The red-shouldered soapberry bug Jadera haematoloma (Hemiptera: Heteroptera: Rhopalidae) is a scentless plant bug native to the US Gulf Coast. It feeds on several native plants of the soapberry family (Sapindaceae) and, since the mid-twentieth century, has adapted to live on the introduced Chinese goldenrain tree (Koelreuteria ssp.). This host shift, along with the abundance of red-shouldered soapberry bugs in urban environments, has made J. haematoloma an excellent model for the study of rapid adaptive evolution (Tsai 2013; Panfilio & Angelini 2018). Indeed, different researchers have examined rapid evolution in beak length (e.g. Carrol & Loye 1987; Yu & Andrés 2014; Cenzer 2016; 2017), wing polyphenism (Carroll et al. 2003; Fawcett et al. 2018), and several other life history traits (Carroll 1991; Carroll et al. 1998). Our lab has been studying appendage development and wing polyphenism in the bugs. And we were interested in its genome sequence as a resource for developmental genetics, to contextualize genotyping and population studies, and as a point of comparison to the genomes of other insects, especially Oncopeltus fasciatus (Panfilio et al. 2019).
The soapberry bug karyotype was first described by Lelia Porter in 1917. Males have 13 chromosomes, and the species appears to use an X0 sex determination system. So there are six pairs of autosomes, and an X that is slightly larger than the smallest autosome (Porter 1917). Based on meiotic behavior, the smallest chromosome has been described as an “m-chromosome”. It does not appear to have chiasmata during meiotic prophase and migrates to the poles early in anaphase (Ueshima 1979). In 2015, Spencer Johnston at Texas A&M used flow cytometry to estimate the genome size of Jadera haematoloma at about 1.95 Gbp. For some context, this is more than 11 times the size of the genome of the fruit fly Drosophila melanogaster or about 61% the size of the human genome.
In 2018, an anonymous gift was made to Colby College to support research in genomics and bioinformatics, and we were given the green light to use these funds for a genome sequencing project. Additional funding was provided by Maine INBRE and the Colby Department of Biology. We contracted Dovetail Genomics for sequencing and assembly. Dovetail offers a combination of library preparation methods, including the use of HiC proximity end-pairing (Pal et al., 2019), which allows for assembly to chromosome length.
To reduce heterozygosity, we chose to sequence a lab population of bugs, originally from Plantation Key in Tavernier, FL, and crossed full siblings for 5 generations. Dovetail made the DNA isolation and prepared libraries from one of these in-bred male bugs.
In August 2019, Dovetail returned the draft genome assembly. The total sequence length from all scaffolds was 2.08 Gbp, very close to the previous estimate. Metrics, such as the distribution of ambiguous nucleotides and repetitive sequences, all indicate that the genome assembly is of high quality. GC content is 34%, typical for true bugs. The assembly length is 2,076.49 Mb with 50,609 scaffolds and an L90 of 7. Seven scaffolds over 1 Mbp contain 89.9% of the sequence and likely represent the seven chromosomes seen in the bug’s karyotype.
We are now in the annotation phase of this project. A preliminary survey using BLAST found orthologs for 80 of 81 candidate genes. Only one gene, knirps, did not have a strong hit to the assembled chromosomes, although it was present on two smaller scaffolds. Interestingly, of the 81 genes searched, none appears on the m-chromosome. The Hox cluster appears to be on chromosome 5.
We are currently using de novo gene prediction methods to further characterize the genome. Gene expression studies are also underway to characterize genes involved in nutritionally dependent plasticity in wing growth and patterning. In the future, the genome sequence will also enable population-level differences among bugs in the wild to be mapped and placed in the context of genes and other genomic features.
Jadera is an excellent model for the study of adaptive evolution, and I would like the eventual publication of this genome to show-case this system’s potential and the varied interests of our small, but growing, Jadera community. Specifically, I am envisioning something modeled after the Oncopeltus genome paper (Panfilio et al. 2019) in which contributors each wrote different sections that highlighted aspects of the genome relevant to their research programs. We are happy to share sequence with anyone who is willing to contribute to the project. So please contact us if you’re interested in collaborating!