A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in<i>Oryza sativa</i>

Bowman, Megan J.; Pulman, Jane A.; Liu, Tiffany L.; Childs, Kevin L.

doi:10.1101/115345

Cited by 1 publication

(1 citation statement)

References 43 publications

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“…Gene prediction was further performed by training SNAP (library 2013‐02‐16) (Korf, 2004 ) and AUGUSTUS v3.3 (Stanke and Morgenstern, 2005 ) as suggested in Bowman et al. ( 2017 ) and the output of the first round of MAKER annotation. After gene prediction the genes in the gff file were renamed and the file was split to produce one gff for each phase.…”

Section: Methodsmentioning

confidence: 99%

Large structural variations in the haplotype‐resolved African cassava genome

et al. 2021

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Summary Cassava (Manihot esculenta Crantz, 2n = 36) is a global food security crop. It has a highly heterozygous genome, high genetic load, and genotype‐dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi‐C to resolve each haplotype of the genome of a farmer‐preferred cassava line, TME7 (Oko‐iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON‐Phase and Hi‐C read data. The ultralong‐range information from Hi‐C sequencing was also used for scaffolding. Comparison of the two phases revealed >5000 large haplotype‐specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele‐specific expression was further explored. RNA‐sequencing data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy‐to‐use web‐based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype‐specific structural variation, gene hemizygosity, and allele‐specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.

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Section: Methodsmentioning

confidence: 99%