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Mol Plant. 2019 Jan 7. pii: S1674-2052(19)30003-6. doi: 10.1016/j.molp.2018.12.023. [Epub ahead of print]

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

Author information

1
Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México. Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, Mexico.
2
Departamento de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Carretera Antigua a Coatepec No. 351, Col. El Haya. C.P. 91070, Xalapa, Veracruz, Mexico.
3
Centro de Investigaciones en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62209 Cuernavaca, Morelos, Mexico.
4
Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Km 6.5 Carretera Celaya-San Miguel de Allende, 38110 Celaya, Guanajuato, Mexico.
5
UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios #1, Col. Los Reyes Iztacala, 54090 Tlanepantla, Edo. de Mex, Mexico. Electronic address: rlira@unam.mx.
6
Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México. Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, Mexico. Electronic address: rlira@unam.mx.

Abstract

Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a whole-genome duplication around 30 Mya, although the evolutionary dynamics of their coding and noncoding genes have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, including the novel genome assembly of Cucurbita argyrosperma, and compared their gene contents with five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report a higher rate of protein-coding gene birth-death rate in the Cucurbita genomes compared to the rest of the Cucurbitaceae family. The genome of C. argyrosperma presented significantly faster evolutionary rates in gene families associated with aspects of pollination and transmembrane transport. LincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita show evidence of birth from the neofunctionalization of previously existing protein-coding genes. Our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes.

KEYWORDS:

Comparative genomics; Cucurbita argyrosperma; Molecular evolution; long noncoding RNA; neofunctionalization; whole-genome duplication

PMID:
30630074
DOI:
10.1016/j.molp.2018.12.023

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