Hyb-seq of Alyssum minutum 541IDA4 - SRA

SRX19448749: Hyb-seq of Alyssum minutum 541IDA4
1 ILLUMINA (Illumina MiSeq) run: 571,229 spots, 171.6M bases, 84.1Mb downloads

Design: The amount of 400-800 ng of Genomic DNA per accession was fragmented to a target fragment size of 500 bp using a Covaris M220 sonicator (Woburn, MA, United States). Sequencing libraries were prepared using the NEBNext UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, MA, United States) following the manufacturers protocol with some modifications. After adaptor ligation, DNA fragments were purified using the QIAquick PCR Purification Kit (Qiagen) and selected to asize range of 500-600 bp using SPRIselect beads (Beckman Coulter, MA, United States). PCR enrichment was then performed with eight cycles using index primers from NEBNext Multiplex Oligos for Illumina. The amplified libraries were cleaned up with AMPure XP beads (Beckman Coulter), measured using a Qubit 2.0 fluorometer (ThermoFisher Scientific, MA, United States), and pooled equimolarly (24 accessions/pool). The pooled libraries were size-selected with SPRIselect beads as described above and measured again with the Qubit 2.0. Aliquots containing 200-350 ng were enriched by hybridization with synthesized RNA baits (26 h at 65C) using the myBaits kit, following the protocol v. 4.01 (Arbor Biosciences, MI, United States). The target-enriched libraries were amplified by PCR with nine cycles using the KAPA HiFi HotStart mix (Kapa Biosystems, Wilmington, MA, United States) and purified with the QIAquick PCR Purification Kit. Enriched and unenriched library aliquots were pooled at a ratio of 2:1, finally purified with AMPure XP beads, and submitted for sequencing with 150-bp paired-end reads on an Illumina MiSeq system.

Submitted by: Plant Science and Biodiversity Centre; Slovak Academy of Sciences

Study: Phylogenomics of the Alyssum montanum-A. repens species complex

PRJNA863918 • SRP388961 • All experiments • All runs

show Abstracthide Abstract

Genome skim data of Alyssum gmelinii and Odontarrhena tortuosa (both tribe Alysseae, Brassicaceae) were generated to develop Hyb-Seq probes for target enrichment in both genera. Then, we reconstructed phylogenetic relationships in the Alyssum montanum-A. repens (Brassicaceae) species complex using these probes targeting 2,081 genes. In addition, we recovered the parentage of several polyploids from this complex.

Sample: Plant sample from Alyssum minutum

SAMN33387256 • SRS16841840 • All experiments • All runs

Organism: Alyssum minutum

Library:

Name: 541IDA4

Instrument: Illumina MiSeq

Strategy: Targeted-Capture

Source: GENOMIC

Selection: Hybrid Selection

Layout: PAIRED

Runs: 1 run, 571,229 spots, 171.6M bases, 84.1Mb

Run	# of Spots	# of Bases	Size	Published
SRR23561746	571,229	171.6M	84.1Mb	2023-02-21

ID:: 26723297

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