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      Characterization of 15 nuclear microsatellite markers for Afzelia africana (Fabaceae) and related species

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          Abstract

          Premise

          Afzelia africana (Fabaceae) is a valuable, internationally vulnerable tree species in tropical Africa. The development of specific simple sequence repeat ( SSR) loci is necessary for population genetic studies in this tree species and its closest relatives.

          Methods And Results

          Fifteen new polymorphic microsatellite markers were developed for A. africana using Illumina next‐generation sequencing. We tested the polymorphism of the 15 loci in three populations in Benin, West Africa. The number of expressed alleles per locus varied from one to 12. The levels of observed and expected heterozygosity ranged from 0.100 to 1.000 and from 0.095 to 0.882, respectively. Most markers successfully amplified in the closely related species A. quanzensis and A. bipindensis, but less so in A. bipindensis.

          Conclusions

          Because of their cross‐amplification ability, these newly developed loci will serve as useful tools for future molecular analyses on A. africana and related species.

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          Most cited references 12

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review.

            Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.
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              A rapid DNA isolation procedure for small amounts of fresh leaf tissue

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                Author and article information

                Contributors
                thierryhouehanou@gmail.com
                Journal
                Appl Plant Sci
                Appl Plant Sci
                10.1002/(ISSN)2168-0450
                APS3
                Applications in Plant Sciences
                John Wiley and Sons Inc. (Hoboken )
                2168-0450
                13 May 2019
                May 2019
                : 7
                : 5 ( doiID: 10.1002/aps3.2019.7.issue-5 )
                Affiliations
                [ 1 ] Laboratory of Applied Ecology Faculty of Agricultural Sciences University of Abomey 01 BP 526 Cotonou Republic of Benin
                [ 2 ] Institute for Ecology and Evolution Professorship for Systematic Botany with Hausknecht Herbarium and Botanical Garden Friedrich Schiller University Jena 07743 Jena Germany
                [ 3 ] Laboratory of Ecology, Botany and Plant Biology Faculty of Agronomy University of Parakou 03 BP 125 Parakou Republic of Benin
                [ 4 ] Laboratoire de Biomathématiques et d'Estimations Forestières Faculté des Sciences Agronomiques Université d'Abomey Calavi 04 BP 1525 Cotonou Republic of Benin
                [ 5 ] Landschaftspflegeverband Suedharz/Kyffhaeuser e.V. 99734 Nordhausen Germany
                Author notes
                [* ]Author for correspondence: thierryhouehanou@ 123456gmail.com
                Article
                APS31249
                10.1002/aps3.1249
                6526647
                © 2019 Houehanou et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 0, Tables: 3, Pages: 5, Words: 4295
                Product
                Funding
                Funded by: Humboldt Foundation
                Categories
                Primer Note
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                Custom metadata
                2.0
                aps31249
                May 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.3 mode:remove_FC converted:20.05.2019

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