GENOMICS & BIOINFORMATICS SERVICE
Who We Are
Introducing TxGen, the Texas A&M AgriLife Genomics and Bioinformatics Service! At TxGen, our mission is to revolutionize genomic research across AgriLife, COALS, and the Texas A&M University System by providing world-class laboratory and bioinformatics expertise. We're dedicated to accelerating genomic research across Texas and the world, and embodying the Aggie Core Values of Service, Excellence, Leadership, Loyalty, Respect, and Integrity.
Led by Dr. Charles Johnson, our team of genomics, bioinformatics, and molecular scientists is committed to meeting the next generation sequencing (NGS) needs of the TAMU system and broader scientific community. With over 13 years of experience running a gene technologies lab and more than 3000 completed projects, we've grown to be one of the leading agrigenomic sequencing facilities in the world. We're proud to be recognized as a center of excellence by both Illumina and PerkinElmer, and to have the capacity to process over 200,000 samples per year and generate enough data to sequence 43,000 human genomes at a cost well below most commercial and academic facilities. Investments in personnel and equipment have been critical to providing genomics and bioinformatics infrastructure for student training, faculty retention, and successful R&D initiatives in the areas of agriculture, life sciences, human health, and veterinary medicine.Allow us to serve you and let's accelerate genomic research together!
- AgriLife gets 1st Illumina GAIIx 2009
- AgriLife gets 2nd Illumina GAIIx 2010
- Roche 454 2010
- Illumina HiSeq 2000 purchase Spring 2012
- Illumina HiSeq 2500v3 upgrade Fall 2012
- Lead AgriLife Genomic Seed Grant (470K)
- Started offering Illumina MiSeq Spring 2013
- Board of Regents approved CBGSE August 2013
- Move to Gateway facility January 2014
- Illumina MiSeq January 2014
- Lead Texas A&M Genomics Seed Grant program (600K) 2014
- Lead Genomics of Plant Water Use Seed Grant (300K) 2014
- Illumina HiSeq 2500v4 Summer 2014
- Oxford Nanopore minION system Fall 2014
- Lead Vet school graduate seed grant program fall 2015
- Lead Vector Borne Disease Genomic Seed Grant (200K) 2016
- Lead Genomics of Plant Water Use Seed Grant (220K) 2016
- Illumina HiSeq 4000 June 2016
- PacBio Sequel Auguest 2016
- OxFord Nanopore minION R9 flowcell
- Lead Vet school graduate research grant program fall 2016
- Illumina Novaseq install May 2017
- PoreCampUSA June 2017
- Plant Gene Editing Seed Grant Program (500k) Dec 2017
- New Lab Grand Opening Oct 2019
- 1st Ag Focused Illumina DREAGN Oct 2019
- 2nd Illumina NovaSeq Dec 2019
- Supported over 1000 researchers drawn from over 65 departments, 10 colleges, and multiple agencies across the Texas A&M System.
- Involved in over 700 state and federal grant submissions, resulting in over $135 millions in new funding for scientists across the TAMU system.
- Launched ten Seed Grant programs- distributing a total of $2.4M in sequencing and bioinformatics services to faculty across the system to generate preliminary data to facilitate outside grant funding. 458 seed grant proposals submitted with over 846 total participants. 106 funded projects, generating $8M in new funding from the first $400k seed grant program.
- Marker Assisted Breeding program
- Launched highly successful genomic seed grant program – produced largest response in AgriLife history
Our Mission: Our mission is to provide exceptional genomics research support to our clients across Texas and the world. We are committed to delivering high-quality, accurate results in a timely and cost-effective manner. Our team upholds the Aggie Core Values of Service, Excellence, Leadership, Loyalty, Respect, and Integrity in all aspects of our work. Through our innovative and reliable services, we aim to be a trusted partner for researchers in advancing the field of genomics research and ultimately improving the lives of people and the environment.
Selfless service: We put the customer at the center of everything we do. We strive to exceed expectations and provide the best possible service to our clients every day.
Excellence : We work tirelessly to exceed the standard in all aspect of our operation. We try harder.
Leadership: “At Texas A&M you learn first to follow, then to develop and practice your leadership skills, and finally you become someone others want to follow.” We are the leaders in genomic technology at Texas A&M
Loyalty: A trust that is built over time
Respect: Respect is not given, but earned. We strive to earn your respect daily and have reputation across the world as one of the top agrigenomic technology labs in the world
Integrity: Aggie Code of Honor states: 'Aggies do not lie, cheat or steal nor tolerate those that do', Enough said
We are currently recruiting for an entry level lab research assistant at TXGen Link to Apply This is a great position for someone wanting to gain experience in high throughput genomic technology in a structured & supportive environment.
Low-pass genotyping is a genotyping approach that involves sequencing DNA samples at a lower coverage depth. In this method, instead of sequencing the entire genome at a high coverage depth, a subset of the genome is sequenced at a lower depth, typically between 0.1x and 5x coverage. This reduced coverage is achieved by sequencing a Read more about Low Cost Genotyping[…]
Large Illumina order arrived today, an outstanding way to head into the summer. Freezers are full! Ready for a busy sequencing summer. Please let us know if we can support your sequencing based research. We work with scientists from around the world and specialize in high throughput, short turn around time projects. 45K views and Read more about A summer of sequencing 2022![…]
May all your sequences be >Q30
In our continuing commitment to the Aggie core value of excellence, Texas A&M AgriLife Genomic and Bioinformatics Service is pleased to announce our new NovaSeq pricing. We have recently added a 2nd Illumina NovaSeq system to our facility. As a consequence, we are able to offer researchers a significant reduction in the cost of sequencing. Read more about New NovaSeq Pricing (Oct, 2019)[…]
Illumina Inc. highlighted the work AgriLife and TxGen in the videos below (>6,200 views) Agriculture Throughout the World is Benefiting from the Latest NGS Technologies- interview with Dr. Johnson Sequencing Complex Plant Genomes at Texas A&M AgriLife https://youtu.be/eecnhlhAn9w Empowering Agrigenomics Across the Globe https://youtu.be/UfBR6FJnQ_o Featured 2019 PAG video https://youtu.be/wSFtVRHe5-k Using the iSeq™ 100 Sequencing System Read more about Illumina Videos and interview[…]
Come Celebrate! October 29th, 2019 The Genomics and Bioinformatics Service (TxGen), part of Texas A&M AgriLife Research, celebrates its 10th year of service to the Texas A&M community, Texas, and scientists around the world with the opening of our new sequencing and bioinformatics facility in the Texas A&M West Campus Research Park. You are invited Read more about Come Celebrate with Us[…]
We are in the process of packing and moving into our new facilities at the Texas A&M Reserach Park, Centeq Building. Please excuse any delays in responding to your emails. We expect to be back to normal operations by the first week in May. Building Address: New Address for TxGen Room 250 Centeq Building A Read more about TxGen Moving Back to Campus[…]
2018 was a landmark sequencing year for @TXGEN and this year is shaping up to be even bigger. We added a 2nd @illumina NovaSeq to meet the growing demand and in collaboration with @PerkinElmer_AG are slashing total sequencing project costs by 40%, or more for 2019. We were named a Center of Excellence by PerkinElmer. Read more about Launching new NovaSeq Service. up to 40% reduction in cost of sequencing[…]
