bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.12.13.571405

De novo genome assembly of four Andean potato weevil species (Premnotrypes,Rhigopsidius), the primary agricultural pest of the potato in South America

Jorgensen, K.·Garcia, O. A.·Alcazar, J.·Walden, K. K. O.·Bigham, A. W.·Moron, N. M.·Cobian, C. V.·Lesnik, J. J.·Fan, C.
View original source ↗Export metadata ↓

Abstract

The Andean potato weevil complex are the most widespread and serious insect pests to potato crops in the Andes. More broadly, genomic assemblies of insect pests are currently lacking in agricultural research, especially those from the order Coleoptera. These genome data are essential for identifying potential underlying mechanisms important to biological control strategies and food security in the highlands. Here, we present the de novo genome assemblies for four species of the Andean potato weevil complex: Premnotrypes vorax, P. suturicallus, P. latithorax, and Rhigopsidius piercei. Genome assemblies exceeded the average size of those from the order Coleoptera and were highly repetitive: for P. vorax (1.33 Gb, 71.51% repetitive), P. latithorax (623 Mb, 59.03% repetitive), P. suturicallus (1.23 Gb, 70.19% repetitive), and R. piercei (1.55 Gb, 71.91% repetitive). We examined genomic regions related to metabolic potato plant detoxification and insecticide resistance using the available Colorado potato beetle (Leptinotarsa decemlineata) genome annotations as a guide. Our analysis of these weevil genomes identified chemosensory receptors and odorant binding proteins that could be related to detecting their hosts, the potato plant (Solanum tuberosum), as well as many genomic regions involved in subverting pesticide resistance. We have generated the first whole-genome assemblies of the Andean potato weevil complex that will be foundational for future agricultural pest management and entomological research in South America. Author SummaryWithin the South American Andean mountains the Andean potato weevil insects are the most widespread and serious pests to potatoes, destroying around 89% of potato harvests a year when insecticides are not used. Here, we collected and performed whole-genome sequencing for the first time for four Andean potato weevil species: Premnotrypes vorax, P. suturicallus, P. latithorax, and Rhigopsidius piercei. After analysis of these genome assemblies, we found that they were large and highly repetitive compared to other published beetle genome data in the order Coleoptera. After further examination of these genome assemblies, we found regions related to metabolic potato plant detoxification, insecticide resistance, and chemosensory and odorant binding protein receptors that could be related to detecting potato plants. These genomic identifications provide novel molecular insight into regions associated with insecticide resistance, metabolic abilities, and environmental receptors, and can serve as a future valuable resource in classifying phylogenetic relationships as well as identifying regions of interest for improved pest management for potato farmers.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jorgensen, K., Garcia, O. A., Alcazar, J., Walden, K. K. O., Bigham, A. W., Moron, N. M., Cobian, C. V., Lesnik, J. J., Fan, C.. 2023-12-13. De novo genome assembly of four Andean potato weevil species (Premnotrypes,Rhigopsidius), the primary agricultural pest of the potato in South America. https://doi.org/10.1101/2023.12.13.571405

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