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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Amaral, Danilo Trabuco [1, 2] ; Bombonato, Juliana Rodrigues [1, 2] ; da Silva Andrade, Sonia Cristina [3] ; Moraes, Evandro Marsola [1] ; Franco, Fernando Faria [1]
Total Authors: 5
[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
Total Affiliations: 3
Document type: Journal article
Source: PLANTA; v. 254, n. 3 SEP 2021.
Web of Science Citations: 0

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)

FAPESP's process: 14/25227-0 - Multilocus phylogenetic analysis to recover evolutionary relationships among species of genus Cereus (Cactaceae; Cereeae)
Grantee:Fernando de Faria Franco
Support type: Regular Research Grants
FAPESP's process: 18/03428-5 - Dimensions US-BIOTA-Sao Paulo: traits as predictors of adaptive diversification along the Brazilian Dry Diagonal
Grantee:Vera Nisaka Solferini
Support type: BIOTA-FAPESP Program - Thematic Grants