2018 was a landmark sequencing year for @TXGEN and this year is shaping up to be even bigger. We added a 2nd @illumina NovaSeq to meet the growing demand and in collaboration with @PerkinElmer_AG are slashing total sequencing project costs by 40%, or more for 2019. pic.twitter.com/wfouiIT7sd — Charlie Johnson (@BioMath) February 1, 2019 Dr. Read more about Twitter Feed Week of Feb 20,1019[…]
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- Cerit Mustafa, Zhen Wang, Mehmet Dogan, Shuhao Yu. Jorge L. Valenzuela-Antelo, Chenggen Chu, Shichen Wang, Qingwu Xue, Amir M. H. Ibrahim, Jackie C. Rudd, Richard Metz, Charles D. Johnson, Shuyu Liu. Mapping QTL for Yield and Its Component Traits Using Wheat (Triticum aestivum L.) RIL Mapping Population from TAM 113 × Gallagher. Agronomy 2023, 13(9), 2402; https://doi.org/10.3390/agronomy13092402
- Kylie G. Bendele , Felix D. Guerrero , Kimberly H. Lohmeyer, Lane D. Foil , Richard P. Metz , Charles D. Johnson Horn fly transcriptome data of ten populations from the southern United States with varying degrees and molecular mechanisms of pesticide resistance. Data in Brief , ISSN 2352-3409,
https://doi.org/10.1016/j.dib.2023.109272 online 30 May 2023
- Ranjita Thapa, Rodante E. Tabien, Charles D. Johnson and Endang M. Septiningsih . Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress. BMC Genomics 2023 https://doi.org/10.1186/s12864-023-09262
- Ze-Tian Fang, Rajan Kapoor, Aniruddha Datta, Shuyu Liu, Matthew A. Stull, Paige G. Seitz, Charles D. Johnson, and Sakiko Okumoto. Transcriptome Analysis of Developing Grains from Wheat Cultivars TAM 111 and TAM 112 Reveal Cultivar-Specific Regulatory Networks Int. J. Mol. Sci. 2022, 23(20), 12660; https://doi.org/10.3390/ijms232012660
- Bed Prakash Bhatta · Takshay Patel · Edgar Correa · Todd C. Wehner · Kevin M. Crosby ·Michael J. Thomson · Richard Metz · Shichen Wang · Marcel Brun · Charles D. Johnson · Subas Malla. Dissection of race 1 anthracnose resistance in a watermelon (Citrullus lanatus var. lanatus) biparental mapping population. Vol.: (0123456789) 1 3 Euphytica (2022) 218:157 https://doi.org/10.1007/s10681-022-03108-7
- Kelsey Michelle Wells, Kai He, Aseem Pandey, Ana Cabello, Dongmei Zhang, Jing Yang, Gabriel Gomez, Yue Liu, Haowu Chang, Xueqiang Li, Hao Zhang, Xuehuang Feng, Luciana Fachini da Costa, Richard Metz, Charles D Johnson, Cameron Lee Martin, Jill Skrobarczyk, Luc R Berghman, Kristin L Patrick, Julian Leibowitz, Allison Ficht, Sing-Hoi Sze, Jianxun Song, Xiaoning Qian, Qing-Ming Qin, Thomas A Ficht, Paul de Figueiredo. Brucella activates the host RIDD pathway to subvert BLOS1-directed immune defense. eLife. 2022; 11: e73625. Published online 2022 May 19. doi: 10.7554/eLife.73625
- Kelsey Michelle Wells, Kai He, Aseem Pandey, Ana Cabello, Dongmei Zhang, Jing Yang, Gabriel Gomez, Yue Liu, Haowu Chang, Xueqiang Li, Hao Zhang, Xuehuang Feng, Luciana Fachini da Costa,Richard Metz,Charles D Johnson, Cameron Lee Martin, Jill Skrobarczyk, Luc R Berghman,Kristin L Patrick,Julian Leibowitz, Allison Ficht, Sing-Hoi Sze,Jianxun Song,Xiaoning Qian,Qing-Ming Qin,Thomas A Ficht, and Paul de Figueiredo. Brucella activates the host RIDD pathway to subvert BLOS1-directed immune defense. eLife. 2022; 11: e73625. Published online 2022 May 19. doi: 10.7554/eLife.73625
- Chenggen Chu, Shichen Wang, Jackie C. Rudd, Amir M. H. Ibrahim, Qingwu Xue, Ravindra N. Devkota, Jason A. Baker, Shannon Baker, Bryan Simoneaux, Geraldine Opena, Haixiao Dong, Xiaoxiao Liu, Kirk E. Jessup, Ming-Shun Chen, Kele Hui, Richard Metz, Charles D. Johnson, Zhiwu S. Zhang & Shuyu Liu . Molecular Breeding volume 42, Article number: 18 (2022). A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding. volume 39 (3), in 2022. DOI https://doi.org/10.1007/s11032-022-01287-8
- C.L. Hunt, L. Yu, M. Cochran, J.-C. Liu, B. McCarl, C.D. Johnson, M. Brun & M. Berquist. A case study approach to high-containment laboratory workflows promoting sustainability, networking, and innovation. Scientific and Technical Review of the OIE. volume 39 (3), in 2021.
- Felix D Guerrero, Noushin Ghaffari, Kylie G Bendele, Richard P Metz, C Michael Dickens, Philip D Blood, Jason Tidwell, Robert J Miller, Adalberto A Pérez de León, Pete D Teel, Charles D Johnson. Raw Pacific Biosciences and Illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus. Data In Brief. Volume 35, 2021, 106852, ISSN 2352-3409, https://doi.org/10.1016/j.dib.2021.106852
- C L Hunt, L Yu, M Cochran, J-C Liu, B Mccarl, C D Johnson, M Brun, M Berquist. A case study approach to high-containment laboratory workflows promoting sustainability, networking and innovation Rev Sci Tech. 2020 Jan;39(3):663-673. doi: 10.20506/rst.39.3.3169.
- Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William K. M. Lai, Richard P. Metz, Charles D. Johnson, Sing-Hoi Sze, B. Franklin Pugh, Bryce E. Nickels, Craig D. Kaplan. Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the “shooting gallery”doi: https://doi.org/10.1101/810127 2020
- Anne N Thorndike ,Jessica L McCurley ,Emily D Gelsomin ,Eric B Rimm,Yuchiao Chang,Bianca Porneala,Emma Anderson, Charles D. Johnson, Douglas E Levy. MP07: Automated, Personalized Feedback and Behavioral Nudges to Improve Workplace Food Choices and Prevent Weight Gain: Choosewell 365 Randomized Controlled Trial. 2 Mar 2020https://doi.org/10.1161/circ.141.suppl_1.MP07Circulation. 2020;141:AMP07
- Christopher M Seabury, David L Oldeschulte, Eric K Bhattarai, Dhruti Legare, Pamela J Ferro, Richard P Metz, Charles D Johnson, Mitchell A Lockwood, Tracy A Nichols. Accurate Genomic Predictions for Chronic Wasting Disease in US White-Tailed Deer G3: Genes, Genomes, Genetics April 1, 2020 vol. 10 no. 4 1433-1441; https://doi.org/10.1534/g3.119.401002
- Nancy H Ing, Kranti Konganti, Noushin Ghaffari, Charles D Johnson, David W Forrest, Charles C Love, Dickson D Varner. Identification and quantification of coding and long non‐coding RNAs in stallion spermatozoa separated by density 03 April 2020 https://doi.org/10.1111/andr.12791 Song, Q., Joshi, M., Wang, S. et al. Comparative Analysis of Root Transcriptome Profiles of Sesame (Sesamum indicum L.) in Response to Osmotic Stress. J Plant Growth Regul (2020). https://doi.org/10.1007/s00344-020-10230-0
- Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M Visbisky, Scott L Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William KM Lai, Richard P Metz, Charles D Johnson, Sing-Hoi Sze, B Franklin Pugh, Bryce E Nickels, Craig D Kaplan. Genome Biol 21, 132 (2020). https://doi.org/10.1186/s13059-020-02040-0
- Yan Yang, Bhoja R. Basnet, Amir M.H. Ibrahim, Jackie C. Rudd, Xianming Chen, Robert L. Bowden, Qingwu Xue, Shichen Wang, Charles D. Johnson, Richard Metz, Richard Esten Mason, Dirk B. Hays, and Shuyu Liu. Developing KASP Markers on a Major Stripe Rust Resistance QTL in a Popular Wheat TAM 111 Using 90K Array and Genotyping-by-Sequencing SNPs. Crop science, vol. 59, january–february 2019
