TITLE

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles

AUTHOR(S)
Oono, Youko; Kawahara, Yoshihiro; Yazawa, Takayuki; Kanamori, Hiroyuki; Kuramata, Masato; Yamagata, Harumi; Hosokawa, Satomi; Minami, Hiroshi; Ishikawa, Satoru; Wu, Jianzhong; Antonio, Baltazar; Handa, Hirokazu; Itoh, Takeshi; Matsumoto, Takashi
PUB. DATE
December 2013
SOURCE
Plant Molecular Biology;Dec2013, Vol. 83 Issue 6, p523
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Rice has developed several morphological and physiological strategies to adapt to phosphate starvation in the soil. In order to elucidate the molecular basis of response to phosphate starvation, we performed mRNA sequencing of 4 rice cultivars with variation in growth response to Pi starvation as indicated by the shoot/root dry weight ratio. Approximately 254 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence and an average of about 5,000 transcripts from each cultivar were found to be responsive under phosphate starvation. Comparative analysis of the RNA-Seq profiles of the 4 cultivars revealed similarities as well as distinct differences in expression of these responsive transcripts. We elucidated a set of core responsive transcripts including annotated and unannotated transcripts commonly expressed in the 4 cultivars but with different levels of expression. De novo assembly of unmapped reads to the Nipponbare genome generated a set of sequence contigs representing potential new transcripts that may be involved in tolerance to phosphate starvation. This study can be used for identification of genes and gene networks associated with environmental stress and the development of novel strategies for improving tolerance to phosphate starvation in rice and other cereal crops.
ACCESSION #
91993160

 

Related Articles

  • Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. Ziwen He; Weiwei Zhai; Haijun Wen; Tian Tang; Yu Wang; Xuemei Lu; Greenberg, Anthony J.; Hudson, Richard R.; Chung-I Wu; Suhua Shi // PLoS Genetics;Jun2011, Vol. 7 Issue 6, Special section p1 

    Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice...

  • Molecular and physiological performance in response to drought stress in Iranian rice cultivars. Akbarpour, M.; Khavari-Nejad, R.; Moumeni, A.; Najafi, F. // Russian Journal of Plant Physiology;Jan2016, Vol. 63 Issue 1, p158 

    The drought is one of the major challenges in rice production in Iran where it is the second most important crop after wheat. Hence, there is an increasing need to develop rice genotypes with drought-tolerant background. Determining drought tolerance mechanisms would be the first priority in...

  • GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops. Shel Swenson, M.; Anderson, Joshua; Ash, Andrew; Gaurav, Prashant; Sükösd, Zsuzsanna; Bader, David A.; Harvey, Stephen C.; Heitsch, Christine E. // BMC Research Notes;2012, Vol. 5 Issue 1, p1 

    Background: Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction...

  • Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: Tertiary climatic shifts and lineage differentiation times. Guillaume Besnard; Rafael Rubio de Casas; Pascal-Antoine Christin; Pablo Vargas // Annals of Botany;Jul2009, Vol. 104 Issue 1, p143 

    Background and Aims The genus Olea (Oleaceae) includes approx. 40 taxa of evergreen shrubs and trees classified in three subgenera, Olea, Paniculatae and Tetrapilus, the first of which has two sections (Olea and Ligustroides). Olive trees (the O. europaea complex) have been the subject of...

  • Molecular Phylogeny of the Lactuca Alliance (Cichorieae Subtribe Lactucinae, Asteraceae) with Focus on Their Chinese Centre of Diversity Detects Potential Events of Reticulation and Chloroplast Capture. Wang, Ze-Huan; Peng, Hua; Kilian, Norbert // PLoS ONE;Dec2013, Vol. 8 Issue 12, p1 

    The first comprehensive molecular phylogenetic reconstruction of the Cichorieae subtribe Lactucinae is provided. Sequences for two datasets, one of the nuclear rDNA ITS region, the other of five concatenated non-coding chloroplast DNA markers including the petD region and the psbA-trnH,...

  • Solution structure of a GAAA tetraloop receptor RNA. Butcher, Samuel E.; Dieckmann, Thorsten; Feigon, Juli // EMBO Journal;12/15/97, Vol. 16 Issue 24, p7490 

    The GAAA tetraloop receptor is an 11-nucleotide RNA sequence that participates in the tertiary folding of a variety of large catalytic RNAs by providing a specific binding site for GAAA tetraloops. Here we report the solution structure of the isolated tetraloop receptor as solved by...

  • Molecular cloning and partial characterisation of the mouse Cyp51 cDNA. Debeljak, Nataša; Horvat, Simon; Komel, Radovan; Rozman, Damjana // Pflugers Archiv European Journal of Physiology;Apr2000, Vol. 439 Issue 7, pr007 

    Northern analysis of the mouse testis and liver RNA show two types of lanosterol 14α-demethylase (CYP51) transcripts, somatic and a testis-specific transcript. At least two CYP51 mRNAs are expressed in liver and testis, while the smallest transcript is expressed only in testis. The partial...

  • Sequencing error correction without a reference genome. Sleep, Julie A.; Schreiber, Andreas W.; Baumann, Ute // BMC Bioinformatics;2013, Vol. 14 Issue 1, p1 

    Background Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced....

  • Sensor and Sensitivity: A Screen for Elite shRNAs. Castanotto, Daniela // Molecular Therapy;May2011, Vol. 19 Issue 5, p823 

    The article presents a study by C. Fellmann and colleagues on the development of RNA interference (RNAi) triggers which help in the drug development. It states that short hairpin RNAs (shRNAs) from nine mammalian transcripts were placed under the doxycycline-inducible promoter with the help of...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics