Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress

BMC Genomics
Mohamed ArishaQiang Li

Abstract

Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt stress is seriously limiting its production and distribution. Due to lacking of reference genome, transcriptome sequencing is offering a rapid approach for crop improvement with promising agronomic traits and stress adaptability. Five cDNA libraries were prepared from the third true leaf of hexaploid sweetpotato at seedlings stage (Xuzi-8 cultivar) treated with 200 mM NaCl for 0, 1, 6, 12, 48 h. Using second and third generation technology, Illumina sequencing generated 170,344,392 clean high-quality long reads that were assembled into 15,998 unigenes with an average length 2178 base pair and 96.55% of these unigenes were functionally annotated in the NR protein database. A number of 537 unigenes failed to hit any homologs which may be considered as novel genes. The current results indicated that sweetpotato plants behavior during the first hour of salt stress was different than the other three time points. Furthermore, expression profiling analysis identified 4, 479, 281, 508 significantly expressed unigenes in salt stress t...Continue Reading

References

Mar 14, 2000·Current Opinion in Plant Biology·J C Cushman, H J Bohnert
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Sep 12, 2002·Annual Review of Plant Biology·Jian-Kang Zhu
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
May 8, 2004·Trends in Plant Science·Wangxia WangArie Altman
Oct 7, 2004·Trends in Plant Science·Ron MittlerFrank Van Breusegem
Dec 14, 2004·Ecotoxicology and Environmental Safety·Asish Kumar Parida, Anath Bandhu Das
Mar 17, 2005·Cellular and Molecular Life Sciences : CMLS·M P Mayer, B Bukau
Nov 29, 2005·Archives of Biochemistry and Biophysics·Shilpi Mahajan, Narendra Tuteja
Jan 18, 2006·The Plant Journal : for Cell and Molecular Biology·Katia MarroccoThomas Kretsch
Jan 9, 2007·Biochimica Et Biophysica Acta·Norio MurataSuleyman I Allakhverdiev
May 1, 2008·Nucleic Acids Research·Stefan GötzAna Conesa
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Nov 17, 2011·Biochemical and Biophysical Research Communications·Hongjian WanYuejian Yang
Feb 18, 2014·Biochemical and Biophysical Research Communications·Niina IdänheimoMichael Wrzaczek
Mar 19, 2014·Trends in Plant Science·Ulrich DeinleinJulian I Schroeder
Oct 7, 2016·Annals of Botany·S NegrãoM Tester
Oct 8, 2016·Cell·Jian-Kang Zhu
Oct 9, 2016·Plant Science : an International Journal of Experimental Plant Biology·Meng GuoMing-Hui Lu

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Citations

Jun 21, 2020·International Journal of Molecular Sciences·Lijuan ZhaoYan Li
May 1, 2021·International Journal of Molecular Sciences·Hong ChenTao Wang

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Methods Mentioned

BETA
environmental stress
salt stress
RNA-seq
Illumina sequencing
RNA Assay
Assay
PCR

Software Mentioned

Blast2GO
PacBio
- tools
house
PASS
samtools
DESeq2R
cogent
Picard
DESeq2

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