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      Genome sequence of mungbean and insights into evolution within Vigna species

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          Abstract

          Mungbean ( Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species ( V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

          Abstract

          Mungbean is a fast-growing and warm-season legume crop, cultivated mainly in Asia. Here, the authors sequence the genomes of both wild and domesticated mungbean varieties and, together with detailed transcriptome data, provide insight into mungbean domestication, polyploidization and speciation.

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          Most cited references21

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          ProtTest: selection of best-fit models of protein evolution.

          Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. ProtTest is available under the GNU license from http://darwin.uvigo.es
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            Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

            A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.
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              LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

              Background Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic genome projects, there are only few high quality genome wide annotations of transposable elements. Therefore, there is a considerable demand for computational identification of transposable elements. LTR retrotransposons, an important subclass of transposable elements, are well suited for computational identification, as they contain long terminal repeats (LTRs). Results We have developed a software tool LTRharvest for the de novo detection of full length LTR retrotransposons in large sequence sets. LTRharvest efficiently delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. A quality validation of LTRharvest against a gold standard annotation for Saccharomyces cerevisae and Drosophila melanogaster shows a sensitivity of up to 90% and 97% and specificity of 100% and 72%, respectively. This is comparable or slightly better than annotations for previous software tools. The main advantage of LTRharvest over previous tools is (a) its ability to efficiently handle large datasets from finished or unfinished genome projects, (b) its flexibility in incorporating known sequence features into the prediction, and (c) its availability as an open source software. Conclusion LTRharvest is an efficient software tool delivering high quality annotation of LTR retrotransposons. It can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB of memory. Its flexibility and small space and run-time requirements makes LTRharvest a very competitive candidate for future LTR retrotransposon annotation projects. Moreover, the structured design and implementation and the availability as open source provides an excellent base for incorporating novel concepts to further improve prediction of LTR retrotransposons.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                11 November 2014
                : 5
                : 5443
                Affiliations
                [1 ]Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University , Seoul 151-921, Korea
                [2 ]Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development , IAARD, Jl. Tentara Pelajar 3A, Bogor 16111, Indonesia
                [3 ]Upland Crop Division, National Institute of Crop Science, Rural Development Administration , Suwon 441-770, Korea
                [4 ]Division of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University , Gwangju 500-757, Korea
                [5 ]Department of Plant Bioscience, College of Natural Resources & Life Science, Pusan National University , Pusan 627-706, Korea
                [6 ]Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University , Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
                [7 ]National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong , Suwon 441-707, Korea
                [8 ]The Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration , Suwon 441-707, Korea
                [9 ]L.H. Bailey Hortorium, Department of Plant Biology, Cornell University , 412 Mann Library, Ithaca, NewYork 14853, USA
                [10 ]Center for Applied Genetic Technologies, University of Georgia , Athens, Georgia, USA
                [11 ]Biotechnology/Molecular Breeding, AVRDC-The World Vegetable Center , 60, Yi-Min Liao, Tainan 74199, Taiwan
                [12 ]Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) , Hyderabad, Andhra Pradesh, India
                [13 ]Plant Genomics and Breeding Institute, Seoul National University , Seoul 151-921, Korea
                Author notes
                Article
                ncomms6443
                10.1038/ncomms6443
                4241982
                25384727
                c49a8afc-b2a7-4a22-b403-4a4427f97924
                Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

                History
                : 03 February 2014
                : 30 September 2014
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