Project Number: 6036-32000-048-08-T
Project Type: Trust Fund Cooperative Agreement
Start Date: Jul 1, 2014
End Date: Jun 30, 2019
Generate and utilize next generation sequence data to identify all of the genes in the Gp-9 non-recombining region (Sb supergene) and to determine which of these genes exhibit complete LD with Gp-9 and with social form in native fire ants.
Component 1: Genes in the Gp-9 non-recombining region. Our linkage map for S. invicta revealed that numerous scaffolds representing ~13Mb of the genome and including >600 genes are linked to Gp-9; evidently, many additional genes in this supergene region remain to be discovered and annotated. To more fully characterize the region (i.e., gene content, regulatory regions, synteny), additional sequence data will be generated to increase breadth of coverage, incorporate existing orphan contigs into the assembly, and fill in gaps in existing scaffolds. A complementary approach will be used consisting of constructing and sequencing single Illumina 20kb mate-pair and three PacBio 7-10kb mate-pair libraries. Given that there is no shortage of approaches to generate the sequence data we require, alternate, complementary strategies will be employed as deemed necessary. Assembly and alignment strategies will follow those used in our previous genome assemblies (e.g., Roche 454 Newbler software, SOAPdenovo, pacBioToCA). Component 2: Genes in complete LD with Gp-9 and social form. The degree of LD between all nucleotide variants within the Sb region, as well as between variants in reference genes outside the region, will be estimated with several different statistics using DnaSP. We predict complete LD over much or all of the supergene interval, with LD decaying rapidly outside the interval and consistently low for unlinked reference genes. We will also determine if Gp-9 haplotype block variation is completely associated with colony social form, as expected if the region constitutes a supergene. Specifically, b-like long haplotypes are predicted to invariably be represented among individuals from polygyne colonies but absent from monogyne colonies in every species.