De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

Abstract

Apricot (Prunus armeniaca) is an important fruit crop worldwide. We have performed a de novo transcriptome assembly for 7 apricot accessions ('Stark Early Orange' (SEO), 'Hacıhaliloğlu' (HH), 'Perfection' , 'Iğdır' , 'Roxana' , 'Esen1' , and 'Esen2'), which yielded a total number of transcripts ranging from 30,363 for 'SEO' to 59,751 for 'Iğdır' . The pool of the reads produced from 7 accessions were assembled into 85,766 transcripts, with an average of 1165.69 nt. Functional annotation (Gene Ontology-GO and Kyoto Encyclopedia of Genes and Genomes-KEGG) was performed successfully for the transcripts. Simple sequence repeats (SSRs) were searched in the transcript pool and 14,722 di-, tri-tetra-, penta-, and hexanucleotide motif loci with a minimum of 5 repetitions for all motifs were identified. Primers were designed for 206 loci, and 72 of them were found to be polymorphic by amplifying diverse 24 apricot accessions, including 7 Plum Pox Virus (PPV)-resistant and 17 PPV-susceptible accessions. In order to test the amplification success of publicly available genomic SSRs (gSSRs) for diverse apricot accessions, an additional 88 published Prunus gSSRs were characterized amplifying the same 24 apricots and only 54 (62%) produced polymorphic bands. The new EST-SSRs could be a reliable source of primers for characterization and mapping studies of apricots, especially because they mostly flank easily scorable tri-and tetranucleotide repeats.

Molecular Characterization of Prunus Cultivars from Romania by Microsatellite Markers

“…The most informative primers in our study were those targeting BPPCT-025, BPPCT-001, BPPCT-002, Pchgms-021, and UDP96-001 loci in peach cultivars, BPPCT-025, BPPCT-001 and UDP96-001 in nectarines, and BPPCT-002, BPPCT-025, Pchgms-004, Pchgms-020 and BPPCT-004 in apricot cultivars. Some of these primers generated either monomorphic or polymorphic patterns, as shown in previous studies [18,22,[54][55][56].…”

Integrated Metabolite and Transcriptome Profiling-Mediated Gene Mining of Sida cordifolia Reveals Medicinally Important Genes

“…Pharmacological properties exhibited by different extracts of Sida cordifolia are antimicrobial, anti-inflammatory, analgesic, anti-ulcer, nephroprotective, anti-diabetic, hepatoprotective, anticancer, and central nervous system depressant activity [ 8 ]. The inevitable identification of genes responsible for the production of various secondary metabolites by S.cordifolia is achieved using the next-generation sequencing technology to unravel the novel transcripts from medicinal plants with respect to secondary metabolite biosynthesis and gene expression analysis [ 9 ]. The technology is employed to generate functional data for non-model plants and EST sequences for the annotation of genes and analysis of targeted discovery.…”