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      Genome-wide analysis of LTR-retrotransposons in oil palm.

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          Abstract

          The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world's largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences.

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          How important are transposons for plant evolution?

          Damon Lisch (2013)
          For decades, transposable elements have been known to produce a wide variety of changes in plant gene expression and function. This has led to the idea that transposable element activity has played a key part in adaptive plant evolution. This Review describes the kinds of changes that transposable elements can cause, discusses evidence that those changes have contributed to plant evolution and suggests future strategies for determining the extent to which these changes have in fact contributed to plant adaptation and evolution. Recent advances in genomics and phenomics for a range of plant species, particularly crops, have begun to allow the systematic assessment of these questions.
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            Rapid recent growth and divergence of rice nuclear genomes.

            Jianxin Ma, Jeffrey L. BENNETZEN (2004)
            By employing the nuclear DNA of the African rice Oryza glaberrima as a reference genome, the timing, natures, mechanisms, and specificities of recent sequence evolution in the indica and japonica subspecies of Oryza sativa were identified. The data indicate that the genome sizes of both indica and japonica have increased substantially, >2% and >6%, respectively, since their divergence from a common ancestor, mainly because of the amplification of LTR-retrotransposons. However, losses of all classes of DNA sequence through unequal homologous recombination and illegitimate recombination have attenuated the growth of the rice genome. Small deletions have been particularly frequent throughout the genome. In >1 Mb of orthologous regions that we analyzed, no cases of complete gene acquisition or loss from either indica or japonica were found, nor was any example of precise transposon excision detected. The sequences between genes were observed to have a very high rate of divergence, indicating a molecular clock for transposable elements that is at least 2-fold more rapid than synonymous base substitutions within genes. We found that regions prone to frequent insertions and deletions also exhibit higher levels of point mutation. These results indicate a highly dynamic rice genome with competing processes for the generation and removal of genetic variation.
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              The impact of transposable elements in environmental adaptation.

              Elena Casacuberta, Josefa González (2013)
              Transposable elements (TEs) play an important role in the responsive capacity of their hosts in the face of environmental challenges. The variety of mechanisms by which TEs influence the capacity of adaptation of the host is as large as the variety of TEs and host genomes. For example, TEs might directly affect the function of individual genes, provide a mechanism for rapidly acquiring new genetic material and disseminate regulatory elements that can lead to the creation of stress-inducible regulatory networks. In this review, we summarize recent examples that are part of an increasing body of evidence suggesting a significant role of TEs in the host response to an ever-changing environment, both in prokaryote and in eukaryote organisms. We argue that in the near future, the increasing availability of genome sequences and the development of new tools to discover and analyse TE insertions will further show the relevant role of TEs in environmental adaptation. © 2013 Blackwell Publishing Ltd.
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                Author and article information

                Journal
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC genomics
                Publisher: Springer Science and Business Media LLC
                ISSN (Electronic): 1471-2164
                ISSN (Print): 1471-2164
                Publication date (Electronic): Oct 15 2015
                Volume: 16
                Affiliations
                [1 ] CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France. thierry.beule@cirad.fr.
                [2 ] CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France. mawusse.agbessi@gmail.com.
                [3 ] IRD, UMR DIADE (IRD, UM), 34394, Montpellier, France. stephane.dussert@ird.fr.
                [4 ] CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France. estelle.jaligot@cirad.fr.
                [5 ] IRD, UMR IPME (IRD, CIRAD, UM), 34394, Montpellier, France. romain.guyot@ird.fr.
                Article
                Publisher Item ID: 10.1186/s12864-015-2023-1
                DOI: 10.1186/s12864-015-2023-1
                PMC ID: 4608283
                PubMed ID: 26470789
                SO-VID: 3e657cc2-e954-4352-929d-d2d3eb50abdf
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