Characterization of full-length transcriptome and mechanisms of sugar accumulation in Annona squamosa fruit

Annona squamosa is a multipurpose fruit tree employed in nutritional, medicinal, and industrial fields. Its fruit is significantly enriched in sugars, making it an excellent species to study sugar accumulation in fruit. However, the scarcity of genomic resources hinders genetic studies in this species. This study aimed at generating large-scale genomic resources in A. squamosa and deciphering the molecular basis of its high sugar content. Herein, we sequenced and characterized the full-length transcriptome of A. squamosa fruit using PacBio Iso-seq. In addition, we analyzed the changes in sugar content over five fruit growth and ripening stages, and we applied RNA-sequencing technology to investigate the changes in gene expression related to sugar accumulation. A total of 783,647 circular consensus sequences were generated, from which we obtained 48,209 high-quality, full-length transcripts. Additionally, 1,838 transcription factors and 1,768 long non-coding RNAs were detected. Furthermore, we identified 10,400 alternative splicing events from 2,541 unigenes having on average 2–4 isoforms. A total of 15,061 simple sequence repeat (SSR) motifs were discovered and up to three primer pairs were designed for each SSR locus. Sugars mainly accumulate during the ripening stage in A. squamosa. Most of the genes involved in sugar transport and metabolism in the fruit were progressively repressed overgrowth and ripening stages. However, sucrose phosphate synthase involved in sucrose synthesis and more importantly, isoamylase, alpha-amylase, beta-amylase, 4-alphaglucanotransferase genes involved in starch degradation displayed positive correlations with sugar accumulation in fruit. Overall, we provide here a high-quality, full-length transcriptome assembly which will facilitate gene discovery and molecular breeding of A. squamosa. We found that starch degradation during fruit ripening was the main channel for sugar accumulation in A. squamosa fruit, and the key genes positively linked to sugar accumulation could be further studied to identify targets for controlling sugar content in A. squamosa fruit.