The genome of a thorny species: comparative genomic analysis among South and North American Cactaceae

Autor(es)

Amaral, Danilo Trabuco ^{[1, 2]} ; Bombonato, Juliana Rodrigues ^{[1, 2]} ; da Silva Andrade, Sonia Cristina ^[3] ; Moraes, Evandro Marsola ^[1] ; Franco, Fernando Faria ^[1]

Afiliação do(s) autor(es)

^[1] Univ Fed Sao Carlos UFSCar, Ctr Human & Biol Sci, Dept Biol, Rodovia Joao Leme Santos, Km 110, SP264, BR-18052780 Sorocaba - Brazil

^[2] Univ Sao Paulo, Fac Philosophy Sci & Languages Ribeirao Preto, Grad Program Comparat Biol, Ribeirao Preto - Brazil

^[3] Univ Sao Paulo, Inst Biociencias, Dept Genet & Evolutionary Biol, Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: PLANTA; v. 254, n. 3 SEP 2021.
• Citações Web of Science: 0

Resumo

Main conclusion The first South American cactus nuclear genome assembly associated with comparative genomic analyses provides insights into nuclear and plastid genomic features, such as size, transposable elements, and metabolic processes related to cactus development. Here, we assembled the partial genome, plastome, and transcriptome of Cereus fernambucensis (Cereeae, Cactaceae), a representative species of the South American core Cactoideae. We accessed other genomes and transcriptomes available for cactus species to compare the heterozygosity level, genome size, transposable elements, orthologous genes, and plastome structure. These estimates were obtained from the literature or using the same pipeline adopted for C. fermabucensis. In addition to the C. fernambucensis plastome, we also performed de novo plastome assembly of Pachycereus pringlei, Stenocereus thurberi, and Pereskia humboldtii based on the sequences available in public databases. We estimated a genome size of similar to 1.58 Gb for C. fernambucensis, the largest genome among the compared species. The genome heterozygosity was 0.88% in C. fernambucensis but ranged from 0.36 (Carnegiea gigantea) to 17.4% (Lophocereus schottii) in the other taxa. The genome lengths of the studied cacti are constituted by a high amount of transposable elements, ranging from similar to 57 to similar to 67%. Putative satellite DNAs are present in all species, excepting C. gigantea. The plastome of C. fernambucensis was similar to 104 kb, showing events of translocation, inversion, and gene loss. We observed a low number of shared unique orthologs, which may suggest gene duplication events and the simultaneous expression of paralogous genes. We recovered 37 genes that have undergone positive selection along the Cereus branch that are associated with different metabolic processes, such as improving photosynthesis during drought stress and nutrient absorption, which may be related to the adaptation to xeric areas of the Neotropics. (AU)

• Processo FAPESP: 14/25227-0 - Análises Filogenéticas Multilocos aplicadas ao entendimento de relações evolutivas entre espécies de Cereus (Cactaceae; Cereeae)
• Beneficiário: Fernando de Faria Franco
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 18/03428-5 - Dimensions US-BIOTA-Sao Paulo: características preditoras da diversificação adaptativa na Diagonal Seca Brasileira
• Beneficiário: Vera Nisaka Solferini
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOTA - Temático