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      Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes

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          Abstract

          Background

          Cotton ( Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD 1), G. barbadense (AD 2), G. raimondii (D 5) and G. arboreum (A 2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium.

          Results

          Six Gossypium mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups ( G. thurberi D 1, G. davidsonii D 3-d and G. trilobum D 8; G. tomentosum AD 3, G. mustelinum AD 4 and G. darwinii AD 5), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of G. arboreum (A 2), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in Gossypium presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of Gossypium. RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of G. raimondii and chromosome A03 of G. hirsutum, respectively, with insertion time less than 1.03 MYA.

          Conclusion

          Ten Gossypium mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes.

          Electronic supplementary material

          The online version of this article (10.1186/s12864-017-4282-5) contains supplementary material, which is available to authorized users.

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          Most cited references56

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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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            tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

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              Fast algorithms for large-scale genome alignment and comparison.

              We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has been used successfully to align the entire human and mouse genomes to each other, and to align numerous smaller eukaryotic and prokaryotic genomes. A new module permits the alignment of multiple DNA sequence fragments, which has proven valuable in the comparison of incomplete genome sequences. We also describe a method to align more distantly related genomes by detecting protein sequence homology. This extension to MUMmer aligns two genomes after translating the sequence in all six reading frames, extracts all matching protein sequences and then clusters together matches. This method has been applied to both incomplete and complete genome sequences in order to detect regions of conserved synteny, in which multiple proteins from one organism are found in the same order and orientation in another. The system code is being made freely available by the authors.
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                Author and article information

                Contributors
                b1301031@cau.edu.cn
                neihs@cau.edu.cn
                yumeiwang001@126.com
                15033153561@163.com
                lishuang2070114@163.com
                zhangld@sjtu.edu.cn
                +86-10-62734748 , jinping_hua@cau.edu.cn
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                13 November 2017
                13 November 2017
                2017
                : 18
                : 876
                Affiliations
                [1 ]ISNI 0000 0004 0530 8290, GRID grid.22935.3f, Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, , China Agricultural University, ; Beijing, 100193 China
                [2 ]ISNI 0000 0004 1758 5180, GRID grid.410632.2, Institute of Cash Crops, Hubei Academy of Agricultural Sciences, ; Wuhan, Hubei 430064 China
                [3 ]ISNI 0000 0004 0368 8293, GRID grid.16821.3c, Department of Plant Science, School of Agriculture and Biology, , Shanghai Jiao Tong University, ; Shanghai, 200240 China
                Article
                4282
                10.1186/s12864-017-4282-5
                5683544
                29132310
                1e79c824-bca2-47b8-8959-bf90e55047db
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.

                History
                : 10 October 2016
                : 7 November 2017
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31671741
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Genetics
                mitochondrial genomes,comparative genomics,multiple dna rearrangement,unique segments,repeat sequences,gossypium

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