Chromium sequencing: the doors open for genomics of obligate plant pathogens
Alistair R McTaggart,
Tuan A Duong,
Vang Quy Le,
Louise S Shuey,
Werner Smidt,
Sanushka Naidoo,
Michael J Wingfield,
Brenda D Wingfield
Affiliations
Alistair R McTaggart
1Department of Biochemistry, Genetics & Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
Tuan A Duong
1Department of Biochemistry, Genetics & Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
Vang Quy Le
3Section of Molecular Diagnostics, Aalborg University Hospital, Denmark
Louise S Shuey
1Department of Biochemistry, Genetics & Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
Werner Smidt
1Department of Biochemistry, Genetics & Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
Sanushka Naidoo
1Department of Biochemistry, Genetics & Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
Michael J Wingfield
1Department of Biochemistry, Genetics & Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
Brenda D Wingfield
1Department of Biochemistry, Genetics & Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
It is challenging to sequence and assemble genomes of obligate plant pathogens and microorganisms because of limited amounts of DNA, comparatively large genomes and high numbers of repeat regions. We sequenced the 1.2 gigabase genome of an obligate rust fungus, Austropuccinia psidii, the cause of rust on Myrtaceae, with a Chromium 10X library. This technology has mostly been applied for single-cell sequencing in immunological studies of mammals. We compared scaffolds of a genome assembled from the Chromium library with one assembled from combined paired-end and mate-pair libraries, sequenced with Illumina HiSeq. Chromium 10X provided a superior assembly, in terms of number of scaffolds, N50 and number of genes recovered. It required less DNA than other methods and was sequenced and assembled at a lower cost. Chromium sequencing could provide a solution to sequence and assemble genomes of obligate plant pathogens where the amount of available DNA is a limiting factor.
