The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

The root transcriptome of Achyranthes bidentata and the identification of the genes involved in... Key message The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone sign- aling and inhibited lignin biosynthesis. Abstract The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called “replanting benefit” is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries pre- pared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecu- tive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Cell Reports Springer Journals

The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

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Publisher
Springer Berlin Heidelberg
Copyright
Copyright © 2018 by Springer-Verlag GmbH Germany, part of Springer Nature
Subject
Life Sciences; Plant Sciences; Cell Biology; Biotechnology; Plant Biochemistry
ISSN
0721-7714
eISSN
1432-203X
D.O.I.
10.1007/s00299-018-2255-z
Publisher site
See Article on Publisher Site

Abstract

Key message The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone sign- aling and inhibited lignin biosynthesis. Abstract The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called “replanting benefit” is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries pre- pared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecu- tive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved

Journal

Plant Cell ReportsSpringer Journals

Published: Jan 17, 2018

References

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