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Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants.

Novikova O, Smyshlyaev G, Blinov A - BMC Genomics (2010)

Bottom Line: Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates.Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes.Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the 'retained' genes theory or by horizontal transmission.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Molecular Genetic Systems, Institute of Cytology and Genetics, Novosibirsk, Russia. novikova@bionet.nsc.ru

ABSTRACT

Background: Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta) suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes.

Results: In present study we preformed in silico analysis of chromodomain-containing LTR retrotransposons in 25 diverse fungi and a number of plant species including spikemoss Selaginella moellendorffii (Lycopodiophyta) coupled with an experimental survey of chromodomain-containing Gypsy LTR retrotransposons from diverse non-seed vascular plants (lycophytes, ferns, and horsetails). Our mining of Gypsy LTR retrotransposons in genomic sequences allowed identification of numerous families which have not been described previously in fungi. Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes. It appeared that one of the clades, namely Tcn1 clade, was present in basidiomycetes and non-seed plants including mosses (Bryophyta) and lycophytes (genus Selaginella).

Conclusions: The interkingdom distribution is not typical for chromodomain-containing LTR retrotransposons clades which are usually very specific for a particular taxonomic group. Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the 'retained' genes theory or by horizontal transmission.

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Neighbor-joining (NJ) phylogenetic trees based on RT and partial Int amino acid sequences of Gypsy LTR retrotransposons including newly described fungal chromodomain-containing LTR retrotransposons. Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The clades are shown on the right. The name of the host species and accession number are indicated for all elements taken from GenBank. Newly identified retrotransposons are highlighted in bold; localization in genomic sequence is indicated for each of them. Genomic sequences of Trichoderma reesei QM6a, Trichoderma virens Gv29-8, Nectria haematococca MPVI, Aspergillus niger ATCC1015, Alternaria brassicicola ATCC 96866, Stagonospora nodorum SN15, Laccaria bicolor S238N, Postia placenta MAD-698, and Sporobolomyces roseus have been taken from The DOE Joint Genome Institute [55]; the following species are available at Broad Institute [54]: Chaetomium globosum CBS 148.51; Fusarium oxysporum 4286 FGSC;Fusarium verticillioides 7600; Aspergillus clavatus NRRL 1; Aspergillus terreus NIH2624; Coccidioides immitis RS; Histoplasma capsulatum NAm1; Uncinocarpus reesii 1704; Sclerotinia sclerotiorum 1980; Botrytis cinerea B05.10; Pyrenophora tritici-repentis Pt-1C-BFP; Coprinus cinereus okayama7#130; Puccinia graminis f. sp. tritici; Batrachochytrium dendrobatidis JEL423. The possible horizontal transmission (HT) is marked. For more details: Additional files 1, 5 and 6.
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Figure 2: Neighbor-joining (NJ) phylogenetic trees based on RT and partial Int amino acid sequences of Gypsy LTR retrotransposons including newly described fungal chromodomain-containing LTR retrotransposons. Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The clades are shown on the right. The name of the host species and accession number are indicated for all elements taken from GenBank. Newly identified retrotransposons are highlighted in bold; localization in genomic sequence is indicated for each of them. Genomic sequences of Trichoderma reesei QM6a, Trichoderma virens Gv29-8, Nectria haematococca MPVI, Aspergillus niger ATCC1015, Alternaria brassicicola ATCC 96866, Stagonospora nodorum SN15, Laccaria bicolor S238N, Postia placenta MAD-698, and Sporobolomyces roseus have been taken from The DOE Joint Genome Institute [55]; the following species are available at Broad Institute [54]: Chaetomium globosum CBS 148.51; Fusarium oxysporum 4286 FGSC;Fusarium verticillioides 7600; Aspergillus clavatus NRRL 1; Aspergillus terreus NIH2624; Coccidioides immitis RS; Histoplasma capsulatum NAm1; Uncinocarpus reesii 1704; Sclerotinia sclerotiorum 1980; Botrytis cinerea B05.10; Pyrenophora tritici-repentis Pt-1C-BFP; Coprinus cinereus okayama7#130; Puccinia graminis f. sp. tritici; Batrachochytrium dendrobatidis JEL423. The possible horizontal transmission (HT) is marked. For more details: Additional files 1, 5 and 6.

Mentions: Twenty monophyletic clades can be recognized in the phylogenetic tree of fungal CHD-containing Gypsy LTR retrotransposons, nine of which have been previously reported [3]. Thirteen clades are specific for ascomycetes (Nessie, Pyret, Maggy, Pyggy, MGLR3, Yeti, Coccy1, Coccy2, Polly, Afut1, Tf1, Ty3, and Afut4), six have been found only in genomes of basidiomycetes (MarY1, Laccy1, Laccy2, Tcn2, Puccy1, and Puccy2) and one clade (Tcn1) is present in both basidiomycetes and chytridiomycetes (Batrachochytrium dendrobatidis JEL423) (Figure 2).


Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants.

