Full-length transcriptome analysis of Zanthoxylum nitidum (Roxb.) DC.

Abstract

Zanthoxylum nitidum (Roxb.) DC. (Z. nitidum) is a type of Chinese Dao-di herb, also called Liangmianzhen, which is widely used to treat arthralgia, rheumatic arthralgia, and stomach pain. However, genomic resources for Z. nitidum are still scarce. This study provides transcriptomic resources for Z. nitidum by applying single-molecule real-time (SMRT) sequencing technology. In total, 456,109 circular consensus sequencing (CCS) reads were generated with a mean length of 2,216 bp from Z. nitidum roots, old stems, young branches, leaves, flowers, and fruits. Of these total reads, 353,932 were full-length nonchimeric (FLNC) reads with an average length of 1,996 bp. A total of 16,163 transcripts with a mean length of 1,171 bp were acquired. Of these transcripts, 14,231 (88%) were successfully annotated using public databases. Across all the 16,163 transcripts, we identified 6,255 long non-coding RNAs (lncRNAs) and 22,780 simple sequence repeats (SSRs). Furthermore, 3,482 transcription factors were identified. Among the SSR loci, 1–3 nucleotide repeats were dominant, occupying 99.36% of the total SSR loci, with mono-, di-, and tri-nucleotide repeats accounting for 61.80%, 19.89%, and 5.02% of the total SSR loci, respectively. A total of 36 out of 100 randomly selected primer pairs were verified to be positive, 20 of which showed polymorphism. These findings enrich the genetic resources available for facilitating future studies and research on relevant topics such as population genetics in Z. nitidum.

Dynamic changes in the levels of metabolites and endogenous hormones during the germination of Zanthoxylum nitidum (Roxb.) DC. Seeds

“… 31 Z. nitidum seeds exhibit PD. 16 The results of this study showed that both stratification and exogenous GA treatment are effective methods for breaking the dormancy of Z. nitidum seeds. The germination method is the same as that used for most physiologically dormant seeds.…”

“…A layer of moist fine sand (60 g of 1–2 mm fine sand +12 g of tap water) was placed onto a culture dish (diameter, 9 cm), and 60 stratified seeds were evenly inoculated onto the dish. 16 The number of germinated seeds was recorded every 5 days until the germination was complete, and each treatment was repeated five times. Fifty seed embryos at each stage were sampled and stored at −80°C for further analysis.…”

“…According to these studies, immersing the seeds in 300 mg/L GA solution for 2 days significantly increased the germination rate from 3.7% to 22%, 15 and layering the seeds onto 100 mg/L GA solution for 1 month significantly increased the germination rate from 0.7% to 47.9%. 16 However, to date there has been still limited research on the physiological and molecular regulatory mechanisms of seed germination.…”