Evolutionary genomics in pumpkins

The wild (left) and domesticated (right) subspecies of Cucurbita argyrosperma.

The evolutionary history of pumpkins (Cucurbita) is peculiar, as they have experienced a whole-genome duplication (WGD) event around 30 Mya. This WGD event allowed pumpkins to evolve novel genomic elements, which likely increased the evolutionary potential (evolvability) of the genus. It is no coincidence that humans were able to domesticate this genus at least six independent times in five different species, displaying several morphological convergences as well as unique traits for each domesticated taxon. Thus, pumpkins serve as a great model to understand the influence of WGDs on the mode and tempo of genome evolution, as well as to understand the basic processes of plant domestication.

Current projects:

Pumpkin paleogenomics.
Evolutionary potential of pseudogenized duplicates.

Publications

An evolutionary genomics view of wild and domesticated Cucurbita species from Mexico

Guillermo Sánchez-de la Vega, Gabriela Castellanos-Morales, Josué Barrera-Redondo, Carmina Martínez-González, Jaime Gasca-Pineda, Emanuel Villafán, Erika Aguirre-Planter, Helena S. Hernández-Rosales, Rafael Lira, Luis E. Eguiarte

Pringer Nature Reference Living Edition, Alejandro Casas, Nivaldo Peroni, Fabiola Parra-Rondinel, Veronica Lema, Xitlali Aguirre-Dugua, Edna Arévalo-Marín, Hernán Alvarado-Sizzo, José Blancas, Biodiversity Management and Domestication in the Neotropics, chapter 3, 1st ed., Springer, Cham, 2025

Population genomics of domesticated Cucurbita ficifolia reveals a recent bottleneck and low gene flow with wild relatives

Xitlali Aguirre-Dugua, Josué Barrera-Redondo, Jaime Gasca-Pineda, Alejandra Vázquez-Lobo, Andrea López-Camacho, Guillermo Sánchez-de la Vega, Gabriela Castellanos-Morales, Enrique Scheinvar, Erika Aguirre-Planter, Rafael Lira-Saade, Luis E. Eguiarte

Plants, vol. 12(23), 2023, p. 3989

The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

Josué Barrera-Redondo, Guillermo Sánchez-de La Vega, Jonás A Aguirre-Liguori, Gabriela Castellanos-Morales, Yocelyn T Gutiérrez-Guerrero, Xitlali Aguirre-Dugua, Erika Aguirre-Planter, Maud I Tenaillon, Rafael Lira-Saade, Luis E Eguiarte

Horticulture Research, vol. 8, Oxford Academic, 2021, p. 109

Recent and historical gene flow in cultivars, landraces, and a wild taxon of Cucurbita pepo in Mexico

Carmina Martínez-González, Gabriela Castellanos-Morales, Josué Barrera-Redondo, Guillermo Sánchez-De La Vega, Helena S Hernández-Rosales, Jaime Gasca-Pineda, Erika Aguirre-Planter, Alejandra Moreno-Letelier, Ana E Escalante, Salvador Montes-Hernández, Rafael Lira-Saade, Luis E Eguiarte

Frontiers in Ecology and Evolution, Frontiers, 2021, p. 307

Landrace diversity and local selection criteria of domesticated squashes and gourds (Cucurbita) in the central Andean mountain range of Peru: Tomayquichua, Huánuco

Josué Barrera-Redondo, Helena S Hernández-Rosales, Verónica Cañedo-Torres, Katia Aréstegui-Alegría, Juan Torres-Guevara, Fabiola Parra, Ignacio Torres-García, Alejandro Casas

Botanical Sciences, vol. 98, 2020, pp. 101-116

Gourds and tendrils of Cucurbitaceae: how their shape diversity, molecular and morphological novelties evolved via whole-genome duplications

Josué Barrera-Redondo, Rafael Lira-Saade, Luis E Eguiarte

Molecular Plant, vol. 13, Elsevier, 2020, pp. 1108-1110

Genomic, transcriptomic and epigenomic tools to study the domestication of plants and animals: a field guide for beginners

Josué Barrera-Redondo, Daniel Piñero, Luis E Eguiarte

Frontiers in Genetics, vol. 11, Frontiers Media SA, 2020, p. 742

Evolutionary dynamics of transferred sequences between organellar genomes in Cucurbita

Xitlali Aguirre-Dugua, Gabriela Castellanos-Morales, Leslie M Paredes-Torres, Helena S Hernández-Rosales, Josué Barrera-Redondo, Guillermo Sánchez-de la Vega, Fernando Tapia-Aguirre, Karen Y Ruiz-Mondragón, Enrique Scheinvar, Paulina Hernández, ..., Luis E Eguiarte

Journal of Molecular Evolution, vol. 87, Springer, 2019, pp. 327-342

The genome of Cucurbita argyrosperma (silver-seed gourd) reveals faster rates of protein-coding gene and long noncoding RNA turnover and neofunctionalization within Cucurbita

Josué Barrera-Redondo, Enrique Ibarra-Laclette, Alejandra Vázquez-Lobo, Yocelyn T Gutiérrez-Guerrero, Guillermo Sánchez de la Vega, Daniel Piñero, Salvador Montes-Hernández, Rafael Lira-Saade, Luis E Eguiarte

Molecular Plant, vol. 12, Elsevier, 2019, pp. 506-520

Historical biogeography and phylogeny of Cucurbita: insights from ancestral area reconstruction and niche evolution

Gabriela Castellanos-Morales, Leslie M Paredes-Torres, Niza Gámez, Helena S Hernández-Rosales, Guillermo Sánchez-de la Vega, Josué Barrera-Redondo, Erika Aguirre-Planter, Alejandra Vázquez-Lobo, Salvador Montes-Hernández, Rafael Lira-Saade, Luis E Eguiarte

Molecular Phylogenetics and Evolution, vol. 128, Elsevier, 2018, pp. 38-54

Domesticación, diversidad y recursos genéticos y genómicos de México: El caso de las calabazas

Luis E Eguiarte, Helena S Hernández-Rosales, Josué Barrera-Redondo, Gabriela Castellanos-Morales, Leslie M Paredes-Torres, Guillermo Sánchez-de la Vega, Karen Y Ruiz-Mondragón, Alejandra Vázquez-Lobo, Salvador Montes-Hernández, Erika Aguirre-Planter, others

TIP. Revista especializada en ciencias químico-biológicas, vol. 21, Universidad Nacional Autónoma de México, Facultad de Estudios Superiores Zaragoza, 2018, pp. 85-101