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Ahmed LT, Alesmail H, Beltran Rodriguez S, Christian R, Coronado J, Elledge AA, Estrada A, Fierro A, Garcia Mora A, Gonzalez K, Gonzalez-Leon S, Guijarro AM, Islas-Quintana J, Juarez-Guido D, Hughey JR, Lara EJ, Lara J, Leonard CT, Lockard KA, Lopez E, Martin S, Martinez M, Mederos B, Medina Pizano A, Medley CJ, Mohsin S, Mumford TF, Muñoz RA, Nachtigall R, Noriega J, Ochoa Cendejas P, Ordaz J, Parra AJ, Pizano J, Reimold M, Rivera K, Rocha A, Rodriguez KC, Tena-Garcia I, Vargas MM, Velasquez J. Complete chloroplast genome of the marine red alga Rhodochorton tenue (Rhodochortonaceae, Rhodophyta) from San Juan Island, Washington. Microbiol Resour Announc 2024; 13:e0106823. [PMID: 38289055 PMCID: PMC10868208 DOI: 10.1128/mra.01068-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
We present the complete chloroplast genome sequence of Rhodochorton tenue from San Juan Island, Washington. The chloroplast genome of R. tenue is 192,037 bp in length, contains 244 genes, and is similar in content to Acrochaetium secundatum. Rhodochorton tenue is genetically distinct from Rhodochorton purpureum from the North Atlantic Ocean.
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Affiliation(s)
- Layla T. Ahmed
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Hiba Alesmail
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | | | - Rachel Christian
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jonathan Coronado
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alice A. Elledge
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - America Estrada
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alena Fierro
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Angel Garcia Mora
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kayla Gonzalez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Samantha Gonzalez-Leon
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Arely M. Guijarro
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jennifer Islas-Quintana
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - David Juarez-Guido
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jeffery R. Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Edward J. Lara
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jamileth Lara
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Carson T. Leonard
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kaylee A. Lockard
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Enzou Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Stephanie Martin
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Miriam Martinez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Brianna Mederos
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alejandro Medina Pizano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Casey J. Medley
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Sarah Mohsin
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Thomas F. Mumford
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, USA
| | - Raphael Araujo Muñoz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Renee Nachtigall
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jannette Noriega
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Pedro Ochoa Cendejas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jessika Ordaz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alberto J. Parra
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Julian Pizano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Michelle Reimold
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Kristalyn Rivera
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Ayleen Rocha
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Karolina C. Rodriguez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Ivan Tena-Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Matthew M. Vargas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jose Velasquez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - On behalf of Hartnell College Genomics Group
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, USA
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Gardner J, LeBoeuf C, Bell P, McGlore O, Tennet H, Alba N, Carroll M, Baert L, Beaton H, Cordell E, Haynes A, Reed C, Lichter K, McCarthy P, McCarthy S, Monchamp T, Roach J, Manies S, Gunville F, Marosok L, Nelson T, Ackerman K, Rudolph J, Stewart M, McCormick K, May S, Falls T, Barrett T, Dale K, Makusha L, McTernana C, Penny-Thomas K, Sullivan K, Narendran P, Robbie J, Smith D, Christensen R, Koehler B, Royal C, Arthur T, Houser H, Renaldi J, Watsen S, Wu P, Lyons L, House B, Yu J, Holt H, Nation M, Vickers C, Watling R, Heptulla R, Trast J, Agarwal C, Newell D, Katikaneni R, Gardner C, Del Rio A, Logan A, Collier H, Rishton C, Whalley G, Ali A, Ramtoola S, Quattrin T, Mastrandea L, House A, Ecker M, Huang C, Gougeon C, Ho J, Pacuad D, Dunger D, May J, O’Brien C, Acerini C, Salgin B, Thankamony A, Williams R, Buse J, Fuller G, Duclos M, Tricome J, Brown H, Pittard D, Bowlby D, Blue A, Headley T, Bendre S, Lewis K, Sutphin K, Soloranzo C, Puskaric J, Madison H, Rincon M, Carlucci M, Shridharani R, Rusk B, Tessman E, Huffman D, Abrams H, Biederman B, Jones M, Leathers V, Brickman W, Petrie P, Zimmerman D, Howard J, Miller L, Alemzadeh R, Mihailescu D, Melgozza-Walker R, Abdulla N, Boucher-Berry C, Ize-Ludlow D, Levy R, Swenson Brousell C, Scott R, Heenan H, Lunt H, Kendall D, Willis J, Darlow B, Crimmins N, Edler D, Weis T, Schultz C, Rogers D, Latham D, Mawhorter C, Switzer C, Spencer W, Konstantnopoulus P, Broder S, Klein J, Bachrach B, Gardner M, Eichelberger D, Knight L, Szadek L, Welnick G, Thompson B, Hoffman R, Revell A, Cherko J, Carter K, Gilson E, Haines J, Arthur G, Bowen B, Zipf W, Graves P, Lozano R, Seiple D, Spicer K, Chang A, Fregosi J, Harbinson J, Paulson C, Stalters S, Wright P, Zlock D, Freeth A, Victory J, Maheshwari H, Maheshwari A, Holmstrom T, Bueno J, Arguello R, Ahern J, Noreika L, Watson V, Hourse S, Breyer P, Kissel C, Nicholson Y, Pfeifer M, Almazan S, Bajaj J, Quinn M, Funk K, McCance J, Moreno E, Veintimilla R, Wells A, Cook J, Trunnel S, Transue D, Surhigh J, Bezzaire D, Moltz K, Zacharski E, Henske J, Desai S, Frizelis K, Khan F, Sjoberg R, Allen K, Manning P, Hendry G, Taylor B, Jones S, Couch R, Danchak R, Lieberman D, Strader W, Bencomo M, Bailey T, Bedolla L, Roldan C, Moudiotis C, Vaidya B, Anning C, Bunce S, Estcourt S, Folland E, Gordon E, Harrill C, Ireland J, Piper J, Scaife L, Sutton K, Wilkins S, Costelloe M, Palmer J, Casas L, Miller C, Burgard M, Erickson C, Hallanger-Johnson J, Clark P, Taylor W, Galgani J, Banerjee S, Banda C, McEowen D, Kinman R, Lafferty A, Gillett S, Nolan C, Pathak M, Sondrol L, Hjelle T, Hafner S, Kotrba J, Hendrickson R, Cemeroglu A, Symington T, Daniel M, Appiagyei-Dankah Y, Postellon D, Racine M, Kleis L, Barnes K, Godwin S, McCullough H, Shaheen K, Buck G, Noel L, Warren M, Weber S, Parker S, Gillespie I, Nelson B, Frost C, Amrhein J, Moreland E, Hayes A, Peggram J, Aisenberg J, Riordan M, Zasa J, Cummings E, Scott K, Pinto T, Mokashi A, McAssey K, Helden E, Hammond P, Dinning L, Rahman S, Ray S, Dimicri C, Guppy S, Nielsen H, Vogel C, Ariza C, Morales L, Chang Y, Gabbay R, Ambrocio L, Manley L, Nemery R, Charlton W, Smith P, Kerr L, Steindel-Kopp B, Alamaguer M, Tabisola-Nuesca E, Pendersen A, Larson N, Cooper-Olviver H, Chan D, Fitz-Patrick D, Carreira T, Park Y, Ruhaak R, Liljenquist D. A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk. Diabetes Care 2018; 41:1887-1894. [PMID: 30002199 PMCID: PMC6105323 DOI: 10.2337/dc18-0087] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/06/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals. RESEARCH DESIGN AND METHODS We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables. RESULTS Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002). CONCLUSIONS The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.
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Affiliation(s)
- Maria J. Redondo
- Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | | | - Andrea K. Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Seth Sharp
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - John M. Wentworth
- Walter and Eliza Hall Institute of Medical Research and Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael N. Weedon
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | | | | | | | | | - Richard A. Oram
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
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