NDLI: Comprehensive Transcriptome Analysis of Response to Nickel Stress in White Birch (Betula papyrifera)

Content Provider	PubMed Central
Author	Theriault, Gabriel Michael, Paul Kabwe, Nkongolo
Editor	Kothe, Erika
Copyright Year	2016
Abstract	White birch (Betula papyrifera) is a dominant tree species of the Boreal Forest. Recent studies have shown that it is fairly resistant to heavy metal contamination, specifically to nickel. Knowledge of regulation of genes associated with metal resistance in higher plants is very sketchy. Availability and annotation of the dwarf birch (B. nana) enables the use of high throughout sequencing approaches to understanding responses to environmental challenges in other Betula species such as B. papyrifera. The main objectives of this study are to 1) develop and characterize the B. papyrifera transcriptome, 2) assess gene expression dynamics of B. papyrifera in response to nickel stress, and 3) describe gene function based on ontology. Nickel resistant and susceptible genotypes were selected and used for transcriptome analysis. A total of 208,058 trinity genes were identified and were assembled to 275,545 total trinity transcripts. The transcripts were mapped to protein sequences and based on best match; we annotated the B. papyrifera genes and assigned gene ontology. In total, 215,700 transcripts were annotated and were compared to the published B. nana genome. Overall, a genomic match for 61% transcripts with the reference genome was found. Expression profiles were generated and 62,587 genes were found to be significantly differentially expressed among the nickel resistant, susceptible, and untreated libraries. The main nickel resistance mechanism in B. papyrifera is a downregulation of genes associated with translation (in ribosome), binding, and transporter activities. Five candidate genes associated to nickel resistance were identified. They include Glutathione S–transferase, thioredoxin family protein, putative transmembrane protein and two Nramp transporters. These genes could be useful for genetic engineering of birch trees.
Related Links	http://dx.doi.org/10.1371/journal.pone.0153762
Starting Page	153762
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	4
Volume Number	11
Language	English
Publisher	Public Library of Science
Publisher Date	2016-04-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla)

Comprehensive Transcriptome Analysis of Developing Xylem Responding to Artificial Bending and Gravitational Stimuli in Betula platyphylla

Correction: Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla)

Decrypting the regulation and mechanism of nickel resistance in white birch (Betula papyrifera) using cross-species metal-resistance genes

Transcriptome Analysis of Litopenaeus vannamei in Response to White Spot Syndrome Virus Infection

Transcriptome Profiling of Sugarcane Roots in Response to Low Potassium Stress

Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress

Sequencing and De Novo Analysis of the Hemocytes Transcriptome in Litopenaeus vannamei Response to White Spot Syndrome Virus Infection

Time Course Transcriptome Changes in Shewanella algae in Response to Salt Stress

Comprehensive Transcriptome Analysis of Response to Nickel Stress in White Birch (Betula papyrifera)

Similar Documents

Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla)

Comprehensive Transcriptome Analysis of Developing Xylem Responding to Artificial Bending and Gravitational Stimuli in Betula platyphylla

Correction: Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla)

Decrypting the regulation and mechanism of nickel resistance in white birch (Betula papyrifera) using cross-species metal-resistance genes

Transcriptome Analysis of Litopenaeus vannamei in Response to White Spot Syndrome Virus Infection

Transcriptome Profiling of Sugarcane Roots in Response to Low Potassium Stress

Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress

Sequencing and De Novo Analysis of the Hemocytes Transcriptome in Litopenaeus vannamei Response to White Spot Syndrome Virus Infection

Time Course Transcriptome Changes in Shewanella algae in Response to Salt Stress

Comprehensive Transcriptome Analysis of Response to Nickel Stress in White Birch (Betula papyrifera)