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


Abstract

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 sci- entific 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 over- come this problem, we sequenced its genome using diverse technologies with sufficient cover- age 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 IrysVR 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 as- sembly of other allotetraploid genomes.

Abstract

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 sci- entific 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 over- come this problem, we sequenced its genome using diverse technologies with sufficient cover- age 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 IrysVR 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 as- sembly of other allotetraploid genomes.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Uncontrolled Keywords:hybrid de novo assembly, finger millet, allotetraploid genome, whole-genome optical mapping
Language:English
Date:September 2017
Deposited On:07 Sep 2017 14:40
Last Modified:07 Sep 2017 14:48
Publisher:Oxford University Press
ISSN:1340-2838
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/dnares/dsx036

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Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)