Dataset Information

Genomic, RNA, and ecological divergences of the Revolver transposon-like multi-gene family in Triticeae.

ABSTRACT: BACKGROUND: Revolver is a newly discovered multi-gene family of transposable elements in the Triticeae genome. Revolver encompasses 2929 to 3041 bp, has 20 bp of terminal inverted repeated sequences at both ends, and contains a transcriptionally active gene encoding a DNA-binding-like protein. A putative TATA box is located at base 221, with a cap site at base 261 and a possible polyadenylation signal AATAAA at base 2918. Revolver shows considerable quantitative variation in wheat and its relatives. RESULTS: Revolver cDNAs varied between 395 and 2,182 bp in length. The first exon exhibited length variation, but the second and third exons were almost identical. These variants in the Revolver family shared the downstream region of the second intron, but varied structurally at the 5' first exon. There were 58 clones, which showed partial homology to Revolver, among 440,000 expressed sequence tagged (EST) clones sourced from Triticeae. In these Revolver homologues with lengths of 360-744 bp, the portion after the 2nd exon was conserved (65-79% homology), but the 1st exon sequences had mutually low homology, with mutations classified into 12 types, and did not have EST sequences with open reading frames (ORFs). By PCR with the 3'-flanking region of a typical genomic clone of Revolver-2 used as a single primer, rye chromosomes 1R and 5R could be simultaneously identified. Extensive eco-geographic diversity and divergence was observed among 161 genotypes of the single species Triticum dicoccoides collected from 18 populations in Israel with varying exposures to abiotic and biotic stresses (soil, temperature, altitude, water availability, and pathogens). CONCLUSIONS: On the base of existing differences between Revolver variants, the molecular markers that can distinguish different rye chromosomes were developed. Eco-geographic diversification of wild emmer T. dicoccoides in Israel and high Revolver copy numbers are associated with higher rainfall and biotic stresses. The remarkable quantitative differences among copy numbers of Revolver in the same species from different ecosystems suggest strong amplification activity within the last 10,000 years. It is the interesting finding because the majority of Triticeae high-copy transposable elements seem to be inactive at the recent time except for BARE-1 element in Hordeum and the fact might be interesting to perceive the processes of plant adaptive evolution.

SUBMITTER: Tomita M

PROVIDER: S-EPMC3203089 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Genomic, RNA, and ecological divergences of the Revolver transposon-like multi-gene family in Triticeae.

Tomita Motonori M Okutani Asuka A Beiles Avigdor A Nevo Eviatar E

BMC evolutionary biology 20110925

<h4>Background</h4>Revolver is a newly discovered multi-gene family of transposable elements in the Triticeae genome. Revolver encompasses 2929 to 3041 bp, has 20 bp of terminal inverted repeated sequences at both ends, and contains a transcriptionally active gene encoding a DNA-binding-like protein. A putative TATA box is located at base 221, with a cap site at base 261 and a possible polyadenylation signal AATAAA at base 2918. Revolver shows considerable quantitative variation in wheat and its ...[more]

PMID: 21943048

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Project description:BackgroundMembers of the Early Salt Induced 3 (Esi3/RCI2/PMP3) gene family in plants have been shown to be induced in response to both biotic and abiotic stresses and to enhance stress tolerance in both transgenic plants and Saccharomyces cerevisiae. Esi3 was first identified as a salt stress induced gene in the salt tolerant wild wheat grass, Lophopyrum elongatum, and subsequently homologous genes in many other species were found to be members of the gene family. These include Arabidopsis thaliana and Oryza sativa where they are referred to as Rare Cold Inducible 2 (RCI2), and Zea mays where they are referred to as Plasma Membrane Protein 3 (PMP3). This study characterizes the Esi3 family members in Triticum aestivum and explores the tissue specific expression patterns of the gene family members as well as their response to a variety of environmental stresses.ResultsThe Esi3 gene family was found to have a total of 29 family members comprised of ten paralogous groups in the hexaploid T. aestivum. Each paralogous group contains three homeologous copies, one in each of the A, B and D genomes with the exception of Esi3-2 which is missing the B copy. The genes of the Esi3 gene family were also identified in four other monocot species, Aegilops tauschii, Hordeum vulgare, Secale cereale and Sorghum bicolor, and were confirmed or corrected for Brachypodium distachyon, Oryza sativa and Zea mays, as well as the dicot Arabidopsis thaliana. Gene expression of the Esi3s was analyzed using tissue-specific, abiotic and biotic stress RNA-Seq 454 sequence libraries and Affymetrix microarray data for T. aestivum.ConclusionsMembers of nearly all paralogous groups of the Esi3 genes in T. aestivum have altered gene expression in response to abiotic or biotic stress conditions. In addition, there are modest differences in gene expression among homeologous members of the gene family. This suggests that the Esi3 gene family plays an important role in the plants response to the stresses presented in this study. The Esi3-9 in T. aestivum has a unique N terminal extension placing it into Group III, a new group for the Esi3/RCI2/PMP3 gene family.

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Dataset Information

Genomic, RNA, and ecological divergences of the Revolver transposon-like multi-gene family in Triticeae.

Publications

Genomic, RNA, and ecological divergences of the Revolver transposon-like multi-gene family in Triticeae.

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