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Lo7 - WGS assemblies

ABSTRACT: Data produced in the phylogenetic analysis of Secale genetic diversity presented in the 2019-2020 rye (Secale cereale L. inbred line 'Lo7') genome assembly release by the International Rye Genome Consortium (IRGSC)

PROVIDER: PRJEB35879 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR3771520_1.fastq.gz	Fastqsanger.gz
	ERR3771520_2.fastq.gz	Fastqsanger.gz
	ERR3771530_1.fastq.gz	Fastqsanger.gz
	ERR3771530_2.fastq.gz	Fastqsanger.gz
	ERR3771521_1.fastq.gz	Fastqsanger.gz

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Project description:The present transcript profiling compares the gene expression during cold-acclimation in different genotypes of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.) and rye (Secale cereale L.) in order to determine factors influencing frost tolerance. Because of its outstanding robustness against adverse environmental conditions rye is considered to be a model species for abiotic stress tolerance. Wheat is moderate frost-tolerant and barley is most sensitive species in this study. The aim of this study elucidate conserved, as well as, species-specific gene regulation across the Triticeae. Furthermore, transcript abundances were correlated between the distinct frost tolerances of genotypes within each species in order to find candidate genes for frost tolerance.

2013-11-30 | GSE47882 | GEO

Secale cereale L. inbred line 'Lo7' Illumina RNA-Seq and PacBio Sequel reads

Project description:Secale cereale L. inbred line 'Lo7' genome assembly paper Rabanus-Wallace et. al

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Centromere misdivision promotes centromeric sequence changes, de novo centromere formation, and centromere expansion

Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids. ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).

2016-04-02 | E-GEOD-63752 | biostudies-arrayexpress

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