Full-length transcriptome analysis of shade-induced promotion of tuber production in Pinellia ternata

Abstract

BackgroundPinellia ternata is native to China and has been used as a traditional herb due to its antiemetic, antitussive, analgesic, and anxiolytic effects. When exposed to strong light intensity and high temperature during the reproductive growth process, P. ternata withers in a phenomenon known as “sprout tumble”, which largely limits tuber production. Shade was previously found to delay sprout tumble formation (STF); however, no information exists regarding this process at the molecular level. Hence, we determined the genes involved in tuber development and STF in P. ternata.ResultsCompared to that with natural sun-light (control), shade significantly induced chlorophyll accumulation, increased chlorophyll fluorescence parameters including initial fluorescence, maximal fluorescence, and qP, and dramatically repressed chlorophyll a:b and NPQ. Catalase (CAT) activity was largely induced by shade, and tuber products were largely increased in this environment. Transcriptome profiles of P. ternata grown in natural sun-light and shaded environments were analyzed by a combination of next generation sequencing (NGS) and third generation single-molecule real-time (SMRT) sequencing. Corrections of SMRT long reads based on NGS short reads yielded 136,163 non-redundant transcripts, with an average N50 length of 2578 bp. In total, 6738 deferentially-expressed genes (DEGs) were obtained from the comparisons, specifically D5S vs D5CK, D20S vs D20CK, D20S vs D5S, and D20CK vs D5CK, of which, 6384 DEGs (94.8%) were generated from the D20S vs D20CK comparison. Gene annotation and functional analyses revealed that these genes were related to auxin signal transduction, polysaccharide and sugar metabolism, phenylpropanoid biosynthesis, and photosynthesis. Moreover, the expression of genes enriched in photosynthesis appeared to be significantly altered by shade. The expression patterns of 16 candidate genes were consistent with changes in their transcript abundance as identified by RNA-Seq, and these might contribute to STF and tuber production.ConclusionThe full-length transcripts identified in this study have provided a more accurate depiction of P. ternata gene transcription. Further, we identified potential genes involved in STF and tuber growth. Such data could serve as a genetic resource and a foundation for further research on this important traditional herb.

Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis

“…Recently, high-throughput sequencing technology especially NGS has been widely used to generate large amounts of omics data of medicinal plants, however, a major limitation of NGS is the length of the short reads, which affected the accuracy of sequence assembly 51 . Single-molecule long-read sequencing offers full-length reads that reduce mis assembles of genes with high sequence identity, greatly improving the accuracy of de novo transcriptome assembly 52 . Therefore, a hybrid sequencing approach combining both short and long-read sequencing technologies provides high-quality and more accurate assemblies for transcriptomic studies in non-model species 53 , 54 .…”

SMRT Sequencing of the Full-Length Transcriptome of the Coelomactra antiquata

“…PacBio RNA-seq has fast sequencing speed, high accuracy, and long readings. Because of the advantages of PacBio RNA-seq, it has been widely used in various species research (Ma et al, 2019;Xue et al, 2019;Luo et al, 2020;Zheng et al, 2020;Chen et al, 2021).…”

“…PacBio RNA-seq has fast sequencing speed, high accuracy, and long readings. Because of the advantages of PacBio RNA-seq, it has been widely used in various species research ( Ma et al, 2019 ; Xue et al, 2019 ; Luo et al, 2020 ; Zheng et al, 2020 ; Chen et al, 2021 ). Because C. antiquata is an important economic shellfish with high medicinal potential, there are many studies now.…”

Regulation Mechanism of Exogenous Brassinolide on Bulbil Formation and Development in Pinellia ternata

“…Pinellia ternata is a perennial herb of the Araceae family and is widely used as a medicinal plant in Asia ( Xue et al, 2019 ). The natural seed setting rate of P. ternata is very low, and it is mostly cultivated by asexual reproduction ( Liu et al, 2012 ).…”