A PacBio single molecule real-time sequencing-based full-length transcriptome atlas of tree tomato (Solanum betaceum Cav.) and mining of simple sequence repeat markers

Deng, Honghong; Zhang, Lu; Liao, Ming’an; Wang, Jin; Liang, Dong; Xia, Hui; Lv, Xiulan; Deng, Qunxian; Wang, Xun; Tang, Yi; Lin, Lijin

doi:10.3389/fpls.2022.1052817

Cited by 2 publications

(1 citation statement)

References 15 publications

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“…Over the past decade, single molecule sequencing technology has been used to characterize the transcriptome diversity in Salvia miltiorrhiza [20], Z. mays [21], Sorghum bicolor [22], Fragaria vesca [23], Phyllostachys edulis [24], Trifolium pratense L. [25], Ricinus communis [26], Ginkgo biloba [27], Populus [28], Solanum betaceum Cav [29] and so on. In these studies, most of the full-length cDNAs were generated by combining in equal amounts total RNA from different tissues and/or did not make replicates.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (Citrullus lanatus)

Yu,

Liufu,

Ren

et al. 2023

IJMS

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Fruit ripening is a highly complicated process that is accompanied by the formation of fruit quality. In recent years, a series of studies have demonstrated post-transcriptional control play important roles in fruit ripening and fruit quality formation. Till now, the post-transcriptional mechanisms for watermelon fruit ripening have not been comprehensively studied. In this study, we conducted PacBio single-molecule long-read sequencing to identify genome-wide alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. In total, 6,921,295 error-corrected and mapped full-length non-chimeric (FLNC) reads were obtained. Notably, more than 42,285 distinct splicing isoforms were derived from 5,891,183 intron-containing full-length FLNC reads, including a large number of AS events associated with fruit ripening. In addition, we characterized 21,506 polyadenylation sites from 11,611 genes, 8703 of which have APA sites. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that fructose and mannose metabolism, starch and sucrose metabolism and carotenoid biosynthesis were both enriched in genes undergoing AS and APA. These results suggest that post-transcriptional regulation might potentially have a key role in regulation of fruit ripening in watermelon. Taken together, our comprehensive PacBio long-read sequencing results offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of watermelon fruit ripening.

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Section: Introductionmentioning

confidence: 99%

Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (Citrullus lanatus)

Yu,

Liufu,

Ren

et al. 2023

IJMS

View full text Add to dashboard Cite

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Abscisic acid promotes selenium absorption, metabolism and toxicity via stress-related phytohormones regulation in Cyphomandra betacea Sendt. (Solanum betaceum Cav.)

Wang,

Lu,

Zhao

et al. 2024

Journal of Hazardous Materials

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A PacBio single molecule real-time sequencing-based full-length transcriptome atlas of tree tomato (Solanum betaceum Cav.) and mining of simple sequence repeat markers

Abstract: and Lin L (2022) A PacBio single molecule real-time sequencingbased full-length transcriptome atlas of tree tomato (Solanum betaceum Cav.) and mining of simple sequence repeat markers.

Cited by 2 publications

References 15 publications

Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (Citrullus lanatus)

Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (Citrullus lanatus)

Abscisic acid promotes selenium absorption, metabolism and toxicity via stress-related phytohormones regulation in Cyphomandra betacea Sendt. (Solanum betaceum Cav.)

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