Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing

Abstract

The use of alternative transcription start or termination sites (aTSS or aTTS) as well as alternative splicing (AS) produce diverse transcript isoforms, playing indispensable roles in the plant development and environmental adaptations. Despite the advances in the finding of the genome-wide alternatively spliced genes in strawberry, it remains unexplored how AS responds to the developmental cues and what relevance do these outcomes have to the gene function. In this study, we have systematically investigated the transcriptome complexity using long-read Oxford Nanopore Technologies along the four successive developmental stages. The full-length cDNA sequencing results unraveled thousands of previously unexplored transcript isoforms raised from aTSS, aTTS, and AS. The relative contributions of these three processes to the complexity of strawberry fruit transcripts were compared. The aTSS and aTTS were more abundant than the AS. Differentially expressed transcripts unraveled the key transitional role of the white fruit stage. Isoform switches of transcripts from 757 genes were observed. They were associated with protein-coding potential change and domain gain or loss as the main consequences. Those genes with switched isoforms take part in the key processes of maturation in the late stages. A case study using yeast two hybrid analysis supported the functional divergence of the two isoforms of the B-box protein 22. Our results provided a new comprehensive overview of the dynamic transcriptomic landscape during strawberry fruit development and maturation.

Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo

“…Intriguingly, most AS-occurring genes were also accompanied by aTSS and aTTS. Furthermore, the frequencies of aTSS and aTTS were more common than that of AS, which was consistent with the observations in human genes [ 30 ] and also similar to the response to fruit development and maturation of strawberry genes [ 10 ].…”

“…Usually, AS events are commonly classified into intron retention, exon skipping, the alternative 5′ splice site, the alternative 3′ splice site, and mutually exclusive exons, and the occurrence of these changes could impact the fate of gene products. Alternative transcription initiation and alternative transcription termination are also important transcriptional regulation processes that contribute to transcript complexity in plants [ 10 ]. Based on single molecular long-read sequencing data, we identified that 27,244 genes produced at least two isoforms in growing culms, suggesting the vital function of AS, aTSS, and aTTS in moso bamboo culm growth.…”

“…It is evident that both pre-transcriptional regulation and post-transcriptional modifications have been involved in numerous physiological and adaptive regulations. Moreover, AS is closely associated with plant growth and development processes [ 10 ], as well as environmental adaptability [ 11 ].…”

Table1.xlsx

“…This study identified 506 sex-biased alternative splicing events in the antennal tissue of Bactrocera dorsalis, with ATSS accounting for 31% of these events. This phenomenon of ATSS having a relatively high proportion in alternative splicing events has also been found in other species (Reyes and Huber, 2018;Chen et al, 2022). Currently, there are a lack of studies on the relationship between ATSS events and inter-sexual differentiation of gene functions in insects.…”

DataSheet3.ZIP

“…This study identified 506 sex-biased alternative splicing events in the antennal tissue of Bactrocera dorsalis, with ATSS accounting for 31% of these events. This phenomenon of ATSS having a relatively high proportion in alternative splicing events has also been found in other species (Reyes and Huber, 2018;Chen et al, 2022). Currently, there are a lack of studies on the relationship between ATSS events and inter-sexual differentiation of gene functions in insects.…”