July 7, 2019  |  

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

Authors: Hatakeyama, Masaomi and Aluri, Sirisha and Balachadran, Mathi Thumilan and Sivarajan, Sajeevan Radha and Patrignani, Andrea and Grüter, Simon and Poveda, Lucy and Shimizu-Inatsugi, Rie and Baeten, John and Francoijs, Kees-Jan and Nataraja, Karaba N and Reddy, Yellodu A Nanja and Phadnis, Shamprasad and Ravikumar, Ramapura L and Schlapbach, Ralph and Sreeman, Sheshshayee M and Shimizu, Kentaro K

Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length?>2.6?Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes.© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Journal: DNA research
DOI: 10.1093/dnares/dsx036
Year: 2017

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