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

Abstract

Pistacia chinensis Bunge (P. chinensis), a dioecious plant species, has been widely found in China. The female P. chinensis plants are more important than male plants in agricultural production, as their seeds can serve as an ideal feedstock for biodiesel. However, the sex of P. chinensis plants is hard to distinguish during the seedling stage due to the scarcity of available transcriptomic and genomic information. In this work, Illumina paired-end RNA sequencing assay was conducted to unravel the transcriptomic profiles of female and male P. chinensis flower buds. In total, 50,925,088 and 51,470,578 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 83,370 unigenes with a mean length of 1.3 kb were screened. Overall, 64,539 unigenes (77.48%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG, and GO databases, 71 of which were putatively related to the floral development of P. chinensis. Additionally, 21,662 simple sequence repeat (SSR) motifs were identified in 17,028 unigenes of P. chinensis, and the mononucleotide motif was the most dominant type of repeats (52.59%) in P. chinensis, followed by dinucleotide (22.29%), trinucleotide (20.15%). The most abundant repeats were AG/CT (13.97%), followed by AAC/GTT (6.75%) and AT/TA (6.10%). Based on these SSR, 983 EST-SSR primers were designed, 151 of which were randomly chosen for validation. Of these validated EST-SSR markers, 25 SSR markers were found to be polymorphic between male and female plants. One SSR marker, namelyPCSSR55, displayed excellent specificity in female plants, which could clearly distinguish between male and female P. chinensis. Altogether, our findings not only reveal that the EST-SSR marker is extremely effective in distinguishing between male and female P. chinensis but also provide a solid framework for sex determination of plant seedlings.

Transcriptome analysis of a tropical medicinal plant, Pistacia weinmannifolia

“…Similarly, it was reported that a comparable number of unigenes were identified and annotated from the transcriptome study of P. chinensis (Choi et al 2019). However, the number of unigenes identified in this study was significantly lower than reports from the transcriptome studies of both P. vera (Karci et al 2020;Moazzzam Jazi et al 2017;Zeng et al 2019) and P. chinensis (Cheng et al 2022;Dong et al 2016). Since several other Pistacia species, including P. atlantica, P. lentiscus, and P. weinmannifolia, are also well known as valuable medicinal plants, it was thought that many genomic studies would have been conducted on these species.…”

Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer

“…In the present study, www.nature.com/scientificreports/ 2,510 SSR loci were identified from 37,538 unigenes in the A. heimuer transcriptome; the SSR frequency of 6.69% was higher than the rates for edible mushrooms such as Auricularia polytricha (4.70%) and Pleurotus eryngii (3.09%) 34,35 , indicating that the A. heimuer transcriptome contains abundant SSR loci. Factors such as database validity, species differences, and SSR search criteria may lead to differences in SSR frequency between A. heimuer and other analyzed species 36,37 . SSR repeat types differ among species, but the dinucleotide and trinucleotide repeat types are dominant 38 .…”

Identification of Sex-Associated Genetic Markers in Pistacia lentiscus var. chia for Early Male Detection

“…Effective sex identification of female and male individual P. vera cultivars has been also achieved using Inter-Simple Sequence Repeat (ISSR) markers [24]. Sex-linked polymorphic EST-SSR markers were also effective in eliminating males in P. vera yet were not able to successfully identify the sex in other Pistacia species [6], except for the transcriptome-based EST-SSR marker identified by Chang et al [25], which was effective in distinguishing between male and female P. chinensis.…”