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

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

Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of <i>Moraceae</i>

<div><p>Improving mulberry leaf production with enhanced leaf quality holds the key to sustain the ever increasing demand for silk. Adoption of modern genomic approaches for crop improvement is severely constrained by the lack of sufficient molecular markers in mulberry. Here, we report development and validation of 206 EST derived SSR markers using transcriptome data generated from leaf tissue of a drought tolerant mulberry genotype, Dudia white. Analysis of transcriptome data containing 10169 EST sequences, revealed 1469 sequences with microsatellite repeat motifs. We designed a total of 264 primers to the most appropriate repeat regions, of which 206 were locus specific. These markers were validated with 25 diverse mulberry accessions and their transferability to closely related species belonging to family <i>Moraceae</i> was examined. Of these markers, 189 revealed polymorphism with up to 8 allelic forms across mulberry species, genotypes and varieties with a mean of 3.5 alleles per locus. The markers also revealed higher polymorphic information content of 0.824 among the accessions. These markers effectively segregated the species and genotypes and hence, can be used for both diversity analysis and in breeding applications. Around 40% of these markers were transferable to other closely related species. Along with the other genic and genomic markers, we report a set of over 750 co-dominant markers. Using these markers we constructed the first genetic linkage map of mulberry exclusively with co-dominant markers.</p></div

Genetic diversity and polymorphic information revealed by markers developed for mulberry and other closely related species.

<p>Genetic diversity and polymorphic information revealed by markers developed for mulberry and other closely related species.</p

Transferability and distribution pattern of mulberry EST-SSR markers in closely related species belonging to <i>Moraceae</i>.

<p>Transferability and distribution pattern of mulberry EST-SSR markers in closely related species belonging to <i>Moraceae</i>.</p

List of mulberry germplasm accessions and species along with other closely related species used for validating the EST-SSR markers developed in mulberry.

<p>List of mulberry germplasm accessions and species along with other closely related species used for validating the EST-SSR markers developed in mulberry.</p

Classification of microsatellite motifs and their frequency among the mulberry EST sequences.

<p>Classification of microsatellite motifs and their frequency among the mulberry EST sequences.</p

Construction of genetic linkage map in mulberry exclusively using co-dominant markers.

<p>Construction of genetic linkage map in mulberry exclusively using co-dominant markers.</p

Validation of genic SSR markers in diverse mulberry accessions.

<p>Validation of genic SSR markers in diverse mulberry accessions.</p

Characterization of EST library for identification of microsatellite motifs.

<p>Characterization of EST library for identification of microsatellite motifs.</p