Sequencing the transcriptome of R570 to explore the complexity of the sugarcane genome [W1019]

Kumar Pazhany Adhini Sudhindra, Perlo Virginie, Botha Frikkie, Furtado Agnelo, O'Keeffe Angela, Karabian Masouleh Ardy, Henry Robert, Aitken Karen S., D'Hont Angélique, Healey Adam, Grimwood Jane, Barry Kerrie W., Schmutz Jeremy. 2020. Sequencing the transcriptome of R570 to explore the complexity of the sugarcane genome [W1019]. In : Abstracts workshops of the PAG XXVIII. San Diego : PAG, Résumé, 443-444. Plant and Animal Genome. 28, San Diego, États-Unis, 11 Janvier 2020/15 Janvier 2020.

Résumé : Sugarcane is a crop of unequivocal importance which can meet requirements for food, feed fiber and fuel. This crop, with a large wealth of genetic resources and a rich breeding history, has only a very nascent genomic history with a monoploid genome sequence. Numerous efforts are underway to unravel the mysteries of this complex crop with advances in sequencing technologies. Efforts to capture the functional part of the genome using transcriptomic studies have long been a priority. R570, a French cultivar has been the most suitable material for many sugarcane genomics studies. In an attempt to utilize the revolutionary technology of long read sequencing, we have carried out isoform sequencing of this representative cultivar with a Pac Bio sequel I system. Recently we have compared sequel II data of the same cultivar from various vegetative and reproductive tissues. A greater sequencing depth may benefit the sugarcane fraternity with a more complete transcriptome and accurate gene annotation. The present study aimed at comparing sequel I and sequel II data for R570 to harness the information contained in the large transcriptome resources and to find novel sources of variation in the light of these recent advances. The results may support future transcriptomic studies in sugarcane to make informed decisions on depth of sequencing and help to unravel the complexities of this transcriptome.

Auteurs et affiliations

• Kumar Pazhany Adhini Sudhindra, University of Queensland (AUS)
• Perlo Virginie, University of Queensland (AUS)
• Botha Frikkie, University of Queensland (AUS)
• Furtado Agnelo, University of Queensland (AUS)
• O'Keeffe Angela, University of Queensland (AUS)
• Karabian Masouleh Ardy, University of Queensland (AUS)
• Henry Robert, University of Queensland (AUS)
• Aitken Karen S., CSIRO (AUS)
• D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA)
• Healey Adam, HudsonAlpha Biotechnology Institute (USA)
• Grimwood Jane, DOE-JGI (USA)
• Barry Kerrie W., United States Department of Energy Joint Genome Institute (USA)
• Schmutz Jeremy, DOE-JGI (USA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/594821/)

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