@article{wu_lau_cao_hamilton_sun_zhou_eserman_gemenet_olukolu_wang_et al._2018, title={Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-06983-8}, DOI={10.1038/s41467-018-06983-8}, abstractNote={Abstract}, number={1}, journal={Nature Communications}, publisher={Springer Nature}, author={Wu, Shan and Lau, Kin H. and Cao, Qinghe and Hamilton, John P. and Sun, Honghe and Zhou, Chenxi and Eserman, Lauren and Gemenet, Dorcus C. and Olukolu, Bode A. and Wang, Haiyan and et al.}, year={2018}, month={Nov} }
 @article{burford reiskind_coyle_daniels_labadie_reiskind_roberts_roberts_schaff_vargo_2016, title={Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa}, volume={16}, ISSN={1755-098X}, url={http://dx.doi.org/10.1111/1755-0998.12527}, DOI={10.1111/1755-0998.12527}, abstractNote={Abstract}, number={6}, journal={Molecular Ecology Resources}, publisher={Wiley}, author={Burford Reiskind, M. O. and Coyle, K. and Daniels, H. V. and Labadie, P. and Reiskind, M. H. and Roberts, N. B. and Roberts, R. B. and Schaff, J. and Vargo, E. L.}, year={2016}, month={May}, pages={1303–1314} }
 @article{burke_scholl_bird_schaff_colman_crowell_diener_gordon_graham_wang_et al._2015, title={The plant parasite Pratylenchus coffeae carries a minimal nematode genome}, volume={17}, ISSN={["1388-5545"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938097712&partnerID=MN8TOARS}, DOI={10.1163/15685411-00002901}, abstractNote={Here we report the genome sequence of the lesion nematode, Pratylenchus coffeae, a significant pest of banana and other staple crops in tropical and sub-tropical regions worldwide. Initial analysis of the 19.67 Mb genome reveals 6712 protein encoding genes, the smallest number found in a metazoan, although sufficient to make a nematode. Significantly, no developmental or physiological pathways are obviously missing when compared to the model free-living nematode Caenorhabditis elegans, which possesses approximately 21 000 genes. The highly streamlined P. coffeae genome may reveal a remarkable functional plasticity in nematode genomes and may also indicate evolutionary routes to increased specialisation in other nematode genera. In addition, the P. coffeae genome may begin to reveal the core set of genes necessary to make a multicellular animal. Nematodes exhibit striking diversity in the niches they occupy, and the sequence of P. coffeae is a tool to begin to unravel the mechanisms that enable the extraordinary success of this phylum as both free-living and parasitic forms. Unlike the sedentary endoparasitic root-knot nematodes (Meloidogyne spp.), P. coffeae is a root-lesion nematode that does not establish a feeding site within the root. Because the P. coffeae nematode genome encodes fewer than half the number of genes found in the genomes of root-knot nematodes, comparative analysis to determine genes P. coffeae does not carry may help to define development of more sophisticated forms of nematode-plant interactions. The P. coffeae genome sequence may help to define timelines related to evolution of parasitism amongst nematodes. The genome of P. coffeae is a significant new tool to understand not only nematode evolution but animal biology in general.}, number={6}, journal={NEMATOLOGY}, author={Burke, Mark and Scholl, Elizabeth H. and Bird, David McK. and Schaff, Jennifer E. and Colman, Steven D. and Crowell, Randy and Diener, Stephen and Gordon, Oksana and Graham, Steven and Wang, Xinguo and et al.}, year={2015}, pages={621–637} }
 @article{schilling_nepomuceno_schaff_muddiman_daniels_reading_2014, title={Compartment Proteomics Analysis of White Perch (Morone americana) Ovary Using Support Vector Machines}, volume={13}, ISSN={["1535-3907"]}, DOI={10.1021/pr401067g}, abstractNote={Compartment proteomics enable broad characterization of target tissues. We employed a simple fractionation method and filter-aided sample preparation (FASP) to characterize the cytosolic and membrane fractions of white perch ovary tissues by semiquantitative tandem mass spectrometry using label-free quantitation based on normalized spectral counts. FASP depletes both low-molecular-weight and high-molecular-weight substances that could interfere with protein digestion and subsequent peptide separation and detection. Membrane proteins are notoriously difficult to characterize due to their amphipathic nature and association with lipids. The simple fractionation we employed effectively revealed an abundance of proteins from mitochondria and other membrane-bounded organelles. We further demonstrate that support vector machines (SVMs) offer categorical classification of proteomics data superior to that of parametric statistical methods such as analysis of variance (ANOVA). Specifically, SVMs were able to perfectly (100% correct) classify samples as either membrane or cytosolic fraction during cross-validation based on the expression of 242 proteins with the highest ANOVA p-values (i.e., those that were not significant for enrichment in either fraction). The white perch ovary cytosolic and membrane proteomes and transcriptome presented in this study can support future investigations into oogenesis and early embryogenesis of white perch and other members of the genus Morone.}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Schilling, Justin and Nepomuceno, Angelito and Schaff, Jennifer E. and Muddiman, David C. and Daniels, Harry V. and Reading, Benjamin J.}, year={2014}, month={Mar}, pages={1515–1526} }
