Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant

Abstract

Background: Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implicated in cold acclimation by affecting gene expression in various ways, yet little information is known about how AS influences cold responses in tea plant (Camellia sinensis).Results: In this study, the AS transcriptional landscape was characterized in the tea plant genome using highthroughput RNA-seq during cold acclimation. We found that more than 41% (14,103) of genes underwent AS events. We summarize the possible existence of 11 types of AS events, including the four common types of intron retention (IR), exon skipping (ES), alternative 5′ splice site (A5SS), and alternative 3′ splice site (A3SS); of these, IR was the major type in all samples. The number of AS events increased rapidly during cold treatment, but decreased significantly following de-acclimation (DA). It is notable that the number of differential AS genes gradually increased during cold acclimation, and these genes were enriched in pathways relating to oxidoreductase activity and sugar metabolism during acclimation and de-acclimation. Remarkably, the AS isoforms of bHLH transcription factors showed higher expression levels than their full-length ones during cold acclimation. Interestingly, the expression pattern of some AS transcripts of raffinose and sucrose synthase genes were significantly correlated with sugar contents. Conclusion: Our findings demonstrated that changes in AS numbers and transcript expression may contribute to rapid changes in gene expression and metabolite profile during cold acclimation, suggesting that AS events play an important regulatory role in response to cold acclimation in tea plant.

HAK/KUP/KT family potassium transporter genes are involved in potassium deficiency and stress responses in tea plants (Camellia sinensis L.): expression and functional analysis

“…In addition to grow in plains, most tea plants grow in the wild in mountainous and hilly areas and often face potassium starvation. Generally, K + -starved tea plants are greatly vulnerable to various stress types, both biotic (pests, fungal diseases) and abiotic (drought, cold, high temperature) [ 9 , 61 , 65 ]. Potassium improves the resistance of tea plants to these stresses and promotes the synthesis and partitioning of photosynthate [ 8 , 12 , 65 ].…”

CsLAZY1 mediates shoot gravitropism and branch angle in tea plants (Camellia sinensis)

“…First-strand cDNA was synthesized from total RNA using the PrimeScript RT Reagent Kit (cat RR036A, Takara, Japan) following the manufacturer’s protocol. A 10 μl total reaction volume, including 5 μl TB Green Enzyme, 1.2 μl cDNA, 3.2 μl water and 0.6 μl primer, was used for qRT-PCR, and the process was performed as described previously in detail [ 38 , 39 ]. The CsGAPDH gene was selected as the internal control, and the relative gene expression values were analyzed using the 2 −△Ct method [ 40 ].…”

Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Pinus taeda L.) in North America

“…Chen et al (2020) compiled recent publications focused on AS studies in different tree species at various stages of development and in response to various stresses. The group, highlighted major contributions in the study of AS in woody species that have been focused on development and stress-responses, including fruit ripening (Mica et al, 2010;Gupta et al, 2015), flower morphogenesis (Ai et al, 2012), wood formation (Xu et al, 2014), drought stress (Guo et al, 2017;Ding et al, 2020), and cold stress (Xiao and Nassuth, 2006;Rahman et al, 2014;Li et al, 2020). Strategies to advance in the functional analysis of AS in woody species have been proposed (Chen et al, 2020).…”