Functional identification of lncRNAs in sweet cherry (Prunus avium) pollen tubes via transcriptome analysis using single-molecule long-read sequencing

Abstract

Sweet cherry (Prunus avium) is a popular fruit with high nutritional value and excellent flavor. Although pollen plays an important role in the double fertilization and subsequent fruit production of this species, little is known about its pollen tube transcriptome. In this study, we identified 16,409 transcripts using single-molecule sequencing. After filtering 292 transposable elements, we conducted further analyses including mRNA classification, gene function prediction, alternative splicing (AS) analysis, and long noncoding RNA (lncRNA) identification to gain insight into the pollen transcriptome. The filtered transcripts could be matched with 3,438 coding region sequences from the sweet cherry genome. GO and KEGG analyses revealed complex biological processes during pollen tube elongation. A total of 2043 AS events were predicted, 7 of which were identified in different organs, such as the leaf, pistil and pollen tube. Using BLASTnt and the Coding-Potential Assessment Tool (CPAT), we distinguished a total of 284 lncRNAs, among which 154 qualified as natural antisense transcripts (NATs). As the NATs could be the reverse complements of coding mRNA sequences, they might bind to coding sequences. Antisense transfection assays showed that the NATs could regulate the expression levels of their complementary sequences and even affect the growth conditions of pollen tubes. In summary, this research characterizes the transcripts of P. avium pollen and lays the foundation for elucidating the physiological and biochemical mechanisms underlying sexual reproduction in the male gametes of this species.

The perennial fruit tree proteogenomics atlas: a spatial map of the sweet cherry proteome and transcriptome

“…Recently, Li et al. (2019) predicted 2043 AS events in sweet cherry pollen tubes using single‐molecule long‐read sequencing. They suggested that RI was the main group, comprising 37.6% of the AS events.…”

“…A high abundance of ES events has been previously reported in peach (Prunus persica; 43%), in contrast to reports on annual plant species such as Arabidopsis, rice (Oryza sativa), maize (Zea mays), and others, where 30% of AS events represent RI (Barbazuk et al, 2008;Marquez et al, 2012;Zhang et al, 2020). Recently, Li et al (2019) predicted 2043 AS events in sweet cherry pollen tubes using single-molecule long-read sequencing. They suggested that RI was the main group, comprising 37.6% of the AS events.…”

Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

“…In addition, some lncRNAs interact with microRNAs (miRNAs), serving as miRNA precursors or competing endogenous RNAs (ceRNAs) to serve as decoys for specific miRNAs, thus protecting the target mRNAs from repression [29][30][31][32] . In recent years, several studies have indicated that lncRNAs play important roles in various biological processes in plants, including roles in organ development, nutrient metabolism, male sterility, and plant immunity [33][34][35][36][37] . In particular, lncRNAs are considered essential regulators of the response to biotic and abiotic stresses in plants 30,[38][39][40] .…”

Whole-Transcriptome Analysis Reveals Long Noncoding RNAs Involved in Female Floral Development of Hickory (Carya cathayensis Sarg.)

“…In plants, although a large number of lncRNAs have been predicted in different biological contexts in quite a few plant species ( Ding et al, 2012 ; Li et al, 2014 ; Shuai et al, 2014 ; Zhang et al, 2014 ; Hao et al, 2015 ), only a handful of plant lncRNAs have been experimentally characterized. Several lines of evidence have shown that these lncRNAs play critical roles in regulating the expression of genes involved in biotic or abiotic stress responses ( Franco-Zorrilla et al, 2007 ; Di et al, 2014 ; Zhu et al, 2014 ; Seo et al, 2017 ; Song et al, 2021 ), vegetative growth ( Ariel et al, 2014 ), fruit development ( Bai et al, 2019 ), reproductive processes ( Ding et al, 2012 ; Zhang et al, 2014 ; Li et al, 2019 ), and flowering time ( Swiezewski et al, 2009 ; Heo and Sung, 2011 ; Kim and Sung, 2017 ) in plant life cycle. In Arabidopsis thaliana , about 6,480 lncRNAs were identified using genome-wide screening of 200 transcriptome data with tissue-specific expression profiles ( Liu et al, 2012 ).…”