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Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana Arabis alpina Arabidopsis lyrata

PROVIDER: GSE54728 | GEO | 2015/02/03

SECONDARY ACCESSION(S): PRJNA237511

REPOSITORIES: GEO

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Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

Project description:Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

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Complete Arabis alpina chloroplast genome sequence and insight into its polymorphism.

Project description:The alpine plant Arabis alpina (alpine rock-cress) is a thoroughly studied species in the fields of perennial plant flowering regulation, phylogeography, and adaptation to harsh alpine climatic conditions. We report the complete A. alpina chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The A. alpina cp circular genome is 152,866 bp in length and built of two inverted repeats of 26,933 bp separated by unique regions: a large single copy of 82,338 bp and a small single copy of 17,938 bp. The genome contains 131 genes, some of them being duplicated in the inverted repeats. Seventy-nine unique protein-coding genes were annotated, together with 29 tRNA genes and 4 ribosomal RNA genes. Sequencing and mapping of 23 additional A. alpina DNA samples enabled to gain insight into the intraspecies polymorphism of the sequenced cp genome. Genetic variability among genomes was detected as 44 indels, most of them being located in noncoding regions, and 130 single-nucleotide polymorphisms, 37 of them corresponding to mutations in coding regions. A. alpina chloroplast genome sequence will be helpful in population studies or investigations of chloroplast functions of this alpine plant species.

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Analysis of TTG1 function in Arabis alpina.

Project description:BACKGROUND: In Arabidopsis thaliana (A. thaliana) the WD40 protein TRANSPARENT TESTA GLABRA1 (TTG1) controls five traits relevant for the adaptation of plants to environmental changes including the production of proanthocyanidin, anthocyanidin, seed coat mucilage, trichomes and root hairs. The analysis of different Brassicaceae species suggests that the function of TTG1 is conserved within the family. RESULTS: In this work, we studied the function of TTG1 in Arabis alpina (A. alpina). A comparison of wild type and two Aattg1 alleles revealed that AaTTG1 is involved in the regulation of all five traits. A detailed analysis of the five traits showed striking phenotypic differences between A. alpina and A. thaliana such that trichome formation occurs also at later stages of leaf development and that root hairs form at non-root hair positions. CONCLUSIONS: The evolutionary conservation of the regulation of the five traits by TTG1 on the one hand and the striking phenotypic differences make A. alpina a very interesting genetic model system to study the evolution of TTG1-dependent gene regulatory networks at a functional level.

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Project description:Arabis alpina (A. alpina) is an arctic-alpine flowering plant in the family Brassicaceae, naturally growing in the tundra of arctic regions and in mountains at southern latitudes. In this study, we first report the assembly of the complete A. alpina mitochondrial (mt) genome using the next-generation sequencing technologies. The A. alpina mt circular genome is 323,159 bp in length and contains 33 protein-coding genes, 18 tRNA genes and 3 rRNA genes. To analyze the phylogenic and evolutional relationship of A. alpina, a neighbour-joining phylogenetic tree was reconstructed based on the mt genome of A. alpina and other 27 plants. The complete A. alpina mt genome will be helpful in population studies or investigations of mt functions of these alpine plant species.

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Project description:Whole-genome resequencing of Arabis alpina populations from Swiss Alps.