Elizaveta Grigoreva from Saint Petersburg State Forestry University in Russia presented at London Callling 2021 on “Whole-genome assembly of guar (Cyamopsis tetragonoloba [L.] Taub.) by second- and third-generation sequencing approaches.” The guar plant is native to India, Pakistan, and the US. It is a legume used in the oil industry as a gelling agent in liquids in oil and gas, according to Grigoreva. There is limited sequence information on the genome. The guar de novo genome assembly approach the team took was genome-guided transcriptome assembly, epigenetics study of guar, and GBS of guar populations. Two sequencing technologies were used: Oxford Nanopore Technologies MinION R9 and Illumina NovaSeq 600. For the MinION, DNA was extracted “using custom method of extraction for palm” and fragmentation with Covaris g-tube. For NovaSeq 600, DNA was extracted following the CTAB method. The MinION ligation sequencing kit 109 was used for five flow cells. Each flow cell was run for fifty or sixty hours. Grigoreva shared images of pore activity that were useful. This helped identify bubbles. Data from five Nanopore flow cells provided 101X coverage and the Illumina run provided 250X coverage. Base calling and filtering was followed by Canu and Flye assembly and polishing with Pilon and Racon. For Illumina, filtering of reads was followed by use of short read assemblers ABySS, Soapdenovo2, Velvet, and SGA. Hybrid assemblies used MaSurCa, hybridSpades, and ABySS. The N50 and assembly metrics suggested that MaSurCa was the best. The assembly was further improved. The genome-guided transcriptome of guar was performed with samples at different time points. Metabolomic and transcriptomic information was combined from samples subjected to long and short-day conditions. the methylation profile from Nanopore sequencing was helpful in several downstream applications.
