Full-length transcriptome sequencing of Arabidopsis seedlings provided new insights into autophagic regulation of photosynthesis

Autophagy is a highly conserved eukaryotic pathway and plays a crucial role in cell survival under stress. Here, we applied a full-length transcriptome approach to study Arabidopsis autophagy mutant (atg5-1) exposed to nitrogen-starvation, using Oxford Nanopore Technologies. A total of 39,033 transcripts were identified, including 11,356 new transcripts. In addition, alternative splicing (AS) events and lncRNAs were also detected between Col-0 (WT) and atg5-1. Differentially expressed transcripts enrichment shown that autophagy upregulates the expression of many stress-responsive genes and inhibits transcription of photosynthesis-associated genes. The results of qRT-PCR showed that the expression patterns of photosynthesis-related genes in the atg5-1 were different under the conditions of nitrogen starvation and carbon starvation. Under nitrogen starvation treatment, many genes related to photosynthesis also exhibited AS. The chlorophyll fluorescence images showed that the Fv/Fm and ΦPSII of old atg5-1 leaves were significantly reduced after nitrogen starvation treatment, but the Y(NPQ) indices were significantly increased compared to those of WT. Taken together, the results provide new insights into how new transcripts, lncRNAs and AS (alternative splicing) are involved in plant autophagy through full-length transcriptome sequencing and suggest a new potential link between autophagy and photosynthesis.