22 results on '"Ka-Shu Wong, Gane"'
Search Results
2. Evolution of genes and genomes on the Drosophila phylogeny
- Author
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Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain
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Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]
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- 2007
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3. Skin colonization by circulating neoplastic clones in cutaneous T-cell lymphoma
- Author
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Iyer, Aishwarya, primary, Hennessey, Dylan, additional, O’Keefe, Sandra, additional, Patterson, Jordan, additional, Wang, Weiwei, additional, Ka-Shu Wong, Gane, additional, and Gniadecki, Robert, additional
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- 2019
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4. RNA Isolation from Plant Tissue v1
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T. J. Johnson, Marc, primary, J. Carpenter, Eric, additional, Tian, Zhijian, additional, Bruskiewich, Richard, additional, N. Burris, Jason, additional, T. Carrigan, Charlotte, additional, W. Chase, Mark, additional, D. Clarke, Neil, additional, Covshoff, Sarah, additional, W. dePamphilis, Claude, additional, P. Edger, Patrick, additional, Goh, Falicia, additional, Graham, Sean, additional, Greiner, Stephan, additional, M. Hibberd, Julian, additional, Jordon-Thaden, Ingrid, additional, M. Kutchan, Toni, additional, Leebens-Mack, James, additional, Melkonian, Michael, additional, Miles, Nicholas, additional, Myburg, Henrietta, additional, Patterson, Jordan, additional, Chris Pires, J., additional, Ralph, Paula, additional, Rolf, Megan, additional, F. Sage, Rowan, additional, Soltis, Douglas, additional, Soltis, Pamela, additional, Stevenson, Dennis, additional, Neal Stewart Jr, C., additional, Surek, Barbara, additional, J. M. Thomsen, Christina, additional, Carlos Villarreal, Juan, additional, Wu, Xiaolei, additional, Zhang, Yong, additional, K. Deyholos, Michael, additional, and Ka-Shu Wong, Gane, additional
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- 2019
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5. RNA Isolation from Plant Tissue Protocol 6: pBIOZOL and Qiagen RNeasy Plant Mini Kit Method v1
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T. J. Johnson, Marc, primary, J. Carpenter, Eric, additional, Tian, Zhijian, additional, Bruskiewich, Richard, additional, N. Burris, Jason, additional, T. Carrigan, Charlotte, additional, W. Chase, Mark, additional, D. Clarke, Neil, additional, Covshoff, Sarah, additional, W. dePamphilis, Claude, additional, P. Edger, Patrick, additional, Goh, Falicia, additional, Graham, Sean, additional, Greiner, Stephan, additional, M. Hibberd, Julian, additional, Jordon-Thaden, Ingrid, additional, M. Kutchan, Toni, additional, Leebens-Mack, James, additional, Melkonian, Michael, additional, Miles, Nicholas, additional, Myburg, Henrietta, additional, Patterson, Jordan, additional, Chris Pires, J., additional, Ralph, Paula, additional, Rolf, Megan, additional, F. Sage, Rowan, additional, Soltis, Douglas, additional, Soltis, Pamela, additional, Stevenson, Dennis, additional, Neal Stewart Jr, C., additional, Surek, Barbara, additional, J. M. Thomsen, Christina, additional, Carlos Villarreal, Juan, additional, Wu, Xiaolei, additional, Zhang, Yong, additional, K. Deyholos, Michael, additional, and Ka-Shu Wong, Gane, additional
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- 2019
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6. Sequencing Protocols for the One Thousand Plant Transcriptomes Initiative v1
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J. Carpenter, Eric, primary, Matasci, Naim, additional, Wu, Shuangxiu, additional, Sun, Jing, additional, Yu, Jun, additional, Rocha Jimenez Vieira, Fabio, additional, Bowler, Chris, additional, G. Dorrell, Richard, additional, Gitzendanner, Matt, additional, Li, Ling, additional, Du, Wensi, additional, Ullrich, Kristian, additional, S. Barker, Michael, additional, H. Leebens-Mack, James, additional, and Ka-Shu Wong, Gane, additional
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- 2019
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7. Human Fetal Astrocytes Infected with Zika Virus Exhibit Delayed Apoptosis and Resistance to Interferon: Implications for Persistence
