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SRX8472921: Seq-Cap of Griffinia alba
1 ILLUMINA (Illumina HiSeq 3000) run: 5.2M spots, 1.6G bases, 622Mb downloads

Design: We contracted with RapidGenomics, Inc. (Gainesville, FL) for sequence capture and initial bioinformatic analysis. We provided two floral transcriptomes previously obtained through Beijing Genomics Institute (Shenzhen, China) from Griffinia liboniana C. Morren and Rauhia staminosa Ravenna for probe design. Putative orthologous single-copy nuclear (SCN) loci for the transcriptomes were identified by MarkerMiner 1.0 (Chamala et al., 2015) using minimum unigene length of 300 bp and the SCN gene reference set of Oryza sativa L. curated by De Smet et al. (2013). MarkerMiner identified 751 SCN orthogroups which were reduced to 735 loci by excluding the orthogroups containing apparent paralogues. DNA libraries were made by random mechanical shearing of our genomic DNA to an average size of 400 bp followed by an end-repair reaction, ligation of an adenine residue to the 3-end of the blunt-end fragments to allow the ligation of barcoded adapters, and PCR-amplification of the library. SureSelect probes (Agilent Technologies, Santa Clara, CA) were used for solution-based target enrichment of a pool of 16 libraries following the SureSelectxt Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library protocol. Data was sequenced using Illumina HiSeq 3000 (Illumina, San Diego, CA) to generate paired-end 100-bp reads.
Submitted by: USDA-ARS
Study: Phylogenomics of the Andean tetraploid clade of the American Amaryllidaceae (subfamily Amaryllidioideae)
show Abstracthide Abstract
The second large clade of the endemic American Amaryllidaceae subfam. Amaryllidoideae constitutes the tetraploid-derived (n = 23) Andean-centered tribes, most of which have 46 chromosomes. Despite progress in resolving phylogenetic relationships of the group with nrDNA, certain subclades were poorly resolved or weakly supported in those previous studies. Sequence capture using anchored hybrid enrichment was employed across 95 species of the clade along with five outgroups and generated sequences of 524 nuclear genes and a partial plastome. Maximum likelihood phylogenetic analyses were conducted on concatenated supermatrices, and coalescent species tree analyses were run on the gene trees, followed by hybridization network, age diversification and biogeographic analyses.
Sample: P02_WE04
SAMN15066134 • SRS6773263 • All experiments • All runs
Organism: Griffinia alba
Library:
Name: P02_WE04
Instrument: Illumina HiSeq 3000
Strategy: Targeted-Capture
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 5.2M spots, 1.6G bases, 622Mb
Run# of Spots# of BasesSizePublished
SRR119273715,223,4081.6G622Mb2020-11-20

ID:
11013686

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