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      Development of microsatellite markers for a monotypic and globally endangered species, Glyptostrobus pensilis (Cupressaceae)

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          Abstract

          Premise of the Study

          Microsatellite markers were developed to facilitate studies of genetic diversity and structure in Glyptostrobus pensilis, a critically endangered and monotypic conifer species.

          Methods and Results

          Using restriction site–associated DNA sequencing ( RAD‐Seq), we developed 10 polymorphic and 27 monomorphic microsatellite markers. Polymorphism was characterized using 333 individuals from nine populations. The number of alleles per locus ranged from one to 14 at the population level. The levels of observed and unbiased expected heterozygosities varied from 0.058 to 0.844 and 0.219 to 0.583, respectively. Nine of these 10 polymorphic markers were successfully cross‐amplified in Taxodium distichum, the species most closely related to G. pensilis.

          Conclusions

          These microsatellite markers can be used to reveal the genetic diversity in existing populations of G. pensilis, enabling its conservation and restoration.

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          Most cited references8

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          msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.

          Brant C Faircloth (2008)
          msatcommander is a platform-independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, fasta-formatted files. Search data and locus-specific primers are written to comma-separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8. msatcommander is available from http://code.google.com/p/msatcommander/. © 2007 The Author.
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            Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.

            Chau-Chung Wu, Jue Ruan, Zechen Chong (2012)
            The innovation of restriction-site associated DNA sequencing (RAD-seq) method takes full advantage of next-generation sequencing technology. By clustering paired-end short reads into groups with their own unique tags, RAD-seq assembly problem is divided into subproblems. Fast and accurately clustering and assembling millions of RAD-seq reads with sequencing errors, different levels of heterozygosity and repetitive sequences is a challenging question. Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top-down manner. And along a guided tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, we show that Rainbow is more competent than the other tools in dealing with RAD-seq data. Source code in C, Rainbow is freely available at http://sourceforge.net/projects/bio-rainbow/files/
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              The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae

              Zhaodong Hao, Tielong Cheng, Renhua Zheng … (2016)
              Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild.
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                Author and article information

                Contributors
                Zheng‐Feng Wang:
                ORCID: https://orcid.org/0000-0002-7599-7891
                wangrj@scbg.ac.cn
                Rui‐Jiang Wang: wzf@scbg.ac.cn
                Journal
                Journal ID (nlm-ta): Appl Plant Sci
                Journal ID (iso-abbrev): Appl Plant Sci
                Journal ID (doi): 10.1002/(ISSN)2168-0450
                Journal ID (publisher-id): APS3
                Title: Applications in Plant Sciences
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Electronic): 2168-0450
                Publication date (Electronic): 05 February 2019
                Publication date Collection: February 2019
                Volume: 7
                Issue: 2 ( doiID: 10.1002/aps3.2019.7.issue-2 )
                Electronic Location Identifier: e01217
                Affiliations
                [ 1 ] Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 People's Republic of China
                [ 2 ] Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 People's Republic of China
                [ 3 ] University of the Chinese Academy of Sciences Beijing 100049 People's Republic of China
                Author notes
                [*] [* ]Authors for correspondence: wangrj@ 123456scbg.ac.cn , wzf@ 123456scbg.ac.cn
                Author information
                https://orcid.org/0000-0002-7599-7891
                Article
                Publisher ID: APS31217
                DOI: 10.1002/aps3.1217
                PMC ID: 6384295
                SO-VID: d8399770-5758-4abf-a0f9-77842a9627b4
                Copyright © © 2019 Wang et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America
                License:

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                Date received : 01 November 2018
                Date accepted : 30 November 2018
                Page count
                Figures: 0, Tables: 3, Pages: 5, Words: 4867
                Funding
                Funded by: Guangzhou Wild Life Conservation and Management Office
                Award ID: SYZFCG‐[2017]032
                Funded by: Guangdong Forestry Department Program for Rare and Endangered Plant Conservation
                Funded by: Botanical Gardens Conservation International (BGCI)
                Funded by: Chinese Academy of Sciences
                Award ID: KFJ‐3W‐No1‐1
                Categories
                Subject: Primer Note
                Subject: Primer Notes
                Custom metadata
                source-schema-version-number 2.0
                component-id aps31217
                cover-date February 2019
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLMPMC version:5.5.9 mode:remove_FC converted:21.02.2019

                Keywords: cupressaceae,endangered species,genetic diversity,genetic markers,glyptostrobus pensilis,rad‐seq
                Data availability:
                Keywords: cupressaceae, endangered species, genetic diversity, genetic markers, glyptostrobus pensilis, rad‐seq

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