University of California, Davis

Contact Info:

Ryan Kim

One Shields Ave

Davis, CA 95616

https://genomecenter.ucdavis.edu/dna_technologies

Grants and Identifiers:

RRID: RRID:SCR_017740

Instrumentation:

Services Provided:

Genomics

Genotyping

Library Services

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Shared Instrumentation Oversight & Maintenance

Relevant Publications:

1.) Zaccaron AZ, Chen LH, Stergiopoulos I (2024 Dec). Transcriptome analysis of two isolates of the tomato pathogen Cladosporium fulvum, uncovers genome-wide patterns of alternative splicing during a host infection cycle. PLoS pathogens, 20(12), e1012791. . PMID: 39693392.

2.) Stevens ET, Van Beeck W, Blackburn B, Tejedor-Sanz S, Rasmussen ARM, Carter ME, Mevers E, Ajo-Franklin CM, Marco ML (2023 Nov 20). Lactiplantibacillus plantarum uses ecologically relevant, exogenous quinones for extracellular electron transfer. mBio, 14(6), e0223423. . PMID: 37982640.

3.) Emami AJ, Sebastian A, Lin YY, Yee CS, Osipov B, Loots GG, Alliston T, Christiansen BA (2022 Apr). Altered canalicular remodeling associated with femur fracture in mice. Journal of orthopaedic research : official publication of the Orthopaedic Research Society, 40(4), 891-900. . PMID: 34129247.

4.) Zaccaron AZ, Chen LH, Samaras A, Stergiopoulos I (2022 Apr). A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome. Microbial genomics, 8(4), . . PMID: 35471194.

5.) Tejedor-Sanz S, Stevens ET, Li S, Finnegan P, Nelson J, Knoesen A, Light SH, Ajo-Franklin CM, Marco ML (2022 Feb 11). Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism. eLife, 11(), . pii: e70684. doi: 10.7554/eLife.70684. PMID: 35147079.

6.) Diner RE, Kaul D, Rabines A, Zheng H, Steele JA, Griffith JF, Allen AE (2021 Aug 31). Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes. mSystems, 6(4), e0057121. doi: 10.1128/mSystems.00571-21. PMID: 34227831.

7.) Lehman PW, Kurobe T, Huynh K, Lesmeister S, Teh SJ (2021). Covariance of Phytoplankton, Bacteria, and Zooplankton Communities Within Microcystis Blooms in San Francisco Estuary. Frontiers in microbiology, 12(), 632264. doi: 10.3389/fmicb.2021.632264. PMID: 34163439.

8.) Curtasu MV, Tafintseva V, Bendiks ZA, Marco ML, Kohler A, Xu Y, Nørskov NP, Nygaard Lærke H, Bach Knudsen KE, Hedemann MS (2020 Nov 12). Obesity-Related Metabolome and Gut Microbiota Profiles of Juvenile Göttingen Minipigs-Long-Term Intake of Fructose and Resistant Starch. Metabolites, 10(11), . . PMID: 33198236.

9.) Wright ME, Yu AO, Marco ML, Panigrahi P (2020 Sep 24). Genome Sequence of Lactiplantibacillus plantarum ATCC 202195, a Probiotic Strain That Reduces Sepsis and Other Infections during Early Infancy. Microbiology resource announcements, 9(39), . . PMID: 32972932.

10.) Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY (2020 Feb 1). Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica. FEMS microbiology ecology, 96(2), . . PMID: 31905236.

11.) Jin J, Kurobe T, Hammock BG, Lam CH, Lin L, Teh SJ (2020 Jan 15). Toxic effects of fluridone on early developmental stages of Japanese Medaka (Oryzias latipes). The Science of the total environment, 700(), 134495. doi: 10.1016/j.scitotenv.2019.134495. PMID: 31693955.

12.) Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY (2020). Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica. PloS one, 15(4), e0231053. doi: 10.1371/journal.pone.0231053. PMID: 32282803.

13.) Arbour TJ, Gilbert B, Banfield JF (2020). Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities. Frontiers in microbiology, 11(), 1694. doi: 10.3389/fmicb.2020.01694. PMID: 32849356.

14.) Kable ME, Riazati N, Kirschke CP, Zhao J, Tepaamorndech S, Huang L (2020). The Znt7-null mutation has sex dependent effects on the gut microbiota and goblet cell population in the mouse colon. PloS one, 15(9), e0239681. doi: 10.1371/journal.pone.0239681. PMID: 32991615.

15.) Dhanapal AP, Crisosto CH (2013 Dec). Association genetics of chilling injury susceptibility in peach (Prunus persica (L.) Batsch) across multiple years. 3 Biotech, 3(6), 481-490. . PMID: 28324420.

Description:

Genotyping on all the Illumina platforms, sequencing on Illumina GAIIx, HiSeq2000, MiSeq,and PacBio RS, array services for NimbleGen and Illumina, chromatin immunoprecipitation and methylated DNA immunoprecipitation services.