Bioinformatics insight in shallow genome sequence: a case study of Corymbia hybrid (C. citriodora × C. torelliana)

Genetic improvement in industrially important Eucalyptus hybrids has been hindered due to the non-availability of functionally relevant genomic or transcriptomic data. Large-scale genomic data discovery has been enabled by the invention of next-generation sequencing (NGS). In this study, NGS was employed to characterize the genomic data of Corymbia hybrids and the development of simple sequence repeat (SSR) markers. A total of ~ 11 Gb raw data with 77.87 million reads were generated through the Illumina HiSeq platform. De novo assembly yielded 2,11,948 contigs (30 × coverage and ~ 387 Mb genome size) with an average length of 150 bp and a read map of up to 88.21%. Further, sequence similarity analyses and annotation of the contigs against the non-redundant protein (Nr) and Gene Ontology (GO) databases identified 548 GO annotations. The annotation of biochemical pathways resulted in 4,684 contigs assigned to 389 Kyoto Encyclopedia of Genes and Genomes (KEGG) maps. A total of 10,501 SSRs were designed out of the 13,321 SSRs that were identified. In silico tests of these SSRs showed successful amplification in C. citriodora (3,789; 36.08%), followed by E. globulus (68; 0.648%), E. grandis (67; 0.638%), and E. camaldulensis (62; 0.590%), all available at the public database NCBI. Notably, a total of 38 in silico SSRs amplied in all four genome sequences. Further, genetic diversity measures for the F₂ recombinant population via four polymorphic SSRs revealed polymorphic information content (PIC), average observed heterozygosity (Ho), and expected heterozygosity (He), which were recorded as 0.184–0.477, 0.493 ± 0.13, and 0.403 ± 0.07, respectively. In addition, the negative value of inbreeding coefficient (F_IS = − 0.197 ± 0.15) signifies that heterozygotes are more frequent in F₂ populations. Overall, the study enriches the genomic and microsatellite data in the genus Corymbia.