from 3 to 18. The observed and expected heterozygosities ranged from 0.3 to 1 and from 0.426 to 0.93, respectively. Only one tested locus significantly deviated from Hardy-Weinberg equilibrium. 18 microsatellite loci were highly polymorphic (PIC > 0.5). These newly isolated microsatellite markers would be useful to study the population genetics and stock management of X. davidi.
Collapse
Affiliation(s)
- Aihuan Guo
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Research Center of East China Sea Fishery Research Institute, Zhejiang Institute of Freshwater Fisheries, 999th South Hangchangqiao Road, Wuxing District, Huzhou, 313000, China
| | - Julin Yuan
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Research Center of East China Sea Fishery Research Institute, Zhejiang Institute of Freshwater Fisheries, 999th South Hangchangqiao Road, Wuxing District, Huzhou, 313000, China.
| | - Qingping Lian
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Research Center of East China Sea Fishery Research Institute, Zhejiang Institute of Freshwater Fisheries, 999th South Hangchangqiao Road, Wuxing District, Huzhou, 313000, China
| | - Ming Li
- Jinhua Fisheries Technology Extension Station, Jinhua, 321000, China
| | - Zhimin Gu
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Research Center of East China Sea Fishery Research Institute, Zhejiang Institute of Freshwater Fisheries, 999th South Hangchangqiao Road, Wuxing District, Huzhou, 313000, China.
| |
Collapse
|
2
|
Zhang X, Qin H, Xie W, Ma Y, Sun W. Comparative population genetic analyses suggest hybrid origin of R hododendron pubicostatum, an endangered plant species with extremely small populations endemic to Yunnan, China. PLANT DIVERSITY 2020; 42:312-318. [PMID: 33094202 PMCID: PMC7567756 DOI: 10.1016/j.pld.2020.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 05/08/2023]
Abstract
Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species. In the present study, we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach. Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus. Interestingly, genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh. pubicostatum. This sympatry should be considered a unimodal hybrid zone, since R h. pubicostatum is predominant here. Unimodal hybrid zones are uncommon in Rhododendron, despite the fact that hybridization frequently occurs in the genus. Issues pertaining to the conservation of R h. pubicostatum resulting from admixture of genetic material from its parental species are discussed.
Collapse
Affiliation(s)
- Xuemei Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hantao Qin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Weijia Xie
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, 650201, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, 650201, China
| |
Collapse
|
3
|
Iguchi A, Nishijima M, Yoshioka Y, Miyagi A, Miwa R, Tanaka Y, Kato S, Matsui T, Igarashi Y, Okamoto N, Suzuki A. Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis. PLoS One 2020; 15:e0228483. [PMID: 32027722 PMCID: PMC7004558 DOI: 10.1371/journal.pone.0228483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/16/2020] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to select a candidate deep-sea amphipod species suitable for connectivity analyses in areas around cobalt-rich ferromanganese crusts (CRCs). We applied DNA barcoding based on the mitochondrial protein-coding gene, cytochrome c oxidase subunit I (COI), to specimens collected from the Xufu Guyot (the JA06 Seamount) off southeastern Minami-Torishima Island in the North Pacific, where CRCs are distributed. We used baited traps to collect 37 specimens. Comparison of COI sequences with public reference databases (GenBank, BOLD) showed that almost all of the specimens belonged to the superfamily Lysianassoidea, which is known to be ubiquitous in deep-sea areas. In a molecular taxonomic analysis of these sequences, we detected 11 clades. One of these clades (group 9) composed of 18 sequences and was identified by DNA barcoding as a putative species belonging to Abyssorchomene, which has been reported from the New Hebrides Trench in the South Pacific. We considered this species to be a candidate for connectivity analysis and analyzed its genome by restriction site–associated DNA sequencing. The results showed that the genetic variation in this species is adequate for analyzing connectivity patterns in CRC areas in the future.