Novikova O, Smyshlyaev G, Blinov A - BMC Genomics (2010)

Neighbor-joining (NJ) phylogenetic trees based on RT and partial Int amino acid sequences of Gypsy LTR retrotransposons including newly described fungal chromodomain-containing LTR retrotransposons. Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The clades are shown on the right. The name of the host species and accession number are indicated for all elements taken from GenBank. Newly identified retrotransposons are highlighted in bold; localization in genomic sequence is indicated for each of them. Genomic sequences of Trichoderma reesei QM6a, Trichoderma virens Gv29-8, Nectria haematococca MPVI, Aspergillus niger ATCC1015, Alternaria brassicicola ATCC 96866, Stagonospora nodorum SN15, Laccaria bicolor S238N, Postia placenta MAD-698, and Sporobolomyces roseus have been taken from The DOE Joint Genome Institute [55]; the following species are available at Broad Institute [54]: Chaetomium globosum CBS 148.51; Fusarium oxysporum 4286 FGSC;Fusarium verticillioides 7600; Aspergillus clavatus NRRL 1; Aspergillus terreus NIH2624; Coccidioides immitis RS; Histoplasma capsulatum NAm1; Uncinocarpus reesii 1704; Sclerotinia sclerotiorum 1980; Botrytis cinerea B05.10; Pyrenophora tritici-repentis Pt-1C-BFP; Coprinus cinereus okayama7#130; Puccinia graminis f. sp. tritici; Batrachochytrium dendrobatidis JEL423. The possible horizontal transmission (HT) is marked. For more details: Additional files 1, 5 and 6.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864245&req=5

Figure 2: Neighbor-joining (NJ) phylogenetic trees based on RT and partial Int amino acid sequences of Gypsy LTR retrotransposons including newly described fungal chromodomain-containing LTR retrotransposons. Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The clades are shown on the right. The name of the host species and accession number are indicated for all elements taken from GenBank. Newly identified retrotransposons are highlighted in bold; localization in genomic sequence is indicated for each of them. Genomic sequences of Trichoderma reesei QM6a, Trichoderma virens Gv29-8, Nectria haematococca MPVI, Aspergillus niger ATCC1015, Alternaria brassicicola ATCC 96866, Stagonospora nodorum SN15, Laccaria bicolor S238N, Postia placenta MAD-698, and Sporobolomyces roseus have been taken from The DOE Joint Genome Institute [55]; the following species are available at Broad Institute [54]: Chaetomium globosum CBS 148.51; Fusarium oxysporum 4286 FGSC;Fusarium verticillioides 7600; Aspergillus clavatus NRRL 1; Aspergillus terreus NIH2624; Coccidioides immitis RS; Histoplasma capsulatum NAm1; Uncinocarpus reesii 1704; Sclerotinia sclerotiorum 1980; Botrytis cinerea B05.10; Pyrenophora tritici-repentis Pt-1C-BFP; Coprinus cinereus okayama7#130; Puccinia graminis f. sp. tritici; Batrachochytrium dendrobatidis JEL423. The possible horizontal transmission (HT) is marked. For more details: Additional files 1, 5 and 6.
Mentions: Twenty monophyletic clades can be recognized in the phylogenetic tree of fungal CHD-containing Gypsy LTR retrotransposons, nine of which have been previously reported [3]. Thirteen clades are specific for ascomycetes (Nessie, Pyret, Maggy, Pyggy, MGLR3, Yeti, Coccy1, Coccy2, Polly, Afut1, Tf1, Ty3, and Afut4), six have been found only in genomes of basidiomycetes (MarY1, Laccy1, Laccy2, Tcn2, Puccy1, and Puccy2) and one clade (Tcn1) is present in both basidiomycetes and chytridiomycetes (Batrachochytrium dendrobatidis JEL423) (Figure 2).

Bottom Line: Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates.Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes.Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the 'retained' genes theory or by horizontal transmission.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Molecular Genetic Systems, Institute of Cytology and Genetics, Novosibirsk, Russia. novikova@bionet.nsc.ru

ABSTRACT

Background: Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta) suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes.

Results: In present study we preformed in silico analysis of chromodomain-containing LTR retrotransposons in 25 diverse fungi and a number of plant species including spikemoss Selaginella moellendorffii (Lycopodiophyta) coupled with an experimental survey of chromodomain-containing Gypsy LTR retrotransposons from diverse non-seed vascular plants (lycophytes, ferns, and horsetails). Our mining of Gypsy LTR retrotransposons in genomic sequences allowed identification of numerous families which have not been described previously in fungi. Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes. It appeared that one of the clades, namely Tcn1 clade, was present in basidiomycetes and non-seed plants including mosses (Bryophyta) and lycophytes (genus Selaginella).

Conclusions: The interkingdom distribution is not typical for chromodomain-containing LTR retrotransposons clades which are usually very specific for a particular taxonomic group. Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the 'retained' genes theory or by horizontal transmission.

Show MeSH
Related in: MedlinePlus