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Boechera holboellii

ABSTRACT: Boechera holboellii overview

PROVIDER: PRJNA61541 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR3929707_1.fastq.gz	Fastqsanger.gz
	SRR3929707_2.fastq.gz	Fastqsanger.gz
	SRR3929708_1.fastq.gz	Fastqsanger.gz
	SRR3929708_2.fastq.gz	Fastqsanger.gz

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Project description:The absence of meiosis and sex are expected to lead to mutation accumulation in asexual (apomictic) plants. We have performed a double-validated analysis of copy number variation (CNV) on 10 biological replicates each of diploid sexual and diploid apomictic Boechera using a high-density (>700K) custom microarray, in order to compare mutation accumulation in the form of CNV between the transcribing regions of their genomes. The Boechera genome demonstrated higher levels of depleted compared to enriched CNV, irrespective of reproductive mode. Genome-wide patterns of CNV revealed four divergent lineages, three of which were characterized by both sexual and apomictic genotypes. Hence genome-wide CNV is reflective of at least 3 independent origins (i.e. expression) of apomixis from different sexual genetic backgrounds. CNV distributions for different families of transposable elements (TEs) were lineage specific, and a trend for enrichment in LINE/L1 and LTR/Copia elements in lineage 3 apomicts is consistent with sex and meiosis being mechanisms for purging genomic parasites. We hypothesize that significant overrepresentation of specific gene ontology classes (e.g. pollen-pistil interaction) in apomicts implies that gene enrichment could be an adaptive mechanism for genome stability in diploid apomicts by providing a polyploid-like system for buffering the effects of deleterious mutations.

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Project description:The expression of 30362 plant genes from uninfected flowers of Boechera stricta, uninfected steam and leaves of B. stricta and infected B. stricta with Puccinia monoica forming pseudoflowers. We hybridized cDNA from each sample to an Arabidopsis thaliana gene expression 4x72K format NimbleGen array (ATH6_60mer_expr). We used a eukaryotic gene expression array design No.5048 from NimbleGen (Cat No. A4511001-00-01). Each 5048 array measures the expression level of 30,362 target genes from Arabidopsis thaliana in a 4-plex format 4x72K with with 72,000 probes per array, a total of two probes per target gene, and 60-mer probe length. Total RNA samples recovered from infected leaves of Boechera stricta with Puccinia monoica (pseudoflowers) and uninfected stem and leaves of B. stricta. Experiments included three/two biological repllicates from each sample. We carried out total RNA extractions for all samples using RNAesy Plant Mini Kit (Qiagen, Cat No. 74904). cDNA synthesis was performed by NimbleGen.

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