Pelaez, J. | Search bioRxiv

bioRxiv2025

Population structure and diversity of common bean (Phaseolus vulgaris L.) landraces in the Peruvian Amazon

Common bean (Phaseolus vulgaris L.) is a globally important legume with significant nutritional and agronomic value. Genetic diversity in Amazonian landraces remains undercharacterized, limiting their utilization in breeding programs. Here we analyzed 647 accessions from the Peruvian Amazon using 18 morphological traits and 23,050 high-quality DArTseq single nucleotide polymorphisms (SNPs). Our results revealed two major genetic groups corresponding to Andean and Mesoamerican gene pools, each subdivided into distinct subgroups, exhibiting high allelic richness and structured diversity. Despite abundant polymorphic loci, observed heterozygosity was low, consistent with the species self-pollinating nature. These findings highlight the Peruvian Amazon as a reservoir of unique genetic variation, underscoring the need for integrated in situ and ex situ conservation strategies. This germplasm offers valuable resources for breeding programs targeting tropical adaptation and resilience, contributing to sustainable agriculture and food security.

plant biology↗

bioRxiv2020

Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long read sequencing allow high quality genome assemblies for tens or even hundreds of species to be generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution within this key group.

evolutionary biology↗