UCE sequences of Mycetosoritis_explicata_534 - SRA

SRX2367888: UCE sequences of Mycetosoritis_explicata_534
1 ILLUMINA (Illumina HiSeq 2500) run: 1.3M spots, 339.6M bases, 210.4Mb downloads

Design: DNA was extracted destructively or non-destructively from worker, male or pupae ants using a DNeasy Blood and TissueKit (Qiagen, CA, USA). We quantified DNA for each sample with Qubit fluorometer (Life Technologies, Inc.) and sheared to a target size of approximately 500-600 bp by sonication (Q800; Qsonica Inc.). The sheared DNA was used as input for a modified genomic DNA library preparation protocol (Kapa Hyper Prep Library Kit, Kapa Biosystems) that incorporated Ňwith-beadÓ cleanup steps (Fisher et al. 2011) and a generic SPRI substitute (Rohland and Reich 2012, speedbeads), as described by (Faircloth et al. 2015). We used TruSeq-style adapters during adapter ligation (Faircloth and Glenn 2012), and PCR amplified 50% of the resulting library volume (15 uL) using a reaction mix of 25 _L HiFi HotStart polymerase (Kapa Biosystems), 2.5 uL each of Illumina TruSeq-style i5 and i7 primers and 5 uL double-distilled water (ddH20). We used the following thermal protocol: 98 C for 45 s; 13 cycles of 98 C for 15 s, 65 _C for 30 s, 72 C for 60 s, and final extension at 72 C for 5 m. After rehydrating in 23uL Elution Buffer (EB) and purifying reactions using speedbeads, we combined groups of eight libraries at equimolar ratios into enrichment pools. This final pool was then size-selected to a fragment range of 250Đ800 bp using the BluePippin size-selection instrument (SageScience, Beverly, MA). Size-selected library pools were sequenced as 3 partial lanes (each of the lanes included other samples) on an Illumina HiSeq 2500 (2x150 rapid run).

Submitted by: National Museum of Natural History

Study: Phylogeny of fungus-farming ant Sericomyrmex

PRJNA354064 • SRP093744 • All experiments • All runs

show Abstracthide Abstract

We use phylogenomic markers, ultraconserved elements (UCEs), to reconstruct evolutionary history, perform dating analyses, and infer species boundaries in the fungus-farming ant genus Sericomyrmex. This is first such attempt for the genus Sericomyrmex, which is known for its difficult taxonomy. Our study is the first to utilize UCEs to recover the relationships of closely related, recently diverged ant species, and we find that UCEs contain enough variation to capture recent species- and population-level divergences. Our analyses indicate that the number of species in Sericomyrmex (11) is less than previously described (19), even though we recognize 3 new species.

Sample:

SAMN06040441 • SRS1814018 • All experiments • All runs

Organism: Xerolitor explicatus

Library:

Name: 534

Instrument: Illumina HiSeq 2500

Strategy: WGS

Source: GENOMIC

Selection: Hybrid Selection

Layout: PAIRED

Runs: 1 run, 1.3M spots, 339.6M bases, 210.4Mb

Run	# of Spots	# of Bases	Size	Published
SRR5044893	1,267,645	339.6M	210.4Mb	2017-02-01

ID:: 3451562

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Recent activity