Biology subjects

Corpuz, R. L.

Publications and source records attributed to Corpuz, R. L..

5 recordsLinked to original sources

bioRxiv2025

An loss of independence: genomic insights into a pest fruit fly-bacterial mutualism

Obligate microbial symbioses are often characterized by streamlined biosynthetic pathways and reduced genomes. The evolutionary process of this reduction first involves an increase in the abundance of non-functional coding genes (pseudogenes) followed by their removal. The olive fruit fly (Bactrocera oleae) harbors an extracellular symbiotic gut bacterium Candidatus Erwinia dacicola, which is crucial to its usage of fruit from the olive genus Olea as a larval food source. In this study, we combined genomics and transcriptomics of Ca. E. dacicola to investigate pathways that facilitate this mutualism. Of 4,675 genes in the Ca. E. dacicola genome, 1,783 were classified as pseudogenes. Some biochemical pathways such as amino acid pathways, biofilm regulator BssS, and 6-phospho-{beta}-glucosidase which are implicated in hydrolyzing oleuropein were complete. However, pathways connected to baseline homeostasis, which would impact cellular functions needed for a bacterium to be free-living, were heavily pseudogenized. Gene selection analyses in Ca. E. dacicola, when compared to related organisms, indicated positive selection on genes related to amino acid metabolism, carbon utilization, transport, and energy production. Our results indicate that Ca. E. dacicola is likely producing amino acids and metabolizing plant phytochemicals. These results reveal that the Ca. E. dacicola genome is undergoing incipient genome erosion in support of an unculturable obligate mutualism. ImportanceMany beneficial bacteria that live inside insects have highly reduced genomes, but little is known about the transitional stages that occur as free-living microbes evolve into obligate symbionts. We show that the olive fruit fly symbiont, Candidatus Erwinia dacicola, retains hallmarks of its plant-associated ancestry while undergoing extensive genome degradation, including the accumulation of mobile DNA elements and inactive genes. At the same time, genes involved in nutrient production, environmental persistence, and host interactions remain functional and are evolving under selection, providing a rare snapshot of how bacterial genomes are reshaped during the evolution of an obligate mutualism. These findings have implications for how obligate gut symbioses are formed and maintained in insect herbivores.

genomics↗

bioRxiv2025

Genome report: chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae)

The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is a specialist of fruits of the genus Olea and is a major pest of commercial olives due to their adverse impacts to olive production. In support of genomic and physiological research of the olive fly, we sequenced, assembled, and annotated two independent genomes, one from a wild-collected male and one from a wild-collected female. The resulting genomes are highly contiguous, collinear, and complete, attesting to the accuracy and quality of both assemblies. In addition to the autosomes captured as single contigs, the X and Y chromosomes were also captured as evidenced by the X chromosome showing diploid coverage in the female assembly compared to haploid coverage in the male assembly and the Y chromosome being entirely absent from the female assembly. These assemblies represent the first full chromosome-level assembly for Olive fly. In addition, a complete genome assembly of a known obligate symbiont to the olive fly, Candidatus Erwinia dacicola, was fully captured. The Ca. E. dacicola we report here is the most contiguous to date, represented with a gapless chromosome and two separate gapless plasmids. These genome assemblies, along with bacterial symbiont assembly, provide foundational resources for future genetic and genomic research in support of its management as an agricultural pest.

genomics↗

bioRxiv2025

CiFi: Accurate long-read chromatin conformation capture with low-input requirements

Hi-C characterizes three-dimensional chromatin organization, facilitates haplotype phasing, and enables genome-assembly scaffolding, but encounters difficulties across complex regions. By coupling chromosome conformation capture (3C) with PacBio HiFi long-read sequencing, here we develop a method (CiFi) that enables analysis of genomic interactions across repetitive regions. Starting with as little as 60,000 cells (sub-microgram DNA), the method produces multi-kilobasepair HiFi reads that contain multiple interacting, concatenated segments ([~]350 bp to 2 kbp). This multiplicity and increase in segment length versus standard short-read-based Hi-C improves read-mapping efficiency and coverage in repetitive regions and enhances haplotype phasing. CiFi pairwise interactions are largely concordant with Hi-C from a human lymphoblastoid cell line, with gains in assigning topologically associating domains across centromeres, segmental duplications, and human disease-associated genomic hotspots. As CiFi requires less input versus established methods, we apply the approach to characterize single small insects: assaying chromatin interactions across the genome from an Anopheles coluzzii mosquito and producing a chromosome-scale scaffolded assembly from a Ceratitis capitata Mediterranean fruit fly. Together, CiFi enables assessment of chromosome-scale interactions of previously recalcitrant low-complexity loci, low-input samples and small organisms.

genomics↗

bioRxiv2024

The genetic basis of the black pupae phenotype in tephritid fruit flies

The remarkable diversity of insect pigmentation offers a captivating avenue for exploring evolution and genetics. In tephritid fruit flies, decoding the molecular pathways underlying pigmentation traits also plays a central role in applied entomology. Mutant phenotypes like the black pupae (bp) have long been used as a component of genetic sexing strains, allowing male-only release in tephritid sterile insect technique applications. However, the genetic basis of bp remains largely unknown. Here, we present independent evidence from classical and modern genetics showing that the bp phenotype in the GUA10 strain of the Mexican fruit fly, Anastrepha ludens, is caused by a large deletion at the ebony locus resulting in the removal of the entire protein-coding region of the gene. Targeted knockout of ebony induced analogous bp phenotypes across six tephritid species spanning over 50 million years of divergent evolution. This functionally validated our findings and allowed for a deeper investigation into the role of Ebony in pigmentation and development in these species. Our study offers fundamental knowledge for developing new sexing strains based on the bp marker and for future evolutionary developmental biology studies in tephritid fruit flies.

genomics↗

bioRxiv2023

Chromosome-scale Genome Assembly of the West Indian Fruit Fly Anastrepha obliqua (Diptera: Tephritidae)

The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the genome using high-fidelity (HiFi) long-read sequencing. This resulted in a highly contiguous contig assembly with 90% of the genome in 10 contigs. The contig assembly was placed in a chromosomal context using synteny with a closely related species, A. ludens, as both are members of the A. fraterculus group. The resulting assembly represents the five autosomes and the X chromosome which represents 95.9% of the genome, and 199 unplaced contigs representing the remaining 4.1%. Orthology analysis across the structural annotation sets of high quality tephritid genomes demonstrates the gene annotations are robust, and identified genes unique to Anastrepha species that may help define their pestiferous nature that can be used as a starting point for comparative genomics. This genome assembly represents the first of this species and will serve as a foundation for future genetic and genomic research in support of its management as an agricultural pest.

genomics↗