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SRX9219531: RADseq of coptotermers formosanus worker
1 ILLUMINA (Illumina HiSeq 2500) run: 6.2M spots, 1.9G bases, 580.6Mb downloads

Design: Total genomic DNA of 365 workers was extracted following a modified Gentra Puregene extraction method (Gentra Systems, Inc. Minneapolis, MN, USA), then libraries were prepared and sequenced at the Texas A&M AgriLife Genomics and Bioinformatics Service facility following the protocol of Peterson et al.48. Briefly, genomic DNA was first digested with the restriction enzymes SphI and EcoRI. Following restriction digestion, each sample was ligated with unique indexed adapters. Then, samples were PCR amplified with iProof High-Fidelity DNA Polymerase (Bio-Rad), and purified using AMPure XP beads (Beckman Coulter Inc.) to make the ddRADseq library. Each library pool was size selected to a range of 300500 bp using the BluePippin system (Sage Science Inc.). Quantity and size distribution were assessed using the Qubit 2.0 Fluorimeter (Life Technologies Corp.) and Bioanalyzer 2100 System (Agilent Technologies). Amplified fragment libraries were then pooled in equimolar amounts and sequenced on six lanes of an Illumina HiSeq 2500 machine to generate 150 bp pairend reads.
Submitted by: Texas A&M University
Study: Global invasion history of Coptotermes formosanus
show Abstracthide Abstract
In this study, we aimed to determine the origin(s) and the number of introduction events of C. formosanus out of eastern Asia and into the US. We sampled this species in both its native and introduced ranges and used double digest restriction-site associated DNA sequencing (ddRADseq48) to obtain markers of high resolution (i.e., single-nucleotide polymorphisms, or SNPs). We first conducted population structure and phylogenetic analyses of the global C. formosanus population to assess genetic structure within its native range and determine the genetic relationship between native and introduced populations. Second, we used approximate Bayesian computation (ABC) to decipher its worldwide routes of invasion. Finally, we investigated introduction-induced effects on population demography, such as population bottlenecks, expansions, migration and admixture, to assess the consequences of the invasion on the global genetic patterns of this species.
Sample:
SAMN16303341 • SRS7453310 • All experiments • All runs
Library:
Name: V0312
Instrument: Illumina HiSeq 2500
Strategy: RAD-Seq
Source: GENOMIC
Selection: Restriction Digest
Layout: PAIRED
Runs: 1 run, 6.2M spots, 1.9G bases, 580.6Mb
Run# of Spots# of BasesSizePublished
SRR127471176,239,3461.9G580.6Mb2020-11-01

ID:
12007389

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