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SRX2424879: UCE target enrichment of Pseudomyrmex_veneficus_D0624: whole organsim
1 ILLUMINA (Illumina HiSeq 2500) run: 4.6M spots, 1.2G bases, 587.6Mb downloads

Design: DNA was extracted from single ants, usually workers or worker pupae, using the DNeasy Blood and Tissue Kit (Qiagen Inc., Valencia, California, U.S.A.), and quantified using a Qubit fluorometer (HS Assay Kit, Life Technologies Inc., Carlsbad, CA). We sheared 10-138 ng input DNA to a target size of approximately 600 bp by sonication using a Diagenode BioRuptor (Diagenode Inc., Denville, NJ), and this product served as input for a modified genomic DNA library preparation protocol (Kapa Hyper Prep Library Kit, Kapa Biosystems) that included SPRI bead cleanup using an AMPure substitute and custom dual-indexing barcodes (iTru). For UCE enrichment we pooled 8Đ10 libraries together at equimolar concentrations and adjusted pool concentrations to 147 ng/_l. For each enrichment we used a total of 500 ng of DNA (3.4 _l each pool), and we performed enrichments using a custom RNA bait library developed for ants and synthesized by MYcroarray (Ann Arbor, MI). The probe set includes 9,446 probes, targeting 2,524 UCE loci. Although the probe set targets loci that are likely to be present across Hymenoptera, it is ant-specific because the probes used were designed from ant genomes only (Harpegnathos saltator and Atta cephalotes). For each enrichment we hybridized the RNA bait libraries to sequencing libraries at 65ĄC for 24 hours and we followed a standardized, in-solution enrichment protocol (version 1.5; protocol available from http://ultraconserved.org). Following enrichment we quantified the DNA concentration of enriched pools using qPCR and we used these values to make an equimolar pool-of-pools, containing up to 102 individual samples. These pools were submitted to the High Throughput Genomics Core Facility, Huntsman Cancer Institute, University of Utah, where they were quality checked, quantified with qPCR, and sequenced on an Illumina HiSeq 2500 (125 cycle paired-end sequencing, v4 chemistry).
Submitted by: University of Utah
Study: The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism
show Abstracthide Abstract
Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. Here we use a phylogenomic approach—ultraconserved element (UCE) sequence capture—to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system the ants receive shelter and food from the hostplant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behavior, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the preexisting mutualism. Initiation of the Pseudomyrmex/Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.
Sample: D0624
SAMN06141958 • SRS1861085 • All experiments • All runs
Library:
Name: Pseudomyrmex_veneficus_D0624
Instrument: Illumina HiSeq 2500
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 4.6M spots, 1.2G bases, 587.6Mb
Run# of Spots# of BasesSizePublished
SRR51125314,633,9311.2G587.6Mb2017-03-01

ID:
3520668

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