Collapse
Affiliation(s)
- Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago-City, Okinawa, Japan
- * E-mail:
| | | | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago-City, Okinawa, Japan
| | - Aika Miyagi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago-City, Okinawa, Japan
| | - Ryuichi Miwa
- Kaiyo Engineering Co., Ltd., Taito-ku, Tokyo, Japan
| | - Yuichiro Tanaka
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Shogo Kato
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Takaaki Matsui
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Yoshiaki Igarashi
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Nobuyuki Okamoto
- Japan Oil, Gas and Metals National Corporation (JOGMEC), Minato-ku, Tokyo, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| |
Collapse
|
4
|
Taboada S, Kenny NJ, Riesgo A, Wiklund H, Paterson GLJ, Dahlgren TG, Glover AG. Mitochondrial genome and polymorphic microsatellite markers from the abyssal sponge Plenaster craigi Lim & Wiklund, 2017: tools for understanding the impact of deep-sea mining. MARINE BIODIVERSITY : A JOURNAL OF THE SENCKENBERG RESEARCH INSTITUTE 2017; 48:621-630. [PMID: 31007772 PMCID: PMC6445405 DOI: 10.1007/s12526-017-0786-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/08/2017] [Accepted: 08/31/2017] [Indexed: 06/09/2023]
Abstract
The abyssal demosponge Plenaster craigi is endemic to the Clarion - Clipperton Zone (CCZ) in the NE Pacific, a region with abundant seafloor polymetallic nodules and of potential interest for mining. Plenaster craigi encrusts on these nodules and is an abundant component of the ecosystem. To assess the impact of mining operations, it is crucial to understand the genetics of this species, because its genetic diversity and connectivity across the area may be representative of other nodule-encrusting invertebrate epifauna. Here we describe and characterize 14 polymorphic microsatellite markers from this keystone species using Illumina MiSeq, tested for 75 individuals from three different areas across the CCZ, including an Area of Particular Environmental Interest (APEI-6) and two areas within the adjacent UK1 mining exploration area. The number of alleles per locus ranged from 3 to 30 (13.33 average alleles for all loci across areas). Observed and expected heterozygosity ranged from 0.909-0.048 and from 0.954-0.255, respectively. Several loci displayed significant deviation from the Hardy-Weinberg equilibrium, which appears to be common in other sponge studies. The microsatellite loci described here will be used to assess the genetic structure and connectivity on populations of the sponge across the CCZ, which will be invaluable for monitoring the impact of mining operations on its habitat. Also, we provide the annotated mitochondrial genome of P. craigi, compare its arrangement with other closely related species, and discuss the phylogenetic framework for the sponge after Maximum Likelihood and Bayesian Inference analyses using nucleotide and amino acid sequences data sets separately.
Collapse
Affiliation(s)
- Sergi Taboada
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Nathan J. Kenny
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Helena Wiklund
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Gordon L. J. Paterson
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Thomas G. Dahlgren
- Uni Research, PO Box 7810, 5020 Bergen, Norway
- Department of Marine Sciences, University of Gothenburg, Box 463, 40530 Gothenburg, Sweden
| | - Adrian G. Glover
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| |
Collapse
|
5
|
Ritchie H, Jamieson AJ, Piertney SB. Genome size variation in deep-sea amphipods. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170862. [PMID: 28989783 PMCID: PMC5627123 DOI: 10.1098/rsos.170862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/16/2017] [Indexed: 06/07/2023]
Abstract
Genome size varies considerably across taxa, and extensive research effort has gone into understanding whether variation can be explained by differences in key ecological and life-history traits among species. The extreme environmental conditions that characterize the deep sea have been hypothesized to promote large genome sizes in eukaryotes. Here we test this supposition by examining genome sizes among 13 species of deep-sea amphipods from the Mariana, Kermadec and New Hebrides trenches. Genome sizes were estimated using flow cytometry and found to vary nine-fold, ranging from 4.06 pg (4.04 Gb) in Paralicella caperesca to 34.79 pg (34.02 Gb) in Alicella gigantea. Phylogenetic independent contrast analysis identified a relationship between genome size and maximum body size, though this was largely driven by those species that display size gigantism. There was a distinct shift in the genome size trait diversification rate in the supergiant amphipod A. gigantea relative to the rest of the group. The variation in genome size observed is striking and argues against genome size being driven by a common evolutionary history, ecological niche and life-history strategy in deep-sea amphipods.
Collapse
Affiliation(s)
- H. Ritchie
- Institute of Biological and Environmental Sciences, University of Aberdeen, Zoology Building, Aberdeen AB24 2TZ, UK
| | - A. J. Jamieson
- Oceanlab, University of Aberdeen, Newburgh, Aberdeenshire AB41 6AA, UK
| | - S. B. Piertney
- Institute of Biological and Environmental Sciences, University of Aberdeen, Zoology Building, Aberdeen AB24 2TZ, UK
| |
Collapse
|
6
|
Taylor ML, Roterman CN. Invertebrate population genetics across Earth's largest habitat: The deep-sea floor. Mol Ecol 2017; 26:4872-4896. [PMID: 28833857 DOI: 10.1111/mec.14237] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/04/2023]
Abstract
Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made.
Collapse
Affiliation(s)
- M L Taylor
- Department of Zoology, University of Oxford, Oxford, UK
| | - C N Roterman
- Department of Zoology, University of Oxford, Oxford, UK
| |
Collapse
|
7
|
Development of Nuclear Microsatellite Loci and Mitochondrial Single Nucleotide Polymorphisms for the Natterjack Toad,Bufo(Epidalea)calamita(Bufonidae), Using Next Generation Sequencing and Competitive Allele Specific PCR (KASPar): Table 1. J Hered 2016; 107:660-665. [DOI: 10.1093/jhered/esw068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/14/2016] [Indexed: 11/14/2022] Open
|