Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress

Abstract

In this study, third-generation full-length (FL) transcriptome sequencing was performed of loquat using single-molecule real-time(SMRT) sequencing from the pooled cDNA of embryos of young loquat fruit under different low temperatures (three biological replicates for treatments of 1˚C,-1˚C, and-3˚C, for 12 h or 24 h) and the control group(three biological replicates for treatments of room temperature), Illumina sequencing was used to correct FL transcriptome sequences. A total of 3 PacBio Iso-Seq libraries (1-2 kb, 2-3 kb and 3-6 kb) and 21 Illumina transcriptome libraries were constructed, a total of 13.41 Gb of clean reads were generated, which included 215,636 reads of insert (ROIs) and 121,654 FL, non-chimaric (FLNC) reads. Transcript clustering analysis of the FLNC reads revealed 76,586 consensus isoforms, and a total of 12,520 high-quality transcript sequences corrected with non-FL sequences were used for subsequent analysis. After the redundant reads were removed, 38,435 transcripts were obtained. A total of 27,905 coding DNA sequences (CDSs) were identified, and 407 long non-coding RNAs (lncRNAs) were ultimately predicted. Additionally, 24,832 simple sequence repeats (SSRs) were identified, and a total of 1,295 alternative splicing (AS) events were predicted. Furthermore, 37,993 transcripts were annotated in eight functional databases. This is the first study to perform SMRT sequencing of the FL transcriptome of loquat. The obtained transcriptomic data are conducive for further exploration of the mechanism of loquat freezing injury and thus serve as an important theoretical basis for generating new loquat material and for identifying new ways to improve loquat cold resistance.

De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses

“…The third-generation single-molecule real-time (SMRT) sequencing platform can capture full length transcripts and avoid the assembly process [30]. SMRT sequencing has been widely used in many plant species such as Arabidopsis pumila [31], rice [32,33], moso bamboo [34], loquat [35], orchid (Bletilla striata) [36], danshen (Salvia miltiorrhiza Bunge) [37] and sugarcane [38] which have provide thousands of high quality full length transcripts and facilitated the identification of alternative splicing. In this study, the upgraded PacBio SMRT Sequel platform was employed to generate a full length transcriptome of A. glabrata.…”

Multi-omics analysis provides new insights into the changes of important nutrients and fructose metabolism in loquat bud sport mutant

“…Intriguingly, our previous studies have unveiled a bud sport mutant derived from the yellow-fleshed Dongting loquat, which displayed an alluring white flesh phenotype ( Sun et al., 2012 , 2017 ). This white-fleshed mutant, known as TBW, remarkably differs from the wild type (TBY) in terms of fructose content, flesh texture, maturity, and cold tolerance, highlighting its great potential for breeding purposes ( Sun et al., 2011 ; Li et al., 2016 ; Chen et al., 2017 ; Li et al., 2017 , 2020 ; Pan et al., 2020 ). Recent studies have shown that TBW has a 321-bp deletion in the PSY2A gene, which encodes a rate-limiting enzyme involved in carotenoid synthesis.…”

EjFAD8 Enhances the Low-Temperature Tolerance of Loquat by Desaturation of Sulfoquinovosyl Diacylglycerol (SQDG)

“…Loquat is native to the subtropical regions of humid heat, and its phylogeny is influenced by climatic environments, making it very sensitive to low temperatures [ 2 , 3 ]. The loquat differs from other fruit trees in that its phenological period is generally autumn–winter flowering and fruiting, so its flower and juvenile fruit development is highly susceptible to low-temperature stress, resulting in reduced yields [ 4 , 5 ]. With the recent increase in extreme weather, low temperatures have become one of the most common stressors in plants, with cold and frost damage greatly impacting plant growth and development [ 6 ].…”