Closing Gaps in the Genome of the Fire Ant Solenopsis invicta
Date Issued
2014
Date
2014
Author(s)
Huang, Xinyu Toby
Abstract
With the rapid development of new sequencing technologies and the drastic reduction to sequencing costs, genome wide sequencing studies can now be applied to non-model organisms that do not have established reference genomes. The recent publication of the genome of the invasive fire ant Solenopsis invicta is a good example of how such new advances in next generation sequencing technologies can be readily adopted for an economically and ecologically important non-model species. Nevertheless, limitations of the sequencing and assembly technologies create difficulties in achieving complete coverage of the entire genome. These newly assembled genomes are considered draft genomes, because they contain many gaps of unknown bases within and in between scaffolds. This project aims to resolve some of these gaps on linkage group 16 (LG 16) of the S. invicta draft genome by using a combination of PCR, cloning, and Sanger sequencing techniques. LG 16, or LG S (“social”), corresponds to a chromosome implicated to have important roles in the genetic control of the fire ant’s social behavior. A total of 279 gap closures were attempted inside and outside a special non-recombining region on LG 16. While larger inter-scaffold gaps were closed by screening for BAC clones that span across scaffolds. Sequencing results revealed a 10% higher proportion of repetitive elements inside the supergene than that of outside. These patterns are consistent with assembly biases which might support previous predictions regarding the accumulation of deleterious elements in the non-recombining region. These resolved gap sequences, in combination with BAC sequences that span inter-scaffold gaps would not only allow for the assembly of a more complete genome, but may also contribute to revealing important genomic features such as repetitive elements and genomic repeats in the social chromosome.
Subjects
入侵紅火蟻
基因體組裝
基因體間隙
基因體重複
重複序列
Type
thesis
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