PUBLICATIONS

(Separated by categories Centromeres, Genomics and Bioinformatics, Biodiversity and DNA Barcoding and Miscellaneous)

 

Centromeres

Xie Z, Presting G. 2016. Chromatin immunoprecipitation to study the plant epigenome, In: Plant Cytogenetics, in press.

Schneider K, Xie Z, Wolfgruber TK, Presting G. 2016. Inbreeding drives maize centromere evolution. Proc Natl Acad Sci USA. 113(8):E987-E996. DOI: 10.1073/pnas.1522008113

Wolfgruber TK, Nakashima MM, Schneider KL, Sharma A, Xie Z, Albert PS, Xu R, Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting G. 2016. High quality maize centromere 10 sequence reveals evidence of frequent recombination events. Front. Plant Sci. 7:308. DOI: 10.3389/fpls.2016.003

Sharma A and Presting G. 2014. Evolution of Centromeric Retrotransposons in Grasses. Genome Biology and Evolution. DOI: 10.1093/gbe/evu096. 08.

Presting G. 2013. Maize centromeres, In: Plant Centromere Biology, Jiang J, Birchler J A, eds. John Wiley & Sons, pp. 25-38.

Sharma A, Wolfgruber TK, Presting G. 2013. Tandem repeats derived from centromeric retrotransposons. BMC Genomics, 14:142.

Birchler JA and Presting G. 2012. Retrotransposon insertion targeting: a mechanism for homogenization of centromere sequences on nonhomologous chromosomes. Genes and Development 26:638-640.

Birchler JA, Gao Z, Sharma A, Presting G and Han F. 2011. Epigenetic aspects of centromere function in plants. Current Opinion in Plant Biology, 14:217-222.

Gent JI, Schneider KL, Topp CN, Rodriguez C, Presting GG and Dawe RK. 2011. Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning. Epigenetics & Chromatin, 4:3 DOI:10.1186/1756-8935-4-3.

Shi J, Wolf SE, Burke JM, Presting GG, Ross-Ibarra J, Dawe RK. 2010. Widespread Gene Conversion in Centromere Cores. PLoS Biol 8(3): e1000327. DOI:10.1371/journal.pbio.1000327.

Wolfgruber TK, Presting G. 2010. JunctionViewer: customizable annotation software for repeat-rich genomic regions. BMC Bioinformatics, 11:23. DOI:10.1186/1471-2105-11-23.

Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo D-H, Shi J, Lee H, Gao Z, Han F, Xu R, Allison J, Birchler JA, Jiang J, Dawe RK, Presting G. 2009. Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons. PLoS Genet 5(11): e1000743. DOI:10.1371/journal.pgen.1000743.

Sharma A, Schneider KL and Presting G. 2008. Sustained retrotransposition is mediated by nucleotide deletions and inter-element recombinations. Proc Natl Acad Sci USA, 105:15470-15474.

Sharma A, Presting G. 2008. Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity. Mol Gen Genomics, 279:133–147.

Luce A, Sharma A, Mollere O, Wolfgruber TK, Nagaki K, Jiang J, Presting G, Dawe RK. 2006. Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-PCR. Genetics 174:1057-61.

Hudakova S, Michalek W, Presting G, ten Hoopen R, dos Santos K, Jasencakova Z, Schubert I. 2001. Sequence organization of barley centromeres. Nucl. Acids Res. 29:5029-5035.

Houben A, Wako T, Furushima-Shimogawara R, Presting G, Kunzel G, Schubert I and Fukui K. 1999. The cell cycle dependent phosphorylation of histone H3 is correlated with the condensation of plant mitotic chromosomes. Plant Journal 18:675-679.

Presting G, Malysheva L, Fuchs J and Schubert I. 1998. A Ty3/GYPSY retrotransposon-like sequence localizes to the centromeric region of cereal chromosomes. Plant Journal 16:721-728.

Presting G, Frary A, Pillen KP and Tanksley SD. 1996. Telomere-homologous sequences occur near the centromeres of many tomato chromosomes. Mol. Gen. Genet. 251:526-531.

Frary A, Presting G and Tanksley SD. 1995. Molecular mapping of the centromeres of tomato chromosomes 7 and 9. Mol. Gen. Genet. 250:295-304.

 

 

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney W, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy M, McMahan L, Buren PV, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia J, Deragon J, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton DS, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. 2009. The B73 maize genome: complexity, diversity and dynamics. Science, 326:1112-1115.

