Transcriptome analysis of a medicinal plant, Pistacia chinensis

Abstract

Pistacia chinensis Bunge has not only been used as a medicinal plant to treat various illnesses but its young shoots and leaves have also been used as vegetables. In addition, P. chinensis is used as a rootstock for Pistacia vera (pistachio). Here, the transcriptome of P. chinensis was sequenced to enrich genetic resources and identify secondary metabolite biosynthetic pathways using Illumina RNA-seq methods. De novo assembly resulted in 18,524 unigenes with an average length of 873 bp from 19 million RNA-seq reads. A Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation tool assigned KO (KEGG orthology) numbers to 6,553 (36.2%) unigenes, among which 4,061 unigenes were mapped into 391 different metabolic pathways. For terpenoid backbone and carotenoid biosynthesis pathways, 44 and 22 unigenes encode enzymes corresponding to 30 and 16 entries, respectively. Twentytwo unigenes encode proteins for 16 entries of the carotenoid biosynthesis pathway. As for the phenylpropanoid and flavonoid biosynthesis pathways, 63 and 24 unigenes were homologous to 17 and 14 entry proteins, respectively. Mining of simple sequence repeat identified 2,599 simple sequence repeats from P. chinensis unigenes. The results of the present study provide a valuable resource for in-depth studies on comparative and functional genomics to unravel the underlying mechanisms of the medicinal properties of Pistacia L.

Differential expression of genes in olive leaves and buds of ON- versus OFF-crop trees

“…The output obtained was used as a reference genome for further analysis. This procedure is reliable and strong strategy which has been used for molecular study of wide plant species such as olive 18,20 , pear 60 and pistachio 61 . By de novo assembly strategy, we mapped the majority of clean reads in every library with made contigs and blasted over 69% of the obtained transcripts with available databases.…”

Transcriptome Analysis and Identification of a Female-Specific SSR Marker in Pistacia chinensis Based on Illumina Paired-End RNA Sequencing

“…Similar findings were also reported in V. angularis [ 34 ], B. napus [ 27 ], I. polycarpa [ 36 ], and A. argotaenia [ 39 ]. Taken together, these data indicate that the trinucleotide motif AAG/CTT is common in P. chinensis [ 22 ]. Besides, we also noticed that AT-rich trinucleotide motifs (AAG/CTT, AAT/ATT, AAC/GTT, ACT/AGT, and ATC/ATG > 71%) were more abundant than GC-rich trinucleotide (ACC/GGT, AGG/CCT, AGC/GCT, ACG/CGT, and CCG/CGG, <29%).…”

“…Transcriptome sequencing has been commonly used to screen SSRs in various angiosperm species, including Fragaria × Potentilla (red-flowering strawberry), Amentotaxus argotaenia , Curcuma alismatifolia , Vigna angularis , P. vera, and P. chinensis [ 22 , 33 , 37 , 38 , 39 , 40 , 41 ]. In this study, out of 83,370 unigenes, 17,028 unigenes consisted of SSR motifs, accounting for 20.42% of total sequences, with a SSR distribution density of 1 per 5.1 kb ( Table 4 and Table 5 ).…”

“…Such divergence in the abundance and distribution of SSR motifs among various plant species could be partially explained by the variations between species, SSR search criteria, size of the datasets, sequence redundancy, and types of data mining tools [ 31 , 36 , 52 ]. The nucleotide characteristics of SSRs may be varied in different plants, and trinucleotides showed the highest repetition rate in Amorphophallus konjac and A. bulbifer [ 53 ], C. alismatifolia [ 38 ], Actinidia chinensis [ 54 ], Z. officinale [ 51 ], and P. chinensis [ 22 ]. In contrast, our results demonstrated that dinucleotide SSR was the most abundant type, which were consistent with those of previous studies conducted on V. angularis [ 37 ], Idesia polycarpa [ 36 ], red-flowering strawberry [ 33 ], and P. vera [ 41 ].…”

“…The sex-linked SSR markers were further verified in a large population of P. chinensis plants. To our knowledge, few studies focus on SSR marker discovery in P. chinensis based on RNA-seq application [ 22 ].…”