De novo assembly of the seed transcriptome and search for potential EST-SSR markers for an endangered, economically important tree species: Elaeagnus mollis Diels

Abstract

Seeds of Elaeagnus mollis (Elaeagnaceae) produce an edible oil and contain more vitamin E (Ve) than major oil-seed crops. Despite its economic value, there is no information on its genome sequence. Here, we used the Illumina platform to determine the seed transcriptome of E. mollis to identify the genes related to Ve biosynthesis and potential simple sequence repeat (SSR) markers. In total, 100,999 unigenes were obtained with an average length of 605 bp and N50 of 985 bp. Of these unigenes, 52,256 (51.7%) were annotated in at least one public database (NT, NR, PFAM, SwissProt, KOG, KO, and GO) in searches using blastn/x. The unigene annotation identified 15 unigenes encoding six enzymes (GGR, HPPD, HPT/VTE2, MPBQ-MT/VTE3, TC/VTE1, and γ-TMT/VTE4) putatively involved in Ve biosynthesis. In addition, 16,810 SSRs distributed in 14,057 unigenes were mined. Of these, 2820, 583, and 3423 SSRs were located in the 5′–UTR, coding sequence (CDS), and 3′–UTR regions, respectively, while the remaining 9984 SSRs had undetermined physical locations. The largest group of repeat motifs comprised mononucleotide repeats (70.76%), followed by dinucleotide (15.59%) and trinucleotide (12.10%) repeats. AG/CT (8.69%) and AAG/CTT (4.15%) were the main dinucleotide and trinucleotide repeats, respectively. Furthermore, 9597 SSR-specific primer pairs were designed. Among 100 primer pairs selected randomly to determine their usefulness, 53 proved to be efficient. To the our best of knowledge, this work is the first study of the E. mollis transcriptome and constitutes valuable genomics data for future genetic engineering studies to alter the amount of Ve. The identified potential EST-SSR markers can be used for population genetics studies and assisted-breeding of E. mollis.