NCGR Publications - 2014

De Novo Transcriptomes of a Mixotrophic and a Heterotrophic Ciliate from Marine Plankton.
Luciana F Santoferrara, Stephanie Guida, Huan Zhang, George B McManus.
2014/7/1 PloS one Volume 9 Issue 7.

Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels.
Matyi SA, Ramaraj T, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE.
Genome Announc. 2014 Jul 10;2(4). pii: e00688-14. doi: 10.1128/genomeA.00688-14.

The transcriptome landscape of early maize meiosis.
Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C.
BMC Plant Biol. 2014 May 3;14:118. doi: 10.1186/1471-2229-14-118.

Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium.
Li, X., Han, Y., Wei, Y., Acharya, A., Farmer, A.D., Ho, J., Monteros, M.J., and Brummer, E.C.
(2014). PLoS ONE 9, e84329

Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
Kudapa, H., Azam, S., Sharpe, A.G., Taran, B., Li, R., Deonovic, B., Cameron, C., Farmer, A.D., Cannon, S.B., and Varshney, R.K.
(2014). PLoS ONE 9, e86039

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.
Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V., Archibald, J.M., Bharti, A.K., Bell, C.J., et al.
(2014). PLoS Biol. 12, e1001889.

Phase variation in Myxococcus xanthus yields cells specialized for iron sequestration.
Dziewanowska, K., Settles, M., Hunter, S., Linquist, I., Schilkey, F., and Hartzell
P.L. (2014). PLoS ONE 9, e95189

Molecular and biological characterization of a new isolate of guinea pig cytomegalovirus.
Schleiss MR, McAllister S, Armién AG, Hernandez-Alvarado N, Fernández-Alarcón C, Zabeli JC, Ramaraj T, Crow JA, McVoy MA
Viruses. 2014 Jan 27;6(2):448-75. doi: 10.3390/v6020448.

A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement.
He R, Salvato F, Park JJ, Kim MJ, Nelson W, Balbuena TS, Willer M, Crow JA, May GD, Soderlund CA, Thelen JJ, Gang DR1.
BMC Plant Biol. 2014 Feb 12;14:46. doi: 10.1186/1471-2229-14-46.

Genome and Secretome analysis of the Hemibiotrophic Fungal Pathogen, Moniliophthora roreri, which causes Frosty Pod Rot Disease of Cacao:Mechanisms of the Biotrophic and Necrotrophic Phases.
Lyndel W Meinhardt, Gustavo G L Costa, Daniela PT Thomazella, Paulo J P L Teixeira, Marcelo F Carazzolle, Stephen C Schuster, John E Carlson, Mark J Guiltinan, Piotr Mieczkowski, Andrew Farmer, Thiruvarangan Ramaraj, Jayne Crozier, Robert E Davis, Jonathan Shao, Rachel L Melnick, Goncalo A G Pereira and Bryan A Bailey
BMC Genomics 2014, 15:164

Sequencing-based large-scale genomics approaches with small numbers of isolated maize meiocytes.
Stefanie Dukowic-Schulze, Anitha Sundararajan, Thiruvarangan Ramaraj, Joann Mudge, and Changbin Chen.

Frontiers in Plant Science 2014 Feb 05 5:57.

Improved hybrid genome assemblies of two Bacteroides xylanisolvens, SD CC 1b and SD CC 2a, obtained using Illumina and 454 sequencing technologies.
Thiruvarangan Ramaraj, Anitha Sundararajan, Faye D. Schilkey, Vito G. Delvecchio, Mildred Donlon, Cherie Ziemer, and Joann Mudge.

Genome announcements 2014 2 (2), e00237-14

Comparative transcriptomics of early meiosis in Arabidopsis and maize.
Dukowic-Schulze S, Harris A, Li J, Sundararajan A, Mudge J, Retzel EF, Pawlowski WP, Chen C

J Genet Genomics. 2014 Mar 20;41(3):139-52. doi: 10.1016/j.jgg.2013.11.007. Epub 2013 Dec 14.

Comprehensive characterization and RNA-Seq profiling of the HD-Zip
transcription factor family in soybean (Glycine max) during
dehydration and salt stress.

Belamkar V, Weeks NT, Bharti AK, Farmer AD, Graham MA, Cannon SB.
BMC Genomics. 2014 Nov 3;15(1):950. PMID: 25362847

Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.
Mukherjee M, Kakarla P, Kumar S, Gonzalez E, Floyd JT, Inupakutika M, Devireddy AR, Tirrell SR, Bruns M, He G, Lindquist IE, Sundararajan A, Schilkey FD, Mudge J, Varela MF
Genomics Discovery, 2014 July 23, 2:1,1. doi: 10.7243/2052-7993-2-1 PMID: 25722857

Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus.
Ramaraj T, Matyi SA, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE. 
Genome Announc. 2014 Oct 9;2(5). pii: e01033-14. doi: 10.1128/genomeA.01033-14. PMID: 25301662

Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism, Polaromonas sp. Strain CG9_12, Determined Using Pacific Biosciences Single-Molecule Real-Time Sequencing Technology.
Smith HJ, Foreman CM, Ramaraj T. 
Genome Announc. 2014 Dec 4;2(6). pii: e01242-14. doi: 10.1128/genomeA.01242-14. PMID: 25477404

Illuminating the Phytophthora capsici Genome 
Kurt Lamour, Jian Hu, Véronique Lefebvre, Joann Mudge, Andrew Howden, Edgar Huitema 
Genomics of Plant-Associated Fungi and Oomycetes: Dicot Pathogens. 2014, Springer: 121-132

High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches. 
Bonhomme M, André O, Badis Y, Ronfort J, Burgarella C, Chantret N, Prosperi JM, Briskine R, Mudge J, Debéllé F, Navier H, Miteul H, Hajri A, Baranger A, Tiffin P, Dumas B, Pilet-Nayel ML, Young ND, Jacquet C. 
New Phytol. 2014 Mar;201(4):1328-42. doi: 10.1111/nph.12611. Epub 2013 Nov 28. PMID: 24283472

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data. 
Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Burow MD. 
PLoS One. 2014 Dec 31;9(12):e115055. doi: 10.1371/journal.pone.0115055. eCollection 2014.  PMID: 25551607

SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China. 
Shrestha S, Hu J, Fryxell RT, Mudge J, Lamour K. 
Mycologia. 2014 Jul-Aug;106(4):676-85. doi: 10.3852/13-165. Epub 2014 Jun 3.  PMID: 24895424

Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea. 
Gujaria-Verma N, Vail SL, Carrasquilla-Garcia N, Penmetsa RV, Cook DR, Farmer AD, Vandenberg A, Bett KE. 
Front Plant Sci. 202014 Dec 5;5:676. doi: 10.3389/fpls.2014.00676. eCollection 2014.  PMID: 25538716