 @article{zhang_franks_liu_kang_keebler_schaff_huang_xiang_2013, title={De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)}, volume={8}, ISSN={1932-6203}, url={https://dx.plos.org/10.1371/journal.pone.0082674}, DOI={10.1371/journal.pone.0082674}, abstractNote={Background Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species. Results The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bi-directional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies. Conclusions The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses. Results of the study also provide markers useful for dogwood phylogenomic studies.}, number={12}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Zhang, Jian and Franks, Robert G. and Liu, Xiang and Kang, Ming and Keebler, Jonathan E. M. and Schaff, Jennifer E. and Huang, Hong-Wen and Xiang, Qiu-Yun (Jenny)}, editor={Wang, TingEditor}, year={2013}, month={Dec}, pages={e82674} }
 @article{thomas_fudali_schaff_liu_scholl_opperman_bird_williamson_2012, title={A sequence-anchored linkage map of the plant-parasitic nematode Meloidogyne hapla reveals exceptionally high genome-wide recombination}, volume={2}, number={7}, journal={G3-Genes Genomes Genetics}, author={Thomas, V. P. and Fudali, S. L. and Schaff, J. E. and Liu, Q. L. and Scholl, E. H. and Opperman, C. H. and Bird, D. M. and Williamson, V. M.}, year={2012}, pages={815–824} }
 @article{mauchline_mohan_davies_schaff_opperman_kerry_hirsch_2010, title={A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans}, volume={50}, ISSN={["0266-8254"]}, DOI={10.1111/j.1472-765x.2010.02830.x}, abstractNote={Aims:  To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR‐based diagnostic tool for P. penetrans.}, number={5}, journal={LETTERS IN APPLIED MICROBIOLOGY}, author={Mauchline, T. H. and Mohan, S. and Davies, K. G. and Schaff, J. E. and Opperman, C. H. and Kerry, B. R. and Hirsch, P. R.}, year={2010}, month={May}, pages={515–521} }
 @article{schaff_mbeunkui_blackburn_bird_goshe_2008, title={A sequence-anchored genetic linkage map for the moss, Physcomitrella patens}, volume={56}, number={5}, journal={Plant Journal}, author={Schaff, J. E. and Mbeunkui, F. and Blackburn, K. and Bird, D. M. and Goshe, M. B.}, year={2008}, pages={840–854} }
 @article{opperman_bird_williamson_rokhsar_burke_cohn_cromer_diener_gajan_graham_et al._2008, title={Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism}, volume={105}, ISSN={["1091-6490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54149092490&partnerID=MN8TOARS}, DOI={10.1073/pnas.0805946105}, abstractNote={
            We have established
            Meloidogyne hapla
            as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence. At 54 Mbp,
            M. hapla
            represents not only the smallest nematode genome yet completed, but also the smallest metazoan, and defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. The
            M. hapla
            genome encodes significantly fewer genes than does the free-living nematode
            Caenorhabditis elegans
            (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous genes suspected to be involved in adaptations to parasitism. In some cases, amplification and tandem duplication have occurred with genes suspected of being acquired horizontally and involved in parasitism of plants. Although
            M. hapla
            and
            C. elegans
            diverged >500 million years ago, many developmental and biochemical pathways, including those for dauer formation and RNAi, are conserved. Although overall genome organization is not conserved, there are areas of microsynteny that may suggest a primary biological function in nematodes for those genes in these areas. This sequence and map represent a wealth of biological information on both the nature of nematode parasitism of plants and its evolution.
          }, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Opperman, Charles H. and Bird, David M. and Williamson, Valerie M. and Rokhsar, Dan S. and Burke, Mark and Cohn, Jonathan and Cromer, John and Diener, Steve and Gajan, Jim and Graham, Steve and et al.}, year={2008}, month={Sep}, pages={14802–14807} }
 @article{schaff_nielsen_smith_scholl_bird_2007, title={Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance}, volume={144}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.106.090241}, DOI={10.1104/pp.106.090241}, abstractNote={Abstract}, number={2}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Schaff, Jennifer E. and Nielsen, Dahlia M. and Smith, Chris P. and Scholl, Elizabeth H. and Bird, David McK.}, year={2007}, month={Apr}, pages={1079–1092} }