Browsing by Autor "Erick Duarte"

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    New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads
    (2023) Laura Natalia González-García; David Guevara-Barrientos; Daniela Lozano‐Arce; Juanita Gil; Jorge Díaz-Riaño; Erick Duarte; Germán I. Andrade; Juan Camilo Bojacá; Maria Camila Hoyos-Sanchez; Christian Chavarro
    Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.
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    Recent evolution, domestication and metabolism of cyanide compounds in Lima bean
    (2025) Jorge Duitama; Erick Duarte; Tatiana García Navarrete; F. J. Pérez Zúñiga; Johanna Stepanian; Viviana Parra; Juan Pablo Londoño; Paula Siaucho; Edwin Bautista; Santiago Jiménez-Serrano
    <title>Abstract</title> The evolution and functional genomics of the biosynthesis of secondary metabolites, including production of hydrogen cyanide (HCN), is a major goal in Lima bean research. This work describes our latest findings in short time evolution, genomics and expression, applied to Lima bean. This includes a chromosome-level assembly for the Andean gene pool and long-read sequencing of wild relatives. Large indels explained by transposable elements affect promoter regions of several genes related to domestication traits. The two major gene pools of P. lunatus diverged within the last million years, but recent insertions of LTRs produced important variations in genome size and composition. A core metabolic network for Phaseolus revealed patterns of variability in RNA expression for genes related to different primary and secondary metabolic processes. The Phaseolus genomes have important differences in the number, location, and expression of genes, which can explain the unique ability of Lima bean across domesticated Phaseolus species for production of HCN.