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Limonta, Daniel, primary, Jovel, Juan, additional, Kumar, Anil, additional, Airo, Adriana, additional, Hou, Shangmei, additional, Saito, Leina, additional, Branton, William, additional, Ka-Shu Wong, Gane, additional, Mason, Andrew, additional, Power, Christopher, additional, and Hobman, Tom, additional
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- 2018
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8. A Survey of Molecular Heterogeneity in Hepatocellular Carcinoma
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Jovel, Juan, primary, Lin, Zhen, additional, O'keefe, Sandra, additional, Willows, Steven, additional, Wang, Weiwei, additional, Zhang, Guangzhi, additional, Patterson, Jordan, additional, Moctezuma‐Velázquez, Carlos, additional, Kelvin, David J., additional, Ka‐Shu Wong, Gane, additional, and Mason, Andrew L., additional
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- 2018
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9. Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis
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Kelly, Steven, primary, Covshoff, Sarah, additional, Wanchana, Samart, additional, Thakur, Vivek, additional, Quick, W. Paul, additional, Wang, Yu, additional, Ludwig, Martha, additional, Bruskiewich, Richard, additional, Fernie, Alisdair R., additional, Sage, Rowan F., additional, Tian, Zhijian, additional, Yan, Zixian, additional, Wang, Jun, additional, Zhang, Yong, additional, Zhu, Xin-Guang, additional, Ka-Shu Wong, Gane, additional, and Hibberd, Julian M., additional
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- 2017
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10. Apparition of the NAC Transcription Factors Predates the Emergence of Land Plants
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Maugarny-Calès, Aude, primary, Gonçalves, Beatriz, additional, Jouannic, Stefan, additional, Melkonian, Michael, additional, Ka-Shu Wong, Gane, additional, and Laufs, Patrick, additional
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- 2016
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11. Cyclotide Discovery in Gentianales Revisited—Identification and Characterization of Cyclic Cystine-Knot Peptides and Their Phylogenetic Distribution in Rubiaceae Plants
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Koehbach, Johannes, Attah, Alfred F., Berger, Andreas, Hellinger, Roland, Kutchan, Toni M., Carpenter, Eric J., Rolf, Megan, Sonibare, Mubo A., Moody, Jones O., Ka-Shu Wong, Gane, Dessein, Steven, Greger, Harald, and Gruber, Christian W.
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Molecular Sequence Data ,food and beverages ,Cystine ,Cyclotides ,Rubiaceae ,Amino Acid Sequence ,Peptides, Cyclic ,Article ,Phylogeny ,Plant Proteins - Abstract
Cyclotides are a unique class of ribosomally synthesized cysteine-rich miniproteins characterized by a head-to-tail cyclized backbone and three conserved disulfide-bonds in a knotted arrangement. Originally they were discovered in the coffee-family plant Oldenlandia affinis (Rubiaceae) and have since been identified in several species of the violet, cucurbit, pea, potato, and grass families. However, the identification of novel cyclotide-containing plant species still is a major challenge due to the lack of a rapid and accurate analytical workflow in particular for large sampling numbers. As a consequence, their phylogeny in the plant kingdom remains unclear. To gain further insight into the distribution and evolution of plant cyclotides, we analyzed ~300 species of >40 different families, with special emphasis on plants from the order Gentianales. For this purpose, we have developed a refined screening methodology combining chemical analysis of plant extracts and bioinformatic analysis of transcript databases. Using mass spectrometry and transcriptome-mining, we identified nine novel cyclotide-containing species and their related cyclotide precursor genes in the tribe Palicoureeae. The characterization of novel peptide sequences underlines the high variability and plasticity of the cyclotide framework, and a comparison of novel precursor proteins from Carapichea ipecacuanha illustrated their typical cyclotide gene architectures. Phylogenetic analysis of their distribution within the Psychotria alliance revealed cyclotides to be restricted to Palicourea, Margaritopsis, Notopleura, Carapichea, Chassalia, and Geophila. In line with previous reports, our findings confirm cyclotides to be one of the largest peptide families within the plant kingdom and suggest that their total number may exceed tens of thousands.
