Abstract
BackgroundCarex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts.ResultsIn this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing.ConclusionsThis study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis.
Highlights
Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation
General properties of PacBio sequencing of C. breviculmis To provide a collection of gene transcripts, we combined the total RNA extracted from C. breviculmis grown under two different conditions in equal amounts to obtain a full-length reference transcriptome using PacBio sequencing
Three cDNA libraries of different sizes (1–2 kb, 2–3 kb and 3– 6 kb) were constructed and sequenced using the PacBio RSII sequencing platform, thereby generating 11.52 Gb of SMRT sequencing raw data consisting of 751,460 raw polymerase reads
Summary
Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The PacBio single-molecule long-read sequencing technology (SMRT sequencing) can obtain full-length splice isoforms directly, without assembly, providing a better opportunity to investigate genome-wide fulllength cDNA molecules [5]. Teng et al BMC Genomics (2019) 20:789 thomaeum [9], Trifolium pretense [10], Medicago sativa [11], Fragaria vesca [5], Arabidopsis thaliana [12] and Phyllostachys edulis [13]. These studies proved the power of SMRT sequencing in transcriptome analysis. With the help of NGS sequencing in error correction, SMRT sequencing may uncover full-length splicing isoforms with complete 3′ and 5′ ends more accurately, better identify differential alternative splicing (AS) events, and provide more accurate profiles of global polyadenylation sites (APA) [13, 14]
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