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Pipeline publication

[…] regions in Kiroba derived from M. glaziovii, investigate their genomic locations, and compare them with the identified QTL regions to infer the source of observed resistance. The varieties for this study were; M. glaziovii, a wild species of Manihot, also known as Ceará or India rubber, Albert, a Tanzanian variety said to be a pure M. esculenta, and Kiroba, one of the parents used in the mapping population reported in this study. DNA extractions, library preparations and sequencing was done as described in Bredeson et al. (). SRA BioSample accession numbers are as follows: Kiroba (SAMN02693378), Albert (SAMN04117017), M. glaziovii (SAMN02693380)., Sequence quality assessment was done using FastQC (Patel and Jain, ). The first 10 bases were trimmed using fastx trimmer and then de novo assembly performed using abyss-pe (Simpson et al., ). Default parameters were used with a k-mer of 64. The purpose of assembling the Kiroba genome was to obtain high quality scaffolds for alignment and SNP analysis. The quality of the Kiroba assembly was assessed by N50 length statistics derived from the abyss-pe output. Based on the results of the assembly, scaffolds and contigs smaller than 200 bp were discarded to avoid using low quality reads in subsequent analysis. Assemblies of M. glaziovii and Albert (M. esculenta), were downloaded from Phytozome v.10 (Goodstein et al., ), and together with the Kiroba assembly, were aligned to v5.1 of the cassava genome assembly, using Bowtie2 (Langmead and Salzberg, ) followed by SNP calling using GATK., The genotype information from the VCF file (the output of GATK pipeline discussed above) was coded as follows; 0/0 = 0, meaning homozygous to the reference, 0/1 = 1, heterozygous to the reference and 1/1 = 2, homozygous alternative. Any SNP with a missing value (−/−) for any genotype was removed. For each SNP, the absolute value for difference between the M. glaziovii and Kiroba (GK) and the difference between Albert and Kiroba (AK) scores were calculated. The final score for the SNP was determined using the equation: Diffscore = AK+ (2 − GK). Any SNP Diffscore value >2 was regarded as indicative of introgression. A loop was created to look at 1,000 bp at a time starting at position 1. The tail of the contig <1,000 bp was not analyzed. Poisso […]

Pipeline specifications

Software tools FastQC, ABySS, Bowtie2, GATK
Databases Phytozome
Organisms Manihot esculenta
Diseases Disease, Necrosis