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ERX2096106: Illumina HiSeq 2000 paired end sequencing
1 ILLUMINA (Illumina HiSeq 2000) run: 17.8M spots, 2.7G bases, 1.7Gb downloads

Submitted by: Centro Nacional de Análisis Genómico
Study: Drosophila guanche genome
show Abstracthide Abstract
Drosophila guanche is a member of the obscura group that originated in the Canary Islands archipelago upon its colonization by D. subobscura. It evolved into a new species in the laurisilva, a laurel forest present in wet regions that in the islands have only minor long-term weather fluctuations. Oceanic island endemic species such as D. guanche can become a model species to investigate not only the relative role of drift and adaptation in speciation processes but also how population size affects nucleotide variation. Moreover, the previous identification of two satellite DNAs in D. guanche makes this species attractive for studying how centromeric DNA evolves. As a prerequisite for its establishment as a model species suitable to address all these questions, we generated a high-quality D. guanche genome sequence composed of 42 cytologically-mapped scaffolds, which are assembled into six super-scaffolds (one per chromosome). The comparative analysis of the D. guanche proteome with that of twelve other Drosophila species identified 151 genes that were subject to adaptive evolution in the D. guanche lineage, with a subset of them being involved in flight and genome stability. For example, the Centromere Identifier (CID) protein, directly interacting with centromeric satellite DNA, shows signals of adaptation in this species. Both genomic analyses and FISH of the two satellites would support an ongoing replacement of centromeric satellite DNA in D. guanche.
Sample: RNA sample from embryos
SAMEA104164777 • ERS1823795 • All experiments • All runs
Library:
Name: 322Q
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: Oligo-dT
Layout: PAIRED
Construction protocol: 500 ng of total RNA were used as the input material and enriched for the m RNA fraction using oligo-dT magnetic beads. The mRNA was fragmented in the presence of divalent metal cations and at high temperature (resulting RNA fragment size was 80- 250 nt, with the major peak at 130nt). After first and second strand cDNA synthesis, the double stranded cDNA was end- repaired, 3 ́adenylated, and thereafter ligated to the Illumina barcoded adapters. After ligation, the product was enriched by 15 cycles of PCR.
Runs: 1 run, 17.8M spots, 2.7G bases, 1.7Gb
Run# of Spots# of BasesSizePublished
ERR203704917,849,7402.7G1.7Gb2018-07-07

ID:
5923514

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