Identification and characterization of sequence variants from a de novo-assembled partial pan-genome of cactus pear (Opuntia L.)

• Published in: South African journal of botany 2024-12, Vol.175, p.241-252
• Main Authors: Maleka, Mathabatha F., Modise, Tsholofelo J., Du Plessis, Morné G., Coetzer, Gesine M.
• Format: Article
• Language: English
• Subjects: agricultural industry; bioinformatics; botany; cactus pears; crops; cultivars; De novo sequence assembly; genetic variation; genome; genus; germplasm; health promotion; Illumina sequencing; Opuntia ficus-indica; Opuntia robusta; Sequence annotation; Simple sequence repeats (SSRs); Single nucleotide polymorphisms (SNPs); species; water storage
• ISSN: 0254-6299
• DOI: 10.1016/j.sajb.2024.10.023

Members of the genus Opuntia exhibit extensive morphological variation that is seemingly linked to their propensity for occupying extreme environments all over the world. The plants are very important to the agriculture industry as they have many health-promoting nutritional and bioactive compounds. Also, as succulents, they are interesting because they develop peculiar stems – which, however, fulfil the role of leaves – that enable the storage of copious amounts of water. Yet, little is known about the genomes of Opuntia species although having such data can give insight into the genetic diversity that regulates the observed morphological variation as well as the molecular processes responsible for the development of succulent leaves. The current study aimed to sequence and de novo assemble a partial reference genome of Opuntia that would be used to find sequence variants for differentiating species and cultivars of this important agricultural crop. Illumina sequencing was performed on 10 cultivars that represented two species (Opuntia ficus-indica and O. robusta) within the South African Opuntia germplasm. Sequence assembly of 214 million filtered high-quality reads generated a 657 Mbp partial pan-genome that represented ∼30 % of a predicted O. ficus-indica genome. Functional annotation of the assembled sequences at different bioinformatic databases revealed many genes relating to diverse developmental pathways as well as water storage. Further, sequence variants including some 60,000 simple sequence repeats (SSRs) and 118,000 biallelic single nucleotide polymorphisms (SNPs) were discovered by mapping reads of each cultivar against the assembled partial reference pan-genome of Opuntia. While the identified number of SNPs is significant it, however, corresponded to moderate and higher frequency variants only (minor allele frequency [MAF] > 0.2). Also, a random selection of 1,000 SNPs genotyped across all specimens were able to differentiate the 10 cultivars and two species studied herein. Overall, the current study reports the first partial reference pan-genome of Opuntia specimens. The generated data should serve as a valuable genetic resource for future studies seeking to analyze diversity-related phenomena or elucidate the molecular development and growth of Opuntia specimens.