Biology subjects

Garavito, A.

Publications and source records attributed to Garavito, A..

3 recordsLinked to original sources

bioRxiv2025

Shotgun sequencing data and SSR mining data of aibika (Abelmoschus manihot, Malvaceae)

Aibika (Abelmoschus manihot) is a tropical leafy vegetable with great potential in the prevention of malnutrition. Its high fibre and micronutrient content makes it a valuable complement to staple foods such as rice and starchy crops consumed in South Asia and the Pacific. The present study is the first to report the development of a set of 21 nuclear single sequence repeat (SSR) markers of A. manihot from genomic sequence data obtained using NGS technology. The DNA library was prepared from a pool of four aibika accessions and sequenced using an Illumina MiSeq system. A total of 1,295,217 pair-end reads were generated. Raw data are available in the European Nucleotide Archive (accession number PRJEB88210; https://www.ebi.ac.uk/ena/browser/view/PRJEB88210). The sequences were assembled using the ABySS software. In total 651,320 contigs were generated. Using MISA Perl script and Primer3 software, we identified 8014 SSR motifs, of which 4637 had a suitable primer design. The contigs were blasted with NCBI-BLAST on okra reference genome. After selection based on motif type, repeat length, amplicon size and occurrence blast, we retained 91 candidate SSR loci, which were tested on 23 aibika accessions. Finally, we validated 21 high quality SSR loci by genotyping 45 accessions from three Pacific countries. The number of alleles per locus ranged from 3 to 21 with an average of 7.81 alleles/locus. The 21 selected SSRs were found to be useful in discriminating between accessions and revealing the diversity structure of A. manihot. They will help to optimize genebanks management and breeding programmes, and guide future collection activities.

molecular biology↗

bioRxiv2025

Viruses and vectors tied to honey bee colony losses

Commercial beekeepers in the US reported severe colony losses early in 2025, as colonies were being staged for their critical role in the almond pollination season in California. Average reported losses since the preceding spring exceeded 60%, with substantial variation among operations. Many colonies were still actively collapsing in January, 2025, when pooled and individual samples were collected then screened for levels of known honey bee pathogens and parasites. Deformed wing virus strains A and B, along with Acute bee paralysis virus, were found at unusually high levels, either in pooled colony samples or in individual bees exhibiting shaking behaviors and morbidity. Differences between these two analyses suggest that direct collections of morbid bees provide a superior diagnostic for causal viruses, a suggestion borne out by confirmation of symptoms and morbidity following isolation and new inoculations. Since these viruses are known to be vectored by parasitic Varroa mites, mites from collapsed colonies were in turn screened for resistance to amitraz, a critical miticide used widely by beekeepers. Miticide resistance was found in all collected Varroa, underscoring the urgent need for new control strategies for this parasite. While viruses are a likely end-stage cause of colony death, other stressors such as nutritional stress and agrochemicals may have also played significant roles.

ecology↗

bioRxiv2023

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred [~]30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

genomics↗