- Jan E Janečka, Brian W Davis, Sharmila Ghosh, Nandina Paria, Pranab J Das, Ludovic Orlando, Mikkel Schubert, Martin K Nielsen, Tom AE Stout, Wesley Brashear, Gang Li, Charles D Johnson, Richard P Metz, Charles C Love, Dickson D Varner, Daniel W Bellott, William J Murphy, Bhanu P Chowdhary, Terje Raudsepp Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nature Communicationsvolume 9, Article number: 2945 (2018)
- NH Ing, K Konganti, N Ghaffari, CD Johnson, DW Forrest, CC Love, DD Varner Functional RNAs in Stallion Sperm: Potential Indicators of Sperm Quality and Contributors to Fertility. Journal of Equine Veterinary Science. Volume 66, July 2018 https://doi.org/10.1016/j.jevs.2018.05.011
- Brun M, Stull MA, Howard E, Hill J, Metz R, Johnson CD (2018) Comparison of MiSeq, iSeq and NovaSeq. In: Texas A&M AgriLife Genomics Bioinforma Serv, pp 2–4. . Comparison of MiSeq, iSeq and NovaSeq. 2018 https://www.txgen.tamu.edu/wp-content/uploads/2018/09/iSeq_MiSeq_NovaSeq-test_v03-1.pdf
- Bin Tian, Shichen Wang, Timothy C. Todd, Charles D. Johnson, Guiliang Tang, and Harold N. Trick Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics 2017. 2 August 2017 18:572 https://doi.org/10.1186/s12864-017-3963-4 Link
- David L. Oldeschulte, Yvette A. Halley, Miranda L. Wilson, Eric K. Bhattarai, Wesley Brashear, Joshua Hill, Richard P. Metz, Charles D. Johnson, Dale Rollins, Markus J. Peterson, Derek M. Bickhart, Jared E. Decker, John F. Sewell and Christopher M. Seabury. Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. G3: Genes, Genomes, Genetics July 17, 2017; Link
- Heidi M. Blank, Ricardo Perez, Chong He, Nairita Maitra, Richard Metz, Joshua Hill, Yuhong Lin, Charles D. Johnson, Vytas A. Bankaitis, Brian K. Kennedy, Rodolfo Aramayo and Michael Polymenis. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. 2017 DOI 10.15252/embj.201695050 | Published online 05.01.2017 The EMBO Journal (2017) e201695050 (Article ID: EMBJ788)
- Noushin Ghaffari, Jordi Abante, Raminder Singh, Philip D. Blood, Charles D. Johnson. Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data July 17 – 21, 2016 ISBN: 978-1-4503-4755-6
- NH Ing, K Konganti, N Ghaffari, CD Johnson, DW Forrest, CC Love, DD Varner. Sequencing of RNA from stallion sperm identifies potential markers of fertility. 2016 Journal of Equine Veterinary Science, S56eS82
- Maria F. Torres, Noushin Ghaffari, Ester A. S. Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson and Lisa J. Vaillancourt. Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction. BMC Genomics 201617:202. DOI:10.1186/s12864-016-2546-0. 8 March 2016
(2015) Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. PLoS ONE 10(12): e0144913. doi: 10.1371/journal.pone.0144913
- Ghaffari, N.; Arshad, O.A.; Jeong, H.; Thiltges, J.; Criscitiello, M.F.; Yoon, Byung-Jun; Datta, A.; Johnson, C.D., “Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline,” Computational Biology and Bioinformatics, IEEE/ACM Transactions on , vol.PP, no.99, pp.1,1 doi: 10.1109/TCBB.2015.2446478
- Masoud Toloue , Jan Risinger , Lindsey Renken , Josh Hill , Noushin Ghaffari , Richard P Metz , Charles D. Johnson , Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification – Mixed Species Plant and Animal Genome XXIII Conference 2015.