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ABSTRACT: Chromosome-level assembly of A. thaliana accession Cvi-0 (AT6911) using PacBio sequencing.

PROVIDER: PRJEB37259 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	CAEFZF01.dat.gz	Other
	CAEFZF01.fasta.gz	Fasta.gz
	CAEFZF01.master.dat	Other

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Transcriptome profiling of ozone responses of Arabidopsis thaliana natural accessions Col-0 and Cvi-0, and a near-isogenig line Col-S with Cvi-0's ozone sensitivity introgressed into Col-0

Project description:Many Arabidopsis thaliana accession show sensitvity to the air pollutant ozone, including the accession Cvi-0 from the Cape Verde Islands. To understand and assist in genetic mapping of loci causing the ozone sensitvity of Cvi-0, transcript profiling was performed in Cvi-0, the tolerant Col-0, and a near isogenic line (Col-S) where ozone sensitivity was introgressesed from Cvi-0 to Col-0 through eight rounds of backcrossing.

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Project description:Chromosome-level assembly of A. thaliana accession Ler-0 (AT7213) using PacBio sequencing.

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Project description:Chromosome-level assembly of A. thaliana accession Col-0 (AT6909) using PacBio sequencing.

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Project description:Chromatin immunoprecipitation analysis of CENH3 in the Arabidopsis thaliana accessions Col-0, Ler-0, Cvi-0 and Tanz-1 was performed in order to align reads to PacBio HiFi genome assemblies which contain complete centromere repeat arrays.

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Project description:Chromosome-level assembly of A. thaliana accession KBS-Mac-74 (AT1741) using PacBio sequencing.

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Bulk segregant sequencing (Bulk-Seq) analysis to identify paternal suppressors of medea in Arabidopsis thaliana

Project description:Arabidopsis thaliana seeds that maternally inherit a medea (mea) mutant allele abort before completing embryogenesis. However, mea seeds can be rescued by pollen from several natural ecotypes of A. thaliana, including the Cape Verdian accession Cvi-0. We developed a method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks. The strategy is to create an F2 population that contains one set of chromosomes from the maternal parent (mea, in a Ler background) but inherits two segregating sets (Ler and Cvi-0) from the other parent. The two paternally segregating sets have opposite effects in mea penetrance: Ler fathers allow full mea seed abortion, while Cvi fathers rescue 90% of medea seeds. Therefore, the two segregating paternal sets are not equally transmitted to the next generation. DNA extracted from pools of viable F2 seedlings was sequenced on an Illumina HiSeq 2000 platform, mapped to the reference TAIR10 A. thaliana genome and the ratio between Ler and Cvi-0 SNPs used to identify chromosomal regions enriched in Cvi-0 sequences. As a control, DNA pools extracted from crosses between a wild-type Ler mother and a hybrid Cvi-0:Ler father were also sequenced. Three biological replicates were made for each pool. Ler-1 x Ler-1:Cvi-0 hybrid viable seedlings pools (each is a biological replicate): WT_pool_1, WT_pool_2, WT_pool_3 mea-1/mea-1; MEA-GR x Ler-1:Cvi-0 hybrid viable seedlings pool (each is a biological replicate): mea_pool_1, mea_pool_2, mea_pool_3

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2011-05-17 | GSE24835 | GEO

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