Aureliano Bombarely

The paper investigates genomic mechanisms underlying independent transitions to terrestrial life across species, finding lineage-specific gene changes that converge functionally.

The paper analyzes population structure in Culex pipiens using genomic data from a WNV hotspot, finding that ecotypes, Wolbachia infection, and habitat type drive genetic variation.

This study examines the evolutionary history of recently diverged Petunia lineages, revealing that most are intermediate stages along a speciation continuum rather than distinct species.

This study evaluates how reference genome choice affects RAD-seq analyses in Petunia and Calibrachoa, finding that closely related genomes yield consistent results while distantly related ones reduce SNP recovery but not evolutionary inference.

The paper presents an avocado pangenome and analyzes NLR gene diversity across lineages, revealing lineage-specific expansions and structural variants.

The paper analyzes genome dynamics in Begonia species to link repetitive element expansion with speciation and genetic isolation across different radiations.

This study benchmarks low-coverage sequencing workflows for eggplant genotyping, finding that 3X coverage with Freebayes achieves high genotypic concordance and sensitivity.

MetPlast quantifies metabolic plasticity using Shannon entropy-based metrics and provides visualization tools, demonstrated on tomato domestication data.

K-seq is a cost-effective genotyping method using Klenow amplification and Illumina sequencing, showing comparable genetic results to WGS and GBS with higher SNP detection.

DeepTE classifies transposable elements using convolutional neural networks, outperforming existing tools in benchmark tests.

The paper presents a high-quality zucchini genome assembly and identifies a whole genome duplication in the Cucurbita genus.