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5. Writing with integrity

Author

Bowden, John A, Green, Pamela J, Ellis, Robert A., Series Editor, Goodyear, Peter, Series Editor, Bowden, John A, and Green, Pamela J

Published
2019
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12. Playing the PhD Game with Integrity: Connecting Research, Professional Practice and Educational Context. Understanding Teaching-Learning Practice

Author

Bowden, John A., Green, Pamela J., Bowden, John A., and Green, Pamela J.

Abstract

This book focuses on integrity throughout the PhD journey and beyond, and is organised around two main themes: (1) integrity in relation to the capabilities developed by doctoral candidates for professional practice; and (2) integrity and coherence at the PhD system level. The working methods of key participants such as PhD candidates, supervisors, university managers, government agencies and politicians are central to achieving integrity goals within PhD programmes. In this context, a number of constructs are developed that inform the practice-based elements of the book in relation to conducting doctoral research, research supervision, academic writing, and research training support systems; in particular, these include our Moral Compass Framework for professional integrity, notions of collective morality, decision-making when faced with 'wicked' problems, connected moral capability and our double-helix model of capability development, negotiated sense in contrast with common sense, completion mindsets and contexts, mindfulness, liminality, and mutual catalysis in joint authorship. While the data the book employs stems from practice-led research within the Australian doctoral system, the conclusions drawn are of global relevance. Throughout the book, wherever appropriate, comparisons are made between the Australian context and other contexts, such as the doctoral systems of the United Kingdom, Europe and the United States.

Published
2019
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13. Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata)

Author

Battelle, Barbara-Anne, Ryan, Joseph F, Kempler, Karen E, Saraf, Spencer R, Marten, Catherine E, Warren, Wesley C, Minx, Patrick J, Montague, Michael J, Green, Pamela J, Schmidt, Skye A, Fulton, Lucinda, Patel, Nipam H, Protas, Meredith E, Wilson, Richard K, and Porter, Megan L

Subjects
Human Genome, Eye Disease and Disorders of Vision, Genetics, Biotechnology, Amino Acid Sequence, Animals, Evolution, Molecular, Eye, Genome, Horseshoe Crabs, Multigene Family, Opsins, Phylogeny, Limulus polyphemus, evolution, opsin, photoreceptors, xiphosuran, Biochemistry and Cell Biology, Evolutionary Biology, Developmental Biology
Abstract

Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.

Published
2016

14. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Author

Olsen, Jeanine L, Rouzé, Pierre, Verhelst, Bram, Lin, Yao-Cheng, Bayer, Till, Collen, Jonas, Dattolo, Emanuela, De Paoli, Emanuele, Dittami, Simon, Maumus, Florian, Michel, Gurvan, Kersting, Anna, Lauritano, Chiara, Lohaus, Rolf, Töpel, Mats, Tonon, Thierry, Vanneste, Kevin, Amirebrahimi, Mojgan, Brakel, Janina, Boström, Christoffer, Chovatia, Mansi, Grimwood, Jane, Jenkins, Jerry W, Jueterbock, Alexander, Mraz, Amy, Stam, Wytze T, Tice, Hope, Bornberg-Bauer, Erich, Green, Pamela J, Pearson, Gareth A, Procaccini, Gabriele, Duarte, Carlos M, Schmutz, Jeremy, Reusch, Thorsten BH, and Van de Peer, Yves

Subjects
Biological Sciences, Genetics, Human Genome, Life Below Water, Acclimatization, Adaptation, Physiological, Cell Wall, Ethylenes, Evolution, Molecular, Gene Duplication, Genes, Plant, Genome, Plant, Metabolic Networks and Pathways, Molecular Sequence Data, Oceans and Seas, Osmoregulation, Phylogeny, Plant Leaves, Plant Stomata, Pollen, Salinity, Salt Tolerance, Seawater, Seaweed, Terpenes, Zosteraceae, Salt-Tolerance, General Science & Technology
Abstract

Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.

