Medicago truncatula forms symbiotic interactions with nitrogen fixing bacteria and mycorrhizal fungi. In order to better understand the genes driving symbiosis as well as other important traits, we resequenced ~285 and identified variants in inbred lines spanning the range of Medicago diversity. In addition, we sequenced and de novo assembled 26 Medicago accessions as well as a mycorrhizal symbiont (Glomus versiforme) and 60 nitrogen-fixing rhizobial symbionts. The resulting sequences and variants allow from population genomic studies and connection of genotype to phenotype through genome-wide association studies (GWAS).
G. Bauchet, K. Bett, C. Cameron, J. Campbell, E. Cannon, S. Cannon, J. Carlson, A. Chan, A. Cleary, T. Close, D. Cook, A. Cooksey, C. Coyne, S. Dash, R. Dickstein, A. Farmer, D. Fernández-Baca, S. Hokin, E. Jones, Y. Kang, M. Monteros, M. Muñoz-Amatriaín, K. Mysore, C. Pislariu, C. Richards, A. Shi, C. Town, M. Udvardi, E. Wettberg, N. Young and P. Zhao.
The future of legume genetic data resources: Challenges, opportunities, and priorities
Legume Science, n/a(n/a), e16, 2019, DOI 10.1002/leg3.16
Legume Information System Legume Federation PeanutBase Medicago HapMap ProjectX. Sun, W. Chen, S. Ivanov, A. MacLean, H. Wight, T. Ramaraj, J. Mudge, M. Harrison and Z. Fei.
Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts
New Phytologist, 221(3), 1556--1573, 2019, DOI 10.1111/nph.15472
Medicago HapMap ProjectK. Moll, P. Zhou, T. Ramaraj, D. Fajardo, N. Devitt, M. Sadowsky, R. Stupar, P. Tiffin, J. Miller, N. Young, K. Silverstein and J. Mudge.
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
BMC Genomics, 18(1), 2017, DOI 10.1186/s12864-017-3971-4
Medicago HapMap ProjectJ. Miller, P. Zhou, J. Mudge, J. Gurtowski, H. Lee, T. Ramaraj, B. Walenz, J. Liu, R. Stupar, R. Denny, L. Song, N. Singh, L. Maron, S. McCouch, W. McCombie, M. Schatz, P. Tiffin, N. Young and K. Silverstein.
Hybrid assembly with long and short reads improves discovery of gene family expansions
BMC Genomics, 18(1), 2017, DOI 10.1186/s12864-017-3927-8
Medicago HapMap ProjectP. Zhou, K. Silverstein, T. Ramaraj, J. Guhlin, R. Denny, J. Liu, A. Farmer, K. Steele, R. Stupar, J. Miller, P. Tiffin, J. Mudge and N. Young.
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
BMC Genomics, 18(1), 2017, DOI 10.1186/s12864-017-3654-1
Legume Federation Medicago HapMap ProjectJ. Yoder, R. Briskine, J. Mudge, A. Farmer, T. Paape, K. Steele, G. Weiblen, A. Bharti, P. Zhou, G. May, N. Young and P. Tiffin.
Phylogenetic Signal Variation in the Genomes of Medicago (Fabaceae)
Systematic Biology, 62(3), 424--438, 2013, DOI 10.1093/sysbio/syt009
Medicago HapMap Project
The National Center for Genome Resources is a not-for-profit research institute that innovates, collaborates, and educates in the field of genomic data science. As leaders in DNA sequence analysis, we partner with government, industry, and academia to drive biological discovery in all kingdoms of life. We deliver value through expertise in experimental design, software, computation, data integration and training a skilled workforce.More
The National Center for Genome Resources, a New Mexico nonprofit corporation ("Company," "NCGR," or "we"), in the operation of this website, www.ncgr.org (the "Website") is committed to protecting the privacy of its online visitors (collectively, "our users" or, as applicable to yourself and your organization, "you").
Other information not treated as personal that may be collected on the Website may include, without limitation, website pages viewed, sites visited before visiting this Website, frequency of visits, clickstream data, browser type, operating system, organization name, articles, internet connection speed, presentations viewed, time spent viewing pages of our website or using certain features of our website, demographic data such as server locations, clickstream data, location services, server location, cookies existing on your computer, search criteria used and results, date and time of access or visits to our website, frequency of visits to our website, connection speed, and other information which does not specifically identify you.
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We use commercially reasonable best efforts to maintain the confidentiality, integrity and security of our users' personal information. Keeping user information secure, and using it only as our users agree, are matters of principle for NCGR. With this in mind, here is our commitment to each user:
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We generally use the information that you provide or that we collect to establish and enhance our relationship with you, and to operate, maintain, enhance, and provide our services and the Website. We may use such information to periodically provide you with information, newsletters or offers about features and services available through our services that may be of interest to you. We may also send information or offers to groups of Users on behalf of other Users or third parties. However, you will have the option to opt out of receiving such information.
We use aggregated information provided by or collected from our users to understand and analyze the usage trends and preferences of our users, to improve the way our services and the Website work and look, and to create new features and functionality. We may use aggregated information about our Users to generate statistics and maps that we deem helpful in the provision of our services or any part thereof. We do not and will not sell analytics that identify personal information of our users without written consent from the user.
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We limit the sharing of personal information outside our Company. We do not sell, license, lease, or otherwise disclose your personal information to third parties, except as noted below:
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We further reserve the right to disclose any of your personal information as we believe appropriate or necessary to take precautions against liability, to investigate and defend against any third party claims or allegations, to assist government enforcement agencies, to protect the security or integrity of the services, or to protect the rights, property or personal safety of our Company, our users, or others.
We may also use and disclose personally identifiable information and non-personally identifiable information: to investigate and help prevent potentially unlawful activity or activities that threaten the integrity of our website or network; to protect and defend our rights or property or the rights or property of others; as required by courts or administrative agencies; and in connection with a financing, sale, merger, or reorganization of our activities or assets.
We do not and will not sell any of your information, including non-personally identifiable or personally identifiable information, to any third party for purposes of advertising, soliciting, or telemarketing. We may use a third party service to collect anonymous visitor information like IP addresses, browser types (such as Firefox), referring pages, pages visited and time spent on a particular service or feature. We collect this information for statistical analysis of web page traffic patterns; to administer our service and servers; to allow for auditing of our services by some third parties who have that right; and for internal purposes to make marketing decisions.
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We limit access to your personal information to those employees who have a legitimate need to access such information to provide you with our services. In keeping with industry standards and practices, we maintain commercially reasonable physical, electronic and procedural safeguards and controls to protect your information. The Website is built upon a secure infrastructure with multiple layers of protection and we use industry standard encryption technologies to safeguard your information.
We have security standards and procedures in place designed to prevent unauthorized access to your accounts and personal information. A key part of this process helps ensure that all information we have about you is accurate and up-to-date. If you ever discover inaccuracies in our data or if your personal information changes, notify us immediately.
The transmission of information via the Internet is not completely secure, and for this reason we cannot guarantee the security of information sent to us electronically. If we learn of a security systems breach, we may attempt to notify you electronically so that you can take appropriate protective steps. We may also post a notice on or through the Website in the event of a security breach. Depending on where you live, you may have a legal right to receive notice of a security breach in writing.
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We are not responsible for removing your personal information from the lists of any third-party services or other third party who has previously been provided your information in accordance with this notice.
REVIEWING, CHANGING OR CORRECTING INFORMATION
You may, of course, decline to share any or all of your personal information with us or ask us to delete your personal information from our systems at any time, in which case we may not be able to provide to you some of the features and functionality found on or through the Website.
OUR COMMITMENT TO CHILDREN'S PRIVACY
We do not knowingly collect personal information on or through our services from persons under 13 years-of-age without their legal guardian's consent. If we learn that personal information has been collected from persons under 13 years-of-age through our services without their legal guardian's consent, then we will take the appropriate steps to delete this information. If you are a parent or guardian and discover that your child under the age of 13 has a registered account with the services or we have received any personally identifiable information of that child without your consent, you may alert us by contacting us.
APPLICABLE LAW AND JURISDICTION
This Privacy Notice shall be governed by, construed and entered in accordance with the laws of the State of New Mexico, United States of America, applicable to contracts deemed to be made within such state, without regard to choice of law or conflict of law provisions thereof. All disputes with respect to this Privacy Notice shall be brought and heard either in the state or federal courts in and for the state of New Mexico, United States of Americe. You consent to the in personam jurisdiction and venue of such courts. YOU HEREBY WAIVE YOUR RIGHT TO A TRIAL BY JURY WITH RESPECT TO ANY CLAIM, ACTION OR PROCEEDING, DIRECTLY OR INDIRECTLY, ARISING OUT OF, OR RELATING TO, THIS AGREEMENT TO THE FULLEST EXTENT PERMITTED BY LAW.
No data transmissions over the Internet can be guaranteed to be 100% secure. Consequently, we cannot ensure or warrant the security of any information you transmit to us and you understand that any information that you transfer to our Company is done at your own risk.
We make reasonable efforts to ensure security on our systems. We have put in place appropriate physical, electronic and administrative procedures to safeguard and secure the information we collect online. However, please note that this is not a guarantee that such information may not be accessed, disclosed, altered or destroyed by breach of our systems.
If we learn of a security systems breach we may attempt to notify you electronically so that you can take appropriate protective steps. By using the service or providing personally identifiable information to us you agree that we can communicate with you electronically regarding security, privacy and administrative issues relating to your use of our services. We may post a notice on our Webpage if a security breach occurs. We may also send an email to you at the email address you have provided to us in these circumstances. Depending on where you live, you may have a legal right to receive notice of a security breach in writing.
Effective November 4, 2019
The National Center for Genome Resources ("NCGR") website (the "Website") is owned and managed by The National Center for Genome Resources, a New Mexico nonprofit corporation ("Owner," or "we" or "us").
THE PURPOSE OF THE WEBSITE IS TO SHARE INFORMATION WITH A PROFESSIONAL AND BUSINESS AUDIENCE CONCERNING GENOMIC DATA SCIENCE.
Owner undertakes to provide accurate and up-to-date information it posts on the Website. However, each User should understand that all information obtained using the Website is subject to change, does not constitute professional advice or opinions, has not been tested or proven, and is provided "AS IS." Accordingly:
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- Passing of time can render information contained in, or linked to, the Website stale. Owner are not responsible for any misimpressions which may result from the use of dated material. Owner does not undertake any duty to verify, update, supplement, correct, comment upon or modify any information contained in the Website or any other site to which it is linked.
You may restrict access to this site using content filtering software or by changing your computer settings (e.g. browser or operating system), as appropriate.
RULES AND RESTRICTIONS ON SUBMISSIONS
1. The Website may contain interactive services, including discussion groups, news groups, bulletin boards, chat rooms, blogs and other social networking features, such as the display of linked content from other sites, which may allow you to post, transmit or submit information, including writings, images, illustrations, audio recordings, and video recordings ("Submissions"). Users should exercise common sense and courtesy with all Submissions. Inappropriate Submissions, which Owner prohibits, would include, for example, comments or materials that:
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- Delete any author attributions, legal notices or proprietary designations or labels in any file that is uploaded;
- Falsify the origin or source of software or other material contained in a file that is uploaded; or
- Violate applicable federal, state or local laws or regulations.
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OWNER'S RIGHT TO MONITOR AND ADMINISTER THE WEBSITE
Owner reserves the right to monitor and administer the Website and, in its sole discretion, to block or remove any content posted to the Website. Owner reserves the right to disallow the use of any particular screen name or e-mail address, or to suspend or terminate any User's access or posting privileges at any time, including individual and group postings. While Owner reserves the right to do so, Owner gives no assurance it does or will do so, as it is not Owner's intention to edit or control content generally.
ACCOUNTS AND SECURITY
To use certain areas of the Website or related features, you may be asked to create an account with a username and password. You agree that the account information you provide us will be and remain accurate. You are responsible for maintaining the strict confidentiality of your account username and password. You are responsible for any activity using your account and password.
Owner does not review all of the sites linked to its Website ("Linked Sites") and is not responsible for the contents of any such Linked Site ("Linked Content"). The inclusion of any link does not imply endorsement by Owner of the Linked Site. Use of any such Linked Site or Linked Content is at the User's own risk.
To use some of the functionality of the Website you may be required to establish an account with a username and password with Linked Sites. As these are unaffiliated sites, we are not responsible for any username, password, or other information these sites may collect. If you are unable to establish accounts on these Linked Sites for any reason, you may not be able to fully utilize the functionality provided by the Site.
OWNERSHIP OF THE WEBSITE AND ITS CONTENTS AND ASSOCIATED TRADEMARKS
The brands, logos and names of specific products or services provided by third parties are owned by those third parties.
The content of the Website, including postings originated by Owner or its providers, and related artwork, graphics and photographic or audiovisual works, are protected by copyright and owned by Owner or third parties who provide such content to Owner. Except as permitted under U.S. Copyright laws, the Website and its contents may not be copied, reproduced, republished or sold, posted, transmitted, distributed, modified, or used for the creation of derivative works without Owner's or applicable third parties' prior written consent.
Owner, to the extent it owns such rights, grants User a non-exclusive, non-transferable, limited license to access, display and/or download a limited and temporary amount of content and pages available within the Website, solely on User's computer and for User's individual use.
Except for the permission expressly granted above to access, display, copy and download the Owner content and pages available within the Website, Owner reserves all rights in the Website and its contents. User may not "mirror" any content or information contained on the Website without Owner's prior written consent. User may not create links to the Website from other sites without Owner's prior written consent and compliance with all applicable laws.
Owner does not claim ownership of or copyrights in User Submissions. User understands that Submissions are not confidential and Owner will be free (without compensation to User) to use or disseminate such Submissions on an unrestricted basis for any purpose. User agrees that Submissions may be published, displayed, copied, distributed, downloaded, or transmitted by Owner or other Website participants, and User grants Owner and all other Users of the Website an irrevocable, unrestricted, perpetual, worldwide, royalty-free license to use, copy, reproduce, display, publish, distribute, transmit, adapt, modify or use for the creation of derivative works (including in digital form) such Submissions.
OWNER MAKES MAKE NO REPRESENTATION OR WARRANTY RELATING TO THE WEBSITE OR ANY INFORMATION AVAILABLE ON THE WEBSITE; ALL EXPRESS OR IMPLIED WARRANTIES OF ANY KIND, INCLUDING WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, ARE HEREBY DISCLAIMED.
OWNER MAKES NO WARRANTY THAT THE WEBSITE, OR ANY COMPUTER, SERVER, DEVICE, SOFTWARE, OR OTHER TECHNOLOGY ASSOCIATED WITH THE WEBSITE, IS FREE OF VIRUSES, WORMS, OR OTHER ELEMENTS OR CODES THAT MANIFEST CONTAMINATING OR DESTRUCTIVE PROPERTIES. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF WARRANTIES, SO THE ABOVE EXCLUSIONS MAY NOT APPLY TO YOU.
LIMITATIONS OF LIABILITY
NEITHER OWNER NOR ITS OFFICERS, DIRECTORS, EMPLOYEES, AGENTS, OR REPRESENTATIVES SHALL BE RESPONSIBLE FOR ANY LOSS OR DAMAGE OF ANY KIND ARISING FROM OR IN ANY WAY RELATING TO (A) THE USE OF OR INABILITY TO USE THE WEBSITE, (B) ERRORS IN OR OMISSIONS FROM WEBSITE CONTENT OR ANY LINKED CONTENT, (C) ANY THIRD PARTY WEB SITES OR CONTENT THEREIN DIRECTLY OR INDIRECTLY ACCESSED THROUGH LINKS IN ANY WEBSITE CONTENT OR LINKED CONTENT, (D) THE UNAVAILABILITY OF THE WEBSITE OR ANY LINKED SITE, OR (E) ANY USE OF THE WEBSITE OR ANY LINKED SITE OR RELIANCE BY THE USER ON ANY INFORMATION OR CONTENT CONTAINED THEREIN.
OWNER SHALL NOT BE LIABLE TO ANY USERS OR ANY OTHER PERSON FOR ANY DIRECT, SPECIAL, INDIRECT, INCIDENTAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES ARISING FROM OR IN ANY WAY RELATING TO THE FOREGOING, EVEN IF THEY HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES OCCURRING.
IN NO EVENT MAY USER BRING ANY CLAIM OR CAUSE OF ACTION AGAINST OWNER MORE THAN ONE (1) YEAR AFTER SUCH CLAIM OR CAUSE OF ACTION ARISES.
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
RESTRICTION, SUSPENSION AND TERMINATION
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: firstname.lastname@example.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