Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA's function in nicotine biosynthesis.

Scientific Reports
Jingjing JinPeijian Cao

Abstract

Tobacco (Nicotiana tabacum) is considered as the model plant for alkaloid research, of which nicotine accounts for 90%. Many nicotine biosynthetic genes have been identified and were known to be regulated by jasmonate-responsive transcription factors. As an important regulator in plant physiological processes, whether small RNAs are involved in nicotine biosynthesis is largely unknown. Here, we combine transcriptome, small RNAs and degradome analysis of two native tobacco germplasms YJ1 and ZY100 to investigate small RNA's function. YJ1 leaves accumulate twofold higher nicotine than ZY100. Transcriptome analysis revealed 3,865 genes which were differently expressed in leaf and root of two germplasms, including some known nicotine and jasmonate pathway genes. By small RNA sequencing, 193 miRNAs were identified to be differentially expressed between YJ1 and ZY100. Using in silico and degradome sequencing approaches, six nicotine biosynthetic genes and seven jasmonate pathway genes were predicted to be targeted by 77 miRNA loci. Three pairs among them were validated by transient expression in vivo. Combined analysis of degradome and transcriptome datasets revealed 51 novel miRNA-mRNA interactions that may regulate nicotine biosynt...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 2, 2000·Plant & Cell Physiology·T ShojiT Hashimoto
May 5, 2001·Annual Review of Plant Physiology and Plant Molecular Biology·Peter J Facchini
Jul 20, 2004·The Plant Cell·Ramanjulu Sunkar, Jian-Kang Zhu
Jul 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·A A BazziniS Asurmendi
Feb 7, 2008·Annual Review of Plant Biology·Jörg Ziegler, Peter J Facchini
May 22, 2008·Plant & Cell Physiology·Tsubasa ShojiTakashi Hashimoto
Jun 11, 2008·Nature Biotechnology·Marcelo A GermanPamela J Green
Sep 26, 2008·PLoS Biology·Carla SchommerDetlef Weigel
Nov 20, 2008·Bioinformatics·Charles Addo-QuayeMichael J Axtell
Nov 1, 2007·Plant Signaling & Behavior·Sadaf Khan, Julie M Stone
Oct 21, 2010·The Plant Cell·Tsubasa ShojiTakashi Hashimoto
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Feng LiBarbara Baker
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 19, 2013·Genome Biology·Nicolas SierroNikolai V Ivanov
Aug 21, 2013·Phytochemistry·Ralph E Dewey, Jiahua Xie
May 1, 1989·Journal of Chemical Ecology·I T Baldwin
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
May 9, 2014·Nature Communications·Nicolas SierroNikolai V Ivanov
Jan 15, 2015·Molecular Genetics and Genomics : MGG·Xuewen Wang, Jeffrey L Bennetzen
Jun 27, 2015·Functional & Integrative Genomics·Hikmet Budak, B Ani Akpinar
Apr 17, 2016·Plant & Cell Physiology·Chonprakun ThagunTsubasa Shoji
Jul 16, 2016·Molekuliarnaia biologiia·N V KorobanN V Melnikova
May 26, 2017·Proceedings of the National Academy of Sciences of the United States of America·Shuqing XuIan T Baldwin
Jun 7, 2017·Plant Physiology·Masataka KajikawaTsubasa Shoji
Jun 15, 2017·Plant Signaling & Behavior·Masataka KajikawaTsubasa Shoji

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Citations

Jun 14, 2021·Journal of Plant Physiology·Ena ŠečićMaria Jose Ladera-Carmona

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Methods Mentioned

BETA
degradome sequencing
Illumina sequencing
RNA-Seq

Software Mentioned

BLAST
BLASTN
PREFeR
bowtie2
psRobot
miR
bowtie
Trimmomatic
miRbase
CleaveLand

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