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- 2013
12. Mesophyll Chloroplast Investment in C3, C4and C2Species of the GenusFlaveria
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Stata, Matt, primary, Sage, Tammy L., additional, Hoffmann, Natalie, additional, Covshoff, Sarah, additional, Ka-Shu Wong, Gane, additional, and Sage, Rowan F., additional
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- 2016
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13. Metagenomic Analysis of Microbiome in Colon Tissue from Subjects with Inflammatory Bowel Diseases Reveals Interplay of Viruses and Bacteria
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Wang, Weiwei, primary, Jovel, Juan, additional, Halloran, Brendan, additional, Wine, Eytan, additional, Patterson, Jordan, additional, Ford, Glenn, additional, OʼKeefe, Sandra, additional, Meng, Bo, additional, Song, Deyong, additional, Zhang, Yong, additional, Tian, Zhijian, additional, Wasilenko, Shawn T., additional, Rahbari, Mandana, additional, Reza, Salman, additional, Mitchell, Troy, additional, Jordan, Tracy, additional, Carpenter, Eric, additional, Madsen, Karen, additional, Fedorak, Richard, additional, Dielemann, Levinus A., additional, Ka-Shu Wong, Gane, additional, and Mason, Andrew L., additional
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- 2015
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14. Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.
- Author
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Johnson, Kim L., Cassin, Andrew M., Lonsdale, Andrew, Ka-Shu Wong, Gane, Soltis, Douglas E., Miles, Nicholas W., Melkonian, Michael, Melkonian, Barbara, Deyholos, Michael K., Leebens-Mack, James, Rothfels, Carl J., Stevenson, Dennis W., Graham, Sean W., Xumin Wang, Shuangxiu Wu, Pires, J. Chris, Edger, Patrick P., Carpenter, Eric J., Bacic, Antony, and Doblin, Monika S.
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- 2017
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15. Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae
- Author
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Tanifuji, Goro, primary, Onodera, Naoko T, additional, Brown, Matthew W, additional, Curtis, Bruce A, additional, Roger, Andrew J, additional, Ka-Shu Wong, Gane, additional, Melkonian, Michael, additional, and Archibald, John M, additional
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- 2014
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16. Peptidomics of Circular Cysteine-Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining.
- Author
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Hellinger, Roland, Koehbach, Johannes, Soltis, Douglas E., Carpenter, Eric J., Ka-Shu Wong, Gane, and Gruber, Christian W.
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- 2015
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17. A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China
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Yu, Jun, primary, Ka-Shu Wong, Gane, additional, Liu, Siqi, additional, Wang, Jian, additional, and Yang, Huanming, additional
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- 2007
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18. Recurrent Loss of Sex Is Associated with Accumulation of Deleterious Mutations in Oenothera.
- Author
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Hollister, Jesse D., Greiner, Stephan, Wei Wang, Jun Wang, Yong Zhang, Ka-Shu Wong, Gane, Wright, Stephen I., and Johnson, Marc T. J.
- Abstract
Sexual reproduction is nearly universal among eukaryotes. Theory predicts that the rarity of asexual eukaryotic species is in part caused by accumulation of deleterious mutations and heightened extinction risk associated with suppressed recombination and segregation in asexual species. We tested this prediction with a large data set of 62 transcriptomes from 29 species in the plant genus Oenothera, spanning ten independent transitions between sexual and a functionally asexual genetic system called permanent translocation heterozygosity. Illumina short-read sequencing and de novo transcript assembly yielded an average of 16.4Mb of sequence per individual. Here, we show that functionally asexual species accumulate more deleterious mutations than sexual species using both population genomic and phylogenetic analysis. At an individual level, asexual species exhibited 1.8 higher heterozygosity than sexual species. Within species, we detected a higher proportion of nonsynonymous polymorphism relative to synonymous variation within asexual compared with sexual species, indicating reduced efficacy of purifying selection. Asexual species also exhibited a greater proportion of transcripts with premature stop codons. The increased proportion of nonsynonymous mutations was also positively correlated with divergence time between sexual and asexual species, consistent with Muller's ratchet. Between species, we detected repeated increases in the ratio of nonsynonymous to synonymous divergence in asexual species compared with sexually reproducing sister taxa, indicating increased accumulation of deleterious mutations. These results confirm that an important advantage of sex is that it facilitates selection against deleterious alleles, which might help to explain the dearth of extant asexual species. [ABSTRACT FROM AUTHOR]
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- 2015
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19. Sampling SNPs
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Yang, Zhiyong, primary, Ka-Shu Wong, Gane, additional, Eberle, Michael A., additional, Kibukawa, Miho, additional, Passey, Douglas A., additional, Hughes, William R., additional, Kruglyak, Leonid, additional, and Yu, Jun, additional
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- 2000
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20. Identification and characterization of insect-specific proteins by genome data analysis.
