Red alder - Frankia symbiosis
Red alder (Alnus rubra Bong.), has significant economic importance, yet is an orphan in terms of scientific understanding of its genetic variability and its relationship with its nitrogen-fixing symbiont Frankia alni. We are developing an omics-based research foundation upon which to base a breeding and improvement program, aimed at further improving tolerance to abiotic stresses and increasing marginal land area devoted to its growth. We aim to develop insights into interactions among tree genotype, rhizosphere microbiome, root transcriptome, symbiont (and other endophyte) transcriptomes, and soil characteristics during a seasonal cycle on good and marginal soil types. Objectives: 1. Create a de novo genome reference assembly of an elite red alder clone that outperforms all other known clones. 2. Create reference genome sequences and epigenomic signatures of the five Frankia strains that result in the best tree performance and symbiosis. 3. Develop a dense set of molecular markers to enable accelerated predictive breeding and improvement. 4. Develop insights into interactions among tree genotype, rhizosphere microbiome, root transcriptome, symbiont (and other endophyte) transcriptomes, and their impacts on juvenile tree growth on good and marginal soils. Methods: 1. PacBio sequencing. De novo assembly and physical map integration. 2. PacBio sequencing with epigenetic modifications determined using the SMRTanalysis suite. 3. Genotyping by sequencing of 350 tree lines using the TASSEL-GBS pipeline. 4. 16s rRNA survey of rhizosphere microbial communities in the field and under experimental conditions. Root and nodule RNA seq (tree roots and and their associated endophytes).
Publications
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C. Bell, J. Sena, D. Fajardo, E. Lavelle, M. Costa, B. Herman, L. Davin, N. Lewis and A. Berry.
A root nodule microbiome sequencing data set from red alder (Alnus rubra Bong.)
Scientific Data, 11(1), 2024, DOI 10.1038/s41597-024-04131-0, PMID 39695182, PMCID PMC11655522
Red alder genomeK. Hixson, Q. Meng, S. Moinuddin, M. Kwon, M. Costa, J. Cort, L. Davin, C. Bell and N. Lewis.
RNA-seq and metabolomic analyses of beneficial plant phenol biochemical pathways in red alder
Frontiers in Plant Science, 15, 2024, DOI 10.3389/fpls.2024.1349635, PMID 39574452, PMCID PMC11578710
Red alder genomeK. Hixson, D. Fajardo, N. Devitt, J. Sena, M. Costa, Q. Meng, C. Boschiero, P. Zhao, E. Baack, V. Paurus, L. Davin, N. Lewis and C. Bell.
Annotated genome sequence of a fast-growing diploid clone of red alder (<i>Alnus rubra</i> Bong.)
G3: Genes, Genomes, Genetics, 13(6), 2023, DOI 10.1093/g3journal/jkad060, PMID 36966434, PMCID PMC10234377
Red alder genomeC. Bell, J. Sena, I. Gifford and A. Berry.
Contiguous Genome Sequence of Frankia sp. Strain ArI3, Isolated from Root Nodules of Alnus rubra Bong
Microbiology Resource Announcements, 10(43), e00800--21, 2021, DOI 10.1128/MRA.00800-21, PMID 34709056
Red alder genome© 2026 National Center for Genome Resources. Privacy Policy | Terms of Use
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.Effective November 4, 2019
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REPRESENTATIONS BY USERS; INDEMNIFICATION
USER IS SOLELY RESPONSIBLE FOR THE CONTENTS OF HIS/HER SUBMISSIONS TO THE WEBSITE. USER REPRESENTS THAT HE/SHE HAS ALL RIGHTS NECESSARY TO POST THE INFORMATION, CONTENT OR MATERIALS SUBMITTED TO THE WEBSITE WITHOUT VIOLATING THE COPYRIGHTS OR ANY OTHER INTELLECTUAL PROPERTY RIGHTS OF THIRD PARTIES, AND THAT NO SUBMISSION BY THE USER WILL VIOLATE APPLICABLE LAWS OR THE RIGHTS OF THIRD PERSONS. USER HEREBY INDEMNIFIES AND AGREES TO HOLD HARMLESS OWNER AND ITS OFFICERS, DIRECTORS, SHAREHOLDERS, EMPLOYEES, AGENTS AND REPRESENTATIVES FROM ANY AND ALL CLAIMS ASSERTED AGAINST THEM AND ANY LIABILITY, LOSS, DAMAGE, COSTS OR EXPENSES (INCLUDING REASONABLE ATTORNEYS' FEES) INCURRED OR SUFFERED BY THEM IN CONNECTION WITH OR ARISING OUT OF USER'S ACTS OR OMISSIONS OR THE MATERIALS OR INFORMATION USER SUBMITS TO THE WEBSITE.
