The importance of sequencing depth for a complex transcriptome [W952]

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. The importance of sequencing depth for a complex transcriptome [W952]. In : Abstracts workshops of the PAG XXVIII. San Diego : PAG, Résumé, 417. Plant and Animal Genome. 28, San Diego, États-Unis, 11 Janvier 2020/15 Janvier 2020.

Résumé : Sugarcane, a unique biological system which has evolved over time to suit the changing human needs is now being manipulated as a source of alternate energy and an array of platform chemicals. Sugarcane is a crop with diverse end uses and applications, a wealth of genetic resources and a rich breeding history. The daunting size and extreme complexity of the genome together with high heterozygosity and variable chromosome numbers has long hampered genomic research in sugarcane. Analysis of the transcriptome using long read sequencing has been reported. Normalization of libraries before sequencing has been widely employed in transcriptome analysis. In the complex sugarcane transcriptome, normalization was found to both reveal more rare sequences and result in the loss of many sequence variants. This suggested the need for deep sequencing to capture the diversity of sequences in sugarcane. Recently, a monoploid genome sequence was generated for the cultivar R570. We now report analysis of the transcriptome of this genotype and the impact of sequencing at greater depth on the recovery of transcripts. The results may guide future transcriptomic studies in sugarcane to make informed decisions on the required depth of sequencing.

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/594829/)

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