Published
2016

16. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

Author

Schulman, Alan H., Yilmaz, Alper, Kalyanaraman, Anantharaman, Hsia, An-Ping, Oliveira, Antonio Costa de, Schnittger, Arp, Meyers, Blake C., Chalhoub, Boulos, Barbazuk, Brad, Sun, Cheng, Dardick, Christopher D., Sullivan, Christopher M., Cass, Cynthia L., Rokhsar, Dan, Garvin, David F., Laudencia-Chingcuanco, Debbie, O'Connor, Devin, Inzé, Dirk, Idziak, Dominika, Bryant, Douglas W., Chapman, Elisabeth J., Pritham, Ellen, Grotewold, Erich, Lindquist, Erika, Murat, Florent, Harmon, Frank, You, Frank M., Haberer, Georg, Tuskan, Gerald A., Lazo, Gerard R., May, Greg D., Mouille, Gregory, Wu, Haiyan, Belcram, Harry, Gundlach, Heidrun, Scheller, Henrik V., Priest, Henry D., Höfte, Herman, Budak, Hikmet, Tice, Hope, Baxter, Ivan, Tanskanen, Jaakko, Carrington, James C., Schnable, James, Thomson, James, Dvorak, Jan, Buchmann, Jan P., Grimwood, Jane, Higgins, Janet, Chang, Jeff H., Kimbrel, Jeffrey A., Bragg, Jennifer N., Schmutz, Jeremy, Pelloux, Jérome, Salse, Jerome, Harholt, Jesper, Wu, Jiajie, Ma, Jianxin, Lai, Jinsheng, Zhai, Jixian, Messing, Joachim, Rose, Jocelyn K. C., Sedbrook, John C., Vogel, John P., Wright, Jonathan, Lail, Kathleen, Barry, Kerrie, Hematy, Kian, Jung, Ki-Hong, Mayer, Klaus, Bartley, Laura E., Zhu, Liucun, Maia, Luciano da C., Tyler, Ludmila, Mueller, Lukas A., Sharma, Manoj K, Spannagl, Manuel, German, Marcelo, Heese, Maren, Byrne, Mary E., Charles, Mathieu, Ganssmann, Matthias, Wang, Mei, Febrer, Melanie, Abrouk, Michael, Bevan, Michael, Vega-Sanchez, Miguel, Luo, Ming-Cheng, Harmon-Smith, Miranda, Huo, Naxin, McKenzie, Neil, Jiang, Ning, Fahlgren, Noah, Anderson, Olin D., Green, Pamela J., Ronald, Pamela, Schnable, Patrick S., Cao, Peijian, and Ulvskov, Peter

Subjects
Brachypodium distachyon, Ehrhartoideae, Pancioideae, Pooideae, renewable energy
Abstract

Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

Published
2009

17. Detailed analysis of a contiguous 22-Mb region of the maize genome.

Author

Wei, Fusheng, Stein, Joshua C, Liang, Chengzhi, Zhang, Jianwei, Fulton, Robert S, Baucom, Regina S, De Paoli, Emanuele, Zhou, Shiguo, Yang, Lixing, Han, Yujun, Pasternak, Shiran, Narechania, Apurva, Zhang, Lifang, Yeh, Cheng-Ting, Ying, Kai, Nagel, Dawn H, Collura, Kristi, Kudrna, David, Currie, Jennifer, Lin, Jinke, Kim, Hyeran, Angelova, Angelina, Scara, Gabriel, Wissotski, Marina, Golser, Wolfgang, Courtney, Laura, Kruchowski, Scott, Graves, Tina A, Rock, Susan M, Adams, Stephanie, Fulton, Lucinda A, Fronick, Catrina, Courtney, William, Kramer, Melissa, Spiegel, Lori, Nascimento, Lydia, Kalyanaraman, Ananth, Chaparro, Cristian, Deragon, Jean-Marc, Miguel, Phillip San, Jiang, Ning, Wessler, Susan R, Green, Pamela J, Yu, Yeisoo, Schwartz, David C, Meyers, Blake C, Bennetzen, Jeffrey L, Martienssen, Robert A, McCombie, W Richard, Aluru, Srinivas, Clifton, Sandra W, Schnable, Patrick S, Ware, Doreen, Wilson, Richard K, and Wing, Rod A

Subjects
Chromosomes, Plant, Sorghum, Zea mays, DNA Transposable Elements, RNA, Plant, Physical Chromosome Mapping, Evolution, Molecular, Gene Rearrangement, Gene Duplication, Base Sequence, Base Pairing, Sequence Homology, Nucleic Acid, Synteny, Mutation, Genes, Plant, Genome, Plant, Open Reading Frames, Molecular Sequence Data, Genetