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

Autor: Amaral DT; Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil.; Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil., Bombonato JR; Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil.; Graduate Program in Comparative Biology, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil., da Silva Andrade SC; Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, Brazil., Moraes EM; Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil., Franco FF; Department of Biology, Center for Human and Biological Sciences, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brazil. franco@ufscar.br.
Jazyk: angličtina
Zdroj: Planta [Planta] 2021 Aug 06; Vol. 254 (3), pp. 44. Date of Electronic Publication: 2021 Aug 06.
DOI: 10.1007/s00425-021-03690-5
Abstrakt: 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 ~ 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 ~ 57 to ~ 67%. Putative satellite DNAs are present in all species, excepting C. gigantea. The plastome of C. fernambucensis was ~ 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.
(© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
Databáze: MEDLINE
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