A pinboard by
Sheina Sim

Postdoctoral research biologist, USDA-ARS


Tephritidae genomics

Tephritid fruit flies are destructive agricultural pests and the subject of exclusion efforts in many countries. Suppression and eradication of invasive tephritids to prevent establishment is facilitated by the release of sterile males using the sterile insect technique (SIT). To address the need for improvements to the sterile insect technique and its requisite genetic sexing strains (GSS), we used a suite of genomic techniques such as whole-genome sequencing, RNA-seq, double-digest RAD-seq, single-molecule sequencing, chromosome conformation capture, long-range sequencing, and targeted gene editing (CRISPR). Using these tools, we developed foundational genomic resources and diagnostic assays for target species in addition to identifying and validating the genetic basis of genetic sexing traits in currently existing genetic sexing strains.


The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species.

Abstract: The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control.The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT.The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.

Pub.: 24 Sep '16, Pinned: 16 Jun '17

A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of White Pupae.

Abstract: Genetic sexing strains (GSS) used in sterile insect technique (SIT) programs are textbook examples of how classical Mendelian genetics can be directly implemented in the management of agricultural insect pests. Though the foundation of traditionally developed GSS are single locus, autosomal recessive traits, their genetic basis are largely unknown. With the advent of modern genomic techniques, the genetic basis of sexing traits in GSS can now be further investigated. This study is the first of its kind to integrate traditional genetic techniques with emerging genomics to characterize a GSS using the tephritid fruit fly pest Bactrocera cucurbitae as a model. These techniques include: whole genome sequencing, the development of a mapping population, linkage map and quantitative trait analysis. The experiment designed to map the genetic sexing trait in B. cucurbitae, wp, also enabled the generation of a chromosome-scale genome assembly by integrating the linkage map with the assembly. Quantitative trait loci analysis revealed SNP loci near position 42 MB on chromosome 3 to be tightly linked to wp Gene annotation and synteny analysis show a near-perfect relationship between chromosomes in B. cucurbitae and Muller Elements A-E in Drosophila melanogaster This chromosome-scale genome assembly is complete, has high contiguity, was generated using a minimal input DNA, and will be used to further characterize the genetic mechanisms underlying wp Knowledge of the genetic basis of genetic sexing traits can be used to improve SIT in this species and expand to other economically important Diptera.

Pub.: 30 Apr '17, Pinned: 16 Jun '17