De novo transcriptome analysis of industrially important agarophyte Gracilaria dura (Rhodophyta: Gracilariacae) revealed differential expression of genes in gametophyte and sporophyte life-phases

Gracilaria dura is the species of choice for commercial aquaculture and quality agarose production. The previous studies have confirmed that the differences in functional traits as well as agar characteristics among life-history stages can be utilised for commercial gains. To enhance our understanding regarding phase differentiation at molecular level, transcriptome analysis was undertaken among tetrasporophyte and female gametophyte collected from the Veraval, Gujarat, India. De novo assembly constructed using an Illumina sequencing platform, yielded 92,645 unigenes in female gametophyte and 146,275 in tetrasporophyte. The similarity search revealed 29.22% and 37.97% unigenes shared homology in non-redundant (Nr) database respectively. Functional annotation with the Kyoto Encyclopedia of Genes and Genomes database assigned unigenes to 23 pathways, majority of them were allocated to carbohydrate metabolism. From significant differentially expressed genes between these life-phases KHN09340.1 and WP_005180746.1 on validation were found 1.2-fold up-regulated and 1.6-fold down-regulated respectively in tetrasporophyte. Further, few differentially expressed genes e.g. IMPDH, LecRK, SAT provide evidence of disparity between life-history phase in stress tolerance, survival and growth, evidence critical for cultivar development. Moreover, a total of 1577 and 3396 simple sequence repeat (SSR) loci were identified in tetrasporophyte and female gametophyte phase respectively. The polymorphism diversity assessed for 5 SSR loci using heterozygosity index, polymorphic information content and marker index, ranged from 0.68–0.72, 0.18–0.193 and 0.036–0.071 respectively. To the best of our knowledge, this is the first data set for G. dura transcriptome that will facilitate understanding of differences in the isomorphic life phases and further studies of the novel mechanisms in red algae.