A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense

Abstract

Background Gnetum is an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening of Gnetum seeds. However, the molecular mechanisms related to this process remain unknown. Results We therefore assembled a full-length transcriptome from immature and mature G. luofuense seeds using PacBio sequencing reads. We identified a total of 5726 novel genes, 9061 alternative splicing events, 3551 lncRNAs, 2160 transcription factors, and we found that 8512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7891 genes upregulated and 6432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening of G. luofuense. Conclusions These findings provide a valuable molecular resource for understanding seed development of gymnosperms.

Transcriptomic Characterization of Nitrate-Enhanced Stevioside Glycoside Synthesis in Stevia (Stevia rebaudiana) Bertoni

“…To further elucidate the underlying mechanism for this, transcriptomic analysis was performed. Further, we validated the RNA-seq data through qRT-PCR detection, as also used in many other studies [38][39][40][41]. Accordingly, the similar expression patterns of specific SG synthesis-related genes from RNA-Seq and qRT-PCR results confirmed the validity of our transcriptome analysis results (Figure 7).…”

Comparative Analyses of Full-Length Transcriptomes Reveal Gnetum luofuense Stem Developmental Dynamics

“…In terms of AS event analysis, results show that intron retention accounts for the largest proportion (32.23%) of the total number of events recorded in G. luofuense stem FLs ( Figure 2A ). This number turns out to be smaller than detected in the female strobili (46%) and the leaves (41.5%), respectively ( Hou et al, 2019a ), but larger than that in the seeds (29.9%) of G. luofuense ( Deng et al, 2020 ). These AS mode proportions have also been reported in Ginkgo biloba L. ( Ye et al, 2019 ) vegetative and reproductive organs as well as in maize and sorghum ( Wang et al, 2018 ).…”

“…The results of APA analysis differ from those of previous studies where transcript numbers declined from one poly(A) site to five poly(A) sites ( Figure 2C ). At the same time, transcript numbers with more than five poly(A) sites make up a relatively small proportion in G. luofuense FLs within the leaves (3.12%), the female strobili (11.14%), and the seeds (3.62%) of G. luofuense ( Deng et al, 2019b ; Hou et al, 2019a , Deng et al, 2020 ). We further examined transcript numbers and found them consistent regardless of APA mode ( Figure 2D ) and were also able to show that the patterns of these events are more conserved compared with their AS counterparts.…”

Endosperm evolution by duplicated and neofunctionalized Type I MADS-box transcription factors

“…The expression data of Type I MADS-box genes in A. thaliana were extracted from Klepicova et al ( 2016) for a spectrum of different organ types and developmental stages and Belmonte et al (2013) for specific compartments in developing seeds. The other transcriptomes used in this study were retrieved from maize (Chen et al 2014;Walley et al 2016), rice (Paul et al 2020), soybean (Chen et al 2021), castor bean (Xu et al 2014), tomato (Pattison et al 2015), coconut (Saensuk et al 2016), avocado (Ge et al 2019), monkeyflower (Flores-Vergara et al 2019), coffee (Ivamoto et al 2017), Nymphaea thermarum (Povilus and Friedman 2021), Picea (Nystedt et al 2013), and Gnetum (Hou et al 2019;Deng et al 2020). Gene identifiers in Supplementary Table…”