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First Insights into the Guar (Cyamopsis tetragonoloba (L.) Taub.) Genome of the ‘Vavilovskij 130’ Accession, Using Second and Third-Generation Sequencing Technologies

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Abstract

Guar (Cyamopsis tetragonoloba (L.) Taub.) is becoming a popular industrial crop in response to industry demand for the guar gum extracted from seeds’ endosperm. Breeding efforts of new guar varieties would greatly benefit from genomic resources developed for marker assisted selection (MAS) purposes. We have undertaken the first steps to establish a whole-genome assembly of the guar ‘Vaviloskij 130’ accession, bred at VIR. Using a combination of second (Illumina short reads) and third generation (Oxford Nanopore long reads) sequencing methods, a dataset of approx. 5X of genome coverage was obtained. We tested assemblers for short reads, namely SOAPdenovo, AbySS and SGA, based on different algorithms. For short reads (Illumina MiSeq and HiSeq data), the better result in terms of total number of scaffolds and total assembly length were obtained with SGA (String Graph Assembler). For Oxford Nanopore dataset, we used the combination of minimap + miniASM assembly, then corrected the assembly with raw Illumina and Nanopore data. The current preliminary de novo assembly of the guar genome covers 1.2 Gb, corresponding to 50% of the genome. The data confirm the phylogeny position of C. tetragoloba as being highly related to the genus Vigna, Abrus, Glycine and Lupinus genomes. This preliminary reference genome paves the way to further detailed diversity and genetic analyses into that important agro-industrial crop.

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ACKNOWLEDGMENTS

The reported study was funded by RFBR according to the research project no. 17-29-08027. We are grateful to the Genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul) for providing computing resources. Sequencing was performed at the Biobank of Research Park of St. Petersburg State University (no. 1259502495). E. Potokina was supported by a “Visiting Scholar” fellowship from Toulouse INP for a short scientific stay at Toulouse INP.

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Authors and Affiliations

  1. Vavilov All-Russian Institute of Plant Genetic Resources, 190000, St. Petersburg, Russia

    E. Grigoreva, P. Ulianich & E. Potokina

  2. EcoLab, Université de Toulouse, CNRS, Auzeville-Tolosane 31326 Castanet-Tolosan Cedex, Toulouse, France

    C. Ben & L. Gentzbittel

  3. Saint-Petersburg State University, 199034, St. Petersburg, Russia

    E. Potokina

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  1. E. Grigoreva
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  2. P. Ulianich
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  3. C. Ben
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  4. L. Gentzbittel
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Correspondence to L. Gentzbittel or E. Potokina.

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Grigoreva, E., Ulianich, P., Ben, C. et al. First Insights into the Guar (Cyamopsis tetragonoloba (L.) Taub.) Genome of the ‘Vavilovskij 130’ Accession, Using Second and Third-Generation Sequencing Technologies. Russ J Genet 55, 1406–1416 (2019). https://doi.org/10.1134/S102279541911005X

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