Sequence capture of UCEs for Rakaia antipodiana - SRA

SRX17306099: Sequence capture of UCEs for Rakaia antipodiana
1 ILLUMINA (Illumina NovaSeq 6000) run: 3.7M spots, 1.1G bases, 390.9Mb downloads

Design: UCE libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems), using up to 250 ng DNA (i.e., half reaction of manufacturers protocol) as starting material. Ampure XP beads were used for all cleanup steps. For samples containing <250 ng total, all DNA was used in library preparation. Target enrichment was performed on pooled libraries using the MYbaits Arachnida 1.1K version 1 kit (Arbor Biosciences, Ann Arbor, MI) following the Target Enrichment of Illumina Libraries v. 1.5 protocol (http://ultraconserved.org/#protocols). Hybridization was conducted at either 60 or 65 C for 24 hours, with a post-hybridization amplification of 18 cycles. Following an additional cleanup, libraries were quantified using a Qubit fluorometer and equimolar mixes were prepared for sequencing.

Submitted by: Harvard University

Study: Raw read data from multiple Cyphophthalmi libraries enriched for ultraconserved elements shared across Arachnida Raw sequence reads

PRJNA860833 • SRP394750 • All experiments • All runs

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Pettalidae is a family of mite harvestmen that inhabits the former circum-Antarctic Gondwanan terranes, including southern South America, South Africa, Madagascar, Sri Lanka, Australia and New Zealand. Australia is home to two pettalid genera, Austropurcellia, in northern NSW and QLD and Karripurcellia, in WA, with a large distributional gap between these two parts of the Australian continent. Here we report specimens of a new pettalid from South Australia, Archaeopurcellia eureka, gen. et sp. nov., closing the large distributional gap of Australian pettalids. Phylogenetic analyses using traditional Sanger markers as well as ultra-conserved elements (UCEs) reveal that the new genus is related to the Chilean Chileogovea, instead of to any of the other East Gondwanan genera. This relationship of an Australian species to a South American clade can be explained by the Antarctic land bridge connecting these two terranes, a connection that was maintained with Australia until 45 mya. The UCE dataset also shows the promise of using museum specimens to resolve relationships within Pettalidae and Cyphophthalmi.

Sample:

SAMN29868485 • SRS14867706 • All experiments • All runs

Organism: Rakaia antipodiana

Library:

Name: Rakaia antipodiana MCZ152061_2

Instrument: Illumina NovaSeq 6000

Strategy: Targeted-Capture

Source: GENOMIC

Selection: Hybrid Selection

Layout: PAIRED

Runs: 1 run, 3.7M spots, 1.1G bases, 390.9Mb

Run	# of Spots	# of Bases	Size	Published
SRR21296977	3,684,632	1.1G	390.9Mb	2022-08-29

ID:: 24126858

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