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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 tree based on RT nucleotide sequences of CHD-containing Gypsy LTR retrotransposons including newly described elements from monilophytes and lycophytes plants (highlighted in bold). Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The name of the host species and accession number are indicated for LTR retrotransposons taken from GenBank. Four diverse clusters of LTR retrotransposons from mosses, monilophytes and lycophytes are shown by arrows. The group of Tcn1-like LTR retrotransposons from mosses (Bryophyta) is also indicated. Previously known clades, clades described in this study, and unclassified lineages (a-f) are shown on the right.
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Figure 4: Neighbor-joining (NJ) phylogenetic tree based on RT nucleotide sequences of CHD-containing Gypsy LTR retrotransposons including newly described elements from monilophytes and lycophytes plants (highlighted in bold). Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The name of the host species and accession number are indicated for LTR retrotransposons taken from GenBank. Four diverse clusters of LTR retrotransposons from mosses, monilophytes and lycophytes are shown by arrows. The group of Tcn1-like LTR retrotransposons from mosses (Bryophyta) is also indicated. Previously known clades, clades described in this study, and unclassified lineages (a-f) are shown on the right.

Mentions: Further phylogenetic analysis revealed that previously described CHD-containing LTR retrotransposons from mosses including PpatensLTR retrotransposons isolated from genomic sequence of moss Physcomitrella patens formed a common branch with Tcn1-like LTR retrotransposons from fungi (Figure 4) [8]. In an attempt to determine the distribution of the Tcn1clade among plants, we used public databases for further survey of LTR retrotransposons including genomic databases for red and green algae, spikemoss Selaginella moellendorffii, and seed plants (see Materials and Methods section). A Tcn1-like LTR retrotransposon search was implemented with BLAST (blastp and blastx). Amino acid sequences of RT and Int domains of known Tcn1-like (Tcn1 from C. neoformans, Ccchromovir1 and Ccchromovir2 from C. cinereus, PcMetavir6 from Phanerochaete chrysosporium, and PpatensLTRs from P. patens) and newly identified retrotransposons (SpoRosTy3-4 and BatDenTy3-1) were used as the queries. The Tcn1-like LTR retrotransposons were identified only in the whole genomic sequence of Selaginella moellendorffii (SM-Tcn1, Figure 4); none of the tested algae or seed plant genomes contained LTR retrotransposons from this clade. It seems that the Tcn1 clade can be found in basidiomycetes and chytridiomycetes fungi as well as non-seed plants (Bryophyta and Lycopodiophyta).


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 tree based on RT nucleotide sequences of CHD-containing Gypsy LTR retrotransposons including newly described elements from monilophytes and lycophytes plants (highlighted in bold). Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The name of the host species and accession number are indicated for LTR retrotransposons taken from GenBank. Four diverse clusters of LTR retrotransposons from mosses, monilophytes and lycophytes are shown by arrows. The group of Tcn1-like LTR retrotransposons from mosses (Bryophyta) is also indicated. Previously known clades, clades described in this study, and unclassified lineages (a-f) are shown on the right.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Neighbor-joining (NJ) phylogenetic tree based on RT nucleotide sequences of CHD-containing Gypsy LTR retrotransposons including newly described elements from monilophytes and lycophytes plants (highlighted in bold). Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are indicated. The name of the host species and accession number are indicated for LTR retrotransposons taken from GenBank. Four diverse clusters of LTR retrotransposons from mosses, monilophytes and lycophytes are shown by arrows. The group of Tcn1-like LTR retrotransposons from mosses (Bryophyta) is also indicated. Previously known clades, clades described in this study, and unclassified lineages (a-f) are shown on the right.
Mentions: Further phylogenetic analysis revealed that previously described CHD-containing LTR retrotransposons from mosses including PpatensLTR retrotransposons isolated from genomic sequence of moss Physcomitrella patens formed a common branch with Tcn1-like LTR retrotransposons from fungi (Figure 4) [8]. In an attempt to determine the distribution of the Tcn1clade among plants, we used public databases for further survey of LTR retrotransposons including genomic databases for red and green algae, spikemoss Selaginella moellendorffii, and seed plants (see Materials and Methods section). A Tcn1-like LTR retrotransposon search was implemented with BLAST (blastp and blastx). Amino acid sequences of RT and Int domains of known Tcn1-like (Tcn1 from C. neoformans, Ccchromovir1 and Ccchromovir2 from C. cinereus, PcMetavir6 from Phanerochaete chrysosporium, and PpatensLTRs from P. patens) and newly identified retrotransposons (SpoRosTy3-4 and BatDenTy3-1) were used as the queries. The Tcn1-like LTR retrotransposons were identified only in the whole genomic sequence of Selaginella moellendorffii (SM-Tcn1, Figure 4); none of the tested algae or seed plant genomes contained LTR retrotransposons from this clade. It seems that the Tcn1 clade can be found in basidiomycetes and chytridiomycetes fungi as well as non-seed plants (Bryophyta and Lycopodiophyta).

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