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      Genetic structure of an endangered species Ormosia henryi in southern China, and implications for conservation

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          Abstract

          Background

          The evergreen broadleaved forest (EBLF) is an iconic vegetation type of East Asia, and it contributes fundamentally to biodiversity-based ecosystem functioning and services. However, the native habitat of EBLFs keeps on decreasing due to anthropogenic activities. Ormosia henryi is a valuable rare woody species in EBLFs that is particularly sensitive to habitat loss. In this study, ten natural populations of O. henryi in southern China were sampled, and then genotyping by sequencing (GBS) was applied to elucidate the standing genetic variation and population structure of this endangered species.

          Results

          In ten O. henryi populations, 64,158 high-quality SNPs were generated by GBS. Based on these markers, a relatively low level of genetic diversity was found with the expected heterozygosity ( He) ranging from 0.2371 to 0.2901. Pairwise F ST between populations varied from 0.0213 to 0.1652, indicating a moderate level of genetic differentiation. However, contemporary gene flow between populations were rare. Assignment test and principal component analysis (PCA) both supported that O. henryi populations in southern China could be divided into four genetic groups, and prominent genetic admixture was found in those populations located in southern Jiangxi Province. Mantel tests and multiple matrix regression with randomization (MMRR) analyses suggested that isolation by distance (IBD) could be the possible reason for describing the current population genetic structure. In addition, the effective population size ( Ne) of O. henryi was extremely small, and showed a continuous declining trend since the Last Glacial Period.

          Conclusions

          Our results indicate that the endangered status of O. henryi is seriously underestimated. Artificial conservation measures should be applied as soon as possible to prevent O. henryi from the fate of extinction. Further studies are needed to elucidate the mechanism that leading to the continuous loss of genetic diversity in O. henryi and help to develop a better conservation strategy.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12870-023-04231-w.

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          Most cited references55

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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              The variant call format and VCFtools

              Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                39191393@qq.com
                13307079666@163.com
                Journal
                BMC Plant Biol
                BMC Plant Biol
                BMC Plant Biology
                BioMed Central (London )
                1471-2229
                26 April 2023
                26 April 2023
                2023
                : 23
                : 220
                Affiliations
                [1 ]GRID grid.452530.5, ISNI 0000 0004 4686 9094, Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, , Jiangxi Academy of Forestry, ; Nanchang, China
                [2 ]Jiangxi Provincial Forestry Science and Technology Experiment Center, Ganzhou, China
                Article
                4231
                10.1186/s12870-023-04231-w
                10131447
                37098472
                31557682-7672-4bb3-b636-f8b985f18e57
                © The Author(s) 2023

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 6 January 2023
                : 15 April 2023
                Funding
                Funded by: Forestry Science and Technology Innovation Project of Jiangxi Forestry Bureau
                Award ID: 20236
                Award ID: 20236
                Award ID: 20236
                Award ID: 20236
                Award Recipient :
                Funded by: Special Fund of Fundamental Research and Talents of Jiangxi Academy of Forestry
                Award ID: 2023521202
                Award ID: 2023521202
                Award ID: 2023521202
                Award ID: 2023521202
                Award ID: 2023521202
                Award ID: 2023521202
                Award Recipient :
                Funded by: Major Programs of Scientific Research and Achievement Popularization of Jiangxi Academy of Forestry
                Award ID: 2017511201
                Award ID: 2017511201
                Award ID: 2017511201
                Award ID: 2017511201
                Award ID: 2017511201
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2023

                Plant science & Botany
                ormosia henryi,population structure,genetic diversity,genotyping by sequencing,conservation

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