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Guojie Zhang, Hongsheng Wang, Junjie Shi, Xiaoling Wang, Hongkun Zheng, Ka-Shu Wong, Gane, Clark, Terry, Wen Wang, Jun Wang, and Le Kang
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PROTEINS ,GENOMES ,GENETICS ,GENOMICS ,EUKARYOTIC cells ,INSECTS - Abstract
Background: Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its proteome that give rise to specialized features. However, proteome determination is an intensive undertaking. Here we present results from a computational method that uses genome analysis to characterize insect and eukaryote proteomes as an approximation complementary to experimental approaches. Results: Homologs in common to Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum, and Apis mellifera were compared to the complete genomes of three non-insect eukaryotes (opisthokonts) Homo sapiens, Caenorhabditis elegans and Saccharomyces cerevisiae. This operation yielded 154 groups of orthologous proteins in Drosophila to be insect-specific homologs; 466 groups were determined to be common to eukaryotes (represented by three opisthokonts). ESTs from the hemimetabolous insect Locust migratoria were also considered in order to approximate their corresponding genes in the insect-specific homologs. Stress and stimulus response proteins were found to constitute a higher fraction in the insect-specific homologs than in the homologs common to eukaryotes. Conclusion: The significant representation of stress response and stimulus response proteins in proteins determined to be insect-specific, along with specific cuticle and pheromone/odorant binding proteins, suggest that communication and adaptation to environments may distinguish insect evolution relative to other eukaryotes. The tendency for low Ka/Ks ratios in the insect-specific protein set suggests purifying selection pressure. The generally larger number of paralogs in the insect-specific proteins may indicate adaptation to environment changes. Instances in our insect-specific protein set have been arrived at through experiments reported in the literature, supporting the accuracy of our approach. [ABSTRACT FROM AUTHOR]
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- 2007
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21. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.
- Author
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Ka-Shu Wong, Gane, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, and Li, Guangyuan
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GENETIC polymorphisms , *GENOMES , *GENETICS , *NUCLEOTIDES , *NUCLEIC acids , *DOMESTIC animals - Abstract
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines-in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100?kilobases. [ABSTRACT FROM AUTHOR]
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- 2004
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22. Mesophyll Chloroplast Investment in C3, C4 and C2 Species of the Genus Flaveria.
- Author
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Stata M, Sage TL, Hoffmann N, Covshoff S, Ka-Shu Wong G, and Sage RF
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- Amino Acid Sequence, Biological Evolution, Carbon Cycle, Flaveria genetics, Mesophyll Cells physiology, Plant Leaves genetics, Plant Leaves physiology, Species Specificity, Chloroplasts metabolism, Flaveria physiology, Photosynthesis
- Abstract
The mesophyll (M) cells of C4 plants contain fewer chloroplasts than observed in related C3 plants; however, it is uncertain where along the evolutionary transition from C3 to C4 that the reduction in M chloroplast number occurs. Using 18 species in the genus Flaveria, which contains C3, C4 and a range of C3-C4 intermediate species, we examined changes in chloroplast number and size per M cell, and positioning of chloroplasts relative to the M cell periphery. Chloroplast number and coverage of the M cell periphery declined in proportion to increasing strength of C4 metabolism in Flaveria, while chloroplast size increased with increasing C4 cycle strength. These changes increase cytosolic exposure to the cell periphery which could enhance diffusion of inorganic carbon to phosphenolpyruvate carboxylase (PEPC), a cytosolic enzyme. Analysis of the transcriptome from juvenile leaves of nine Flaveria species showed that the transcript abundance of four genes involved in plastid biogenesis-FtsZ1, FtsZ2, DRP5B and PARC6-was negatively correlated with variation in C4 cycle strength and positively correlated with M chloroplast number per planar cell area. Chloroplast size was negatively correlated with abundance of FtsZ1, FtsZ2 and PARC6 transcripts. These results indicate that natural selection targeted the proteins of the contractile ring assembly to effect the reduction in chloroplast numbers in the M cells of C4 Flaveria species. If so, efforts to engineer the C4 pathway into C3 plants might evaluate whether inducing transcriptome changes similar to those observed in Flaveria could reduce M chloroplast numbers, and thus introduce a trait that appears essential for efficient C4 function., (© The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2016
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- View/download PDF
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