CHOICE OF LAW AND CONSENT TO FORUM
This Agreement will be interpreted and governed in all respects by the laws of the State of New Mexico, United States of America, without regard to its choice of laws rules. Any dispute arising under these Terms of Use or in connection with the User's use of the Website shall be subject to the exclusive jurisdiction of either the state or federal courts in and for New Mexico, and User and Owner hereby consent to the personal jurisdiction of such courts over them.
RESTRICTION, SUSPENSION AND TERMINATION
We may restrict, suspend, or terminate your access to the Site and/or your ability to avail of any of the services on the Website, including interactive services, at any time if we believe that you have breached these Terms of Use. Any such restriction, suspension, or termination will be without prejudice to any rights that we may have against you in respect of your breach of these Terms of Use. We may also remove the Website as a whole or any sections or features of the Website at any time.
Please note that we have the ability to trace your IP address and if necessary contact your internet service provider in the event of a suspected breach of these Terms of Use.
PROCEDURES FOR REQUESTING THE REMOVAL OF INFRINGING MATERIAL
Owner respect the intellectual property of others. If a person or organization (a "Copyright Owner") believes that his, her or its work has been copied on the Website in a way that constitutes copyright infringement, provide Owner the written information specified below. Please note that this procedure is exclusively for the Copyright Owner to notify Owner that copyrighted material of the Copyright Owner has been infringed. If a Copyright Owner believes that its own copyrighted work has been copied in a way that constitutes copyright infringement and is accessible via the Website, the Copyright Owner may notify Owner's copyright agent in accordance with the following procedures and the Digital Millennium Copyright Act of 1998 (DMCA).
For a complaint to be valid under the DMCA, the Copyright Owner must provide the following information when providing notice of the claimed copyright infringement: (1) a physical or electronic signature of a person authorized to act on behalf of the Copyright Owner; (2) identification of the copyrighted work or other intellectual property that the Copyright Owner owns and claims to have been infringed; (3) identification of the material that the Copyright Owner claims is infringing as well as information reasonably sufficient to permit Owner to locate the material on the Website; (4) the address, telephone number, and e-mail address of the Copyright Owner or its designee; (5) a statement by the Copyright Owner that the Copyright Owner as the complaining party has a good faith belief that use of the material in the manner complained of is not authorized by the Copyright Owner, its agent, or the law; and (6) a statement, made under penalty of perjury, that the information in the notification is accurate, and that the complaining party is authorized to act on behalf of the Copyright Owner of an exclusive right that is allegedly infringed. The foregoing information must be submitted as a written notification to the following Designated Agent:
- Site: www.ncgr.org
- Designated agent for infringement claims: Callum Bell, President
- Address:National Center for Genome Resources2935 Rodeo Park Drive EastSanta Fe, New Mexico 87505
- Telephone of designated agent: 505-982-7840
- E-mail of designated agent: cjb@ncgr.org
WE CAUTION YOU THAT UNDER FEDERAL LAW, IF YOU KNOWINGLY MISREPRESENT THAT ONLINE MATERIAL IS INFRINGING, YOU MAY BE SUBJECT TO CIVIL PENALTIES. THESE INCLUDE MONETARY DAMAGES, COURT COSTS, AND ATTORNEYS' FEES INCURRED BY US, BY ANY COPYRIGHT OWNER, OR BY ANY COPYRIGHT OWNER'S LICENSEE THAT IS INJURED AS A RESULT OF OUR RELYING UPON YOUR MISREPRESENTATION. YOU MAY ALSO BE SUBJECT TO CRIMINAL PROSECUTION FOR PERJURY.
This information should not be construed as legal advice. For further details on the information required for valid DMCA notifications, see 17 U.S.C. 512(c)(3).
NOTE: This information is provided exclusively for notifying the service providers referenced above that the Copyright Owner's own copyrighted material(s) might have been infringed. All other inquiries, including technical requests, reports of e-mail abuse and third party reports of piracy, will not receive a response through this process.
HOW TO CONTACT OWNER
Questions regarding the Terms of Use or any other aspect of the Website can be submitted in writing to: info@ncgr.org