Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

Wu, Bin; Li, Yanni; Li, Jishuang; Xie, Zhenzhen; Luan, Mingbao; Gao, Chunsheng; Shi, Yuhua; Chen, Shilin

doi:10.3390/ijms222111989

Cited by 9 publications

(11 citation statements)

References 114 publications

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“…We indeed find evidence for differential splicing of CsPT1 and multiple other CBGAS-related genes (Figure S1) between a high THC variety (White Cookies) and a high CBD variety (Canna Tsu), but with a small magnitude of difference as well as sample size, and therefore should be confirmed by additional studies. However, in support of our findings, a recent study reported alternative splicing events at the CBGAS locus, as well as others in the cannabinoid biosynthesis pathway, though tests for differential splicing between varieties were not performed (Wu et al 2021).…”

Section: Discussionsupporting

confidence: 90%

Genomic description of critical cannabinoid biosynthesis genes

Innes

Vergara

2023

Botany

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Cannabinoid production is a key attribute of the plant Cannabis sativa and characterizing the genes involved is an essential first step to develop tools for their optimization. We used bioinformatic approaches to annotate and explore variation in the genes coding for enzymes comprising the cannabinoid pathway: olivetol synthase (OLS), olivetolic acid cyclase (OAC), cannabigerolic acid synthase (CBGAS), and the cannabinoid oxidocyclases (THCAS, CBDAS, CBCAS) in multiple C. sativa genome assemblies from diverse lineages. The former three enzymes generate the precursor molecules for the oxidocyclases to produce cannabinoids THC and CBD. We show that duplications of OLS and OAC are consistent across varieties, and that OAC has the least amount of sequence diversity based on phylogenetic comparisons. We also found that one CBGAS-like gene exhibits copy number variation among varieties. We discuss implications of these genes existing on separate chromosomes (with homologs of each found in close proximity), and the significance of CBGAS being located on the X chromosome for cannabinoid production in female plants. This study provides valuable insight on the genomic identity and variation of cannabinoid biosynthesis genes that will benefit future research on the origin and evolution of this pathway, a driver of economic, social, and medicinal value.

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Section: Discussionsupporting

confidence: 90%

Genomic description of critical cannabinoid biosynthesis genes

Innes

Vergara

2023

Botany

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“…In this study, 3 male red deer were selected to collect antler samples at about 30 d, 60 d and 90 d growth stages, so that there were 3 samples from different individuals at each time point. In high-throughput sequencing, every sample pool was a mix of equal amount of RNAs from three individual male deer, as was the case in other studies [ 7 , 40 , 41 , 42 ], which indicated that this method was acceptable. However, studies with at least biological replicates may be more meaningful and acceptable compared with RNA pools, though each pool is collected with at least three samples.…”

Section: Discussionmentioning

confidence: 92%

Integrative Analyses of Antler Cartilage Transcriptome and Proteome of Gansu Red Deer (Cervus elaphus kansuensis) at Different Growth Stages

Chen

Zhang

Jin

et al. 2022

Animals

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The velvet antler is a unique model for cancer and regeneration research due to its periodic regeneration and rapid growth. Antler growth is mainly triggered by the growth center located in its tip, which consists of velvet skin, mesenchyme and cartilage. Among them, cartilage accounts for most of the growth center. We performed an integrative analysis of the antler cartilage transcriptome and proteome at different antler growth stages. RNA-seq results revealed 24,778 unigenes, 19,243 known protein-coding genes, and 5535 new predicted genes. Of these, 2722 were detected with differential expression patterns among 30 d, 60 d, and 90 d libraries, and 488 differentially expressed genes (DEGs) were screened at 30 d vs. 60 d and 60 d vs. 90 d but not at 30 d vs. 90 d. Proteomic data identified 1361 known proteins and 179 predicted novel proteins. Comparative analyses showed 382 differentially expressed proteins (DEPs), of which 16 had differential expression levels at 30 d vs. 60 d and 60 d vs. 90 d but not at 30 d vs. 90 d. An integrated analysis conducted for DEGs and DEPs showed that gene13546 and its coding protein protein13546 annotated in the Wnt signaling pathway may possess important bio-logical functions in rapid antler growth. This study provides in-depth characterization of candidate genes and proteins, providing further insights into the molecular mechanisms controlling antler development.

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“…To decipher the regulation of miRNAs in NATs and STs in C. sativa, we downloaded all the released plant mature miRNA sequences (V 22.1) from miRbase (Kozomara et al, 2019). Then we collected the published miRNA sequences of C. sativa from our previous report (Wu et al, 2021). Then, these miRNAs' targeted NATs and STs were predicted using the psRNATarget server with a penalty score of ≤ 2.5 (Dai et al, 2018).…”

Section: Prediction Of Mirna Targetsmentioning

confidence: 99%

Genome-Wide View and Characterization of Natural Antisense Transcripts in Cannabis Sativa L.

Liu

2023

Preprint

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Natural Antisense Transcripts (NATs) are a kind of complex regulatory RNAs that play vitriol roles in gene expression and regulation. In recent years, due to the tremendous economic and medicinal values of cannabinoids, the genome of Cannabis Sativa L. was sequenced and the the biosynthetic pathway of cannabinoids was deciphered. Moreover, the regulation of non-coding RNAs, including microRNAs and long non-coding RNAs involved in the biosynthesis of cannabinoids were predicted. However, the NATs in C. sativa remain unknown. In this study, we predicted C. sativa NATs genome-wide by a computational pipeline using strand-specific RNA sequencing (ssRNA-Seq) data. Then, we performed a comprehensive analysis and validated the expression profiles by strand-specific quantitative reverse transcription PCR (ssRT-qPCR). As a result, 260 NATs were predicted in C. sativa, including 92 cis- and 168 trans-NATs. The primary type of cis-NATs was sense transcripts (STs) containing NATs. The expression profiles of 92% of transcripts of ssRNA-Seq were consistent with those of the ssRT-qPCR. Functional enrichment analysis demonstrated that the C. sativa NATs potentially participated in growth and development, stress resistance, and the biosynthesis of compounds. Finally, 12 cis- and 278 trans- NAT-ST pairs were predicted to produce 476 cis- and 2342 trans- small interfering RNA (nat-siRNAs), respectively. These nat-siRNAs were potentially involved in the biosynthesis of cannabinoids, fatty acids, and cellulose. All these results will shed light on the regulation of NATs and nat-siRNAs in C. sativa.

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Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

Cited by 9 publications

References 114 publications

Genomic description of critical cannabinoid biosynthesis genes

Genomic description of critical cannabinoid biosynthesis genes

Integrative Analyses of Antler Cartilage Transcriptome and Proteome of Gansu Red Deer (Cervus elaphus kansuensis) at Different Growth Stages

Genome-Wide View and Characterization of Natural Antisense Transcripts in Cannabis Sativa L.

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