Paull RE, Irikura B, Wu P, Turano H, Chen NJ, Blas A, Fellman JK, Gschwend AR, Wai CM, Yu Q, Presting G, Alam M, Ming R. 2008. Fruit development, ripening and quality related genes in the papaya genome. Tropical Plant Biol. 1:246–277.

Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice D, Albert H, Wang M, Zhu YJ, Schatz M, Nagarajan N, Agbayani R, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na J, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Pérez RN, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo M, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen D, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M. 2008. Genome of the transgenic tropical fruit tree papaya (Carica papaya L.). Nature, 452:991-996.

Umylny B, Presting G and Ward WS. 2007. Evidence of Alu expression in dbEST. Archives of Andrology, 53:207-18.

Eustice M, Yu Q, Lai CWJ, Moore PH, Presting G and Ming R. 2007. Development and use of microsatellite markers for genetic analysis in papaya. Tree Genetics and Genomes, 4:333-341, DOI 10.1007/s11295-007-0112-2.

Umylny B, Presting G, Efird J and Ward WS. 2007. Most human Alu and Murine B1 repeats are unique. Journal of Cellular Biochemistry, 102:110-121, DOI: 10.1002/jcb.21278.

Lai CW, Yu Q, Hou S, Skelton RL, Jones MR, Kanako LTJ, Murray J, Eustice M, Agbayani R, Guan P, Moore P, Ming R, Presting G. 2006. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol. Gen. Genomics 276:1-12.

Gabriel DW, Allen C, Schell M, Denny T, Greenberg J, Duan YP, Flores-Cruz Z, Huang Q, Clifford JM, Presting G, Gonzalez ET, Reddy J, Elphinstone J, Swanson J, Yao J, Mulholand V, Liu L, Farmerie W, Patnaikuni M, Balogh B, Norman D, Alvarvez A, Castillo JA, Jones J, Saddler G, Walunas T, Zhukov A and Mikhailova N. 2006. Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2. Mol. Plant Microbe Interactions. 19:69-79.

Lange BM, Presting G. 2004. Genomic survey of metabolic pathways in rice, In: Recent Advances in Phytochemistry, Romeo, John T., ed., Elsevier Science, Amsterdam, pp. 111-137.

Presting G. 2003. Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome. BioInformatics 19(5):579-586.

Sessions A, Burke E, Presting G, Aux G, McElver J, Patton D, Dietrich B, Ho P, Bacwaden J, Ko C, Clarke JD, Cotton D, Bullis D, Snell J, Miguel T, Hutchison D, Kimmerly B, Mitzel T, Katagiri F, Glazebrook J, Law M, Goff SA. 2002. A high-throughput Arabidopsis reverse genetics system. Plant Cell 14(12):2985-94.

Goff SA, Ricke D, Lan T, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange B, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W, Chen L, Cooper B, Park S, Wood T, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller R, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S. 2002. A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica). Science Apr 5 2002: 92-100.

Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA. 2002. An integrated physical and genetic map of the rice genome. Plant Cell 14:1-10.

Wechter WP, Begum D, Presting G, Kim JJ, Wing RA, Kluepfel DA. 2002. Physical mapping, BAC-end sequence analysis, and marker tagging of the soilborne nematicidal bacterium, Pseudomonas synxantha BG33R. OMICS – A Journal of Integrative Biology 6:11-21.

Wing RA, Yu Y, Presting G, Frisch D, Wood T, Woo S-S, Budiman MA, Mao L, Kim HR, Rambo T, Fang E, Blackmon B, Goicoechea JL, Higingbottom S, Sasinowski M, Tomkins J, Dean RA, Soderlund C, McCombie WR, Martienson R, de al Bastide M, Wilson R, Johnson D. 2002. Sequence-tagged connector / DNA fingerprint framework for rice genome sequencing. In: Rice Genetics IV. pp. 215 to 225. The International Rice Research Institute. Science Publishers Inc. New Delhi, India.

Cheng Z, Presting G, Buell CR, Wing RA, Jiang J. 2001. High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157:1749-57.

Presting G, Budiman MA, Wood T, Yu Y, Kim HR, Goicoechea JL, Fang E, Blackman B, Jiang J, Woo SS, Dean RA, Frisch D, Wing RA. 2001. A framework for sequencing the rice genome. In: Rice Biotechnology: Improving yield, stress tolerance and grain quality, Jamie A. Goode and Derek Chadwick, eds., John Wiley & Sons, New York, pp. 236:13-27.

Draye X, Lin YR, Qian XY, Bowers JE, Burow GB, Morrell PL, Peterson DG, Presting G, Ren SX, Wing RA and Paterson AH. 2001. Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. Plant Physiol. 125:1325-41.

Mao L, Wood T, Yu Y, Budiman MA, Woo S, Sasinowski M, Presting G, Frisch D, Goff S, Dean R and Wing R. 2000. Rice transposable elements: a survey of 73,000 sequence-tagged connectors. Genome Res. 7:982-90.

 

Sherwood AR, Carlile AL, Neumann JM, Kociolek JP, Johansen J, Lowe RL, Conklin KY, Presting G. 2014. The Hawaiian Freshwater Algae Biodiversity Survey (2009-2014): systematic and biogeographic trends with an emphasis on the macroalgae. BMC Ecology, 14:28. DOI: 10.1186/s12898-014-0028-2

Campbell MA, Presting G, Bennett MS, Sherwood, AR. 2014. Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive alga Gracilaria salicornia (Rhodophyta). Phycologia, 53:109-116.

Sherwood AR, Wang N, Carlile AL, Neumann JM, Wolfgruber TK, Presting G. 2012. The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource. BMC Ecology, 12:22, DOI:10.1186/1472-6785-12-22.

Yakabe LE, Maccree MM, Sudarshana P, McClean AE, Parker SR, Wechter WP, Presting G, Marutani-Hert M and Kluepfel DA. 2012. Novel PCR primers for detection of genetically diverse virulent Agrobacterium tumefaciens biovar 1 strains. Journal of General Plant Pathology, DOI: 10.1007/s10327-012-0364-z.

Schneider K, Marrero G, Alvarez A and Presting G. 2011. Rapid identification of plant pathogenic bacteria below the species level using a computationally derived DNA marker. PLoS ONE 6(4): e18496. DOI:10.1371/journal.pone.0018496.

Sherwood AR, Sauvage T, Kurihara A, Conklin KY and Presting G. 2010. A comparative analysis of COI, LSU and UPA marker data for the Hawaiian florideophyte Rhodophyta: implications for DNA barcoding of red algae. Cryptogamie-Algologie, 31(4):451-465.

Sherwood AR, Kurihara A, Conklin KY, Sauvage T and Presting G. 2010. The Hawaiian Rhodophyta Biodiversity Survey (2006-2010): a summary of principal findings. BMC Plant Biology, 10:258. DOI:10.1186/1471-2229-10-258.

Wang N, Sherwood AR, Kurihara A, Conklin KY, Sauvage T, Presting G. 2009. The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data. BMC Plant Biology, 9:117.

Sherwood A, Chan YL and Presting G. 2008. Application of universally amplifying plastid primers to environmental sampling of a stream periphyton community. Mol Ecol Resour, 8 (5), 1011-1014.

Sherwood AR, Vis ML, Entwisle TJ, Necchi O and Presting G. 2008. Contrasting intra- versus inter-specific sequence variation for representatives of the Batrachospermales (Rhodophyta): a comparison of two markers. Phycological Research, 56:269-279.

Sherwood AR, Presting G. 2007. Universal primers amplify a 23S rDNA plastid marker in eukaryoric algae and cyanobacteria. Journal of Phycology, 43:605-608.

Presting G. 2006. Identification of conserved regions in the plastid genome – implications for DNA barcoding and biological function. Canadian Journal of Botany, 84:1434-1443.

Jenkins DM, Chami B, Kreuzer M, Presting G, Alvarez A, Liaw BY. 2006. Hybridization probe for femtomolar quantification of selected nucleic acid sequences on a disposable electrode. Anal Chem. 78:2314-8.

 

Ori N, Eshed Y, Paran I, Presting G, Aviv D, Tanksley SD, Zamir D and Fluhr R. 1997. The I2C family from the wilt disease resistance locus I2 belongs to the nucleotide binding, leucine-rich repeat family of plant resistance genes. Plant Cell 9:521-532.

Presting G, Smith OPS and Brown CR. 1995. Resistance to potato leafroll virus in potato plants transformed with the coat protein gene or with vector control constructs. Phytopathology 85:436-442.

Presting G and Helgeson JP. 1994. Media and protocols for the isolation of independent mutants and transformants from Nicotiana plumbaginifolia protoplasts. Plant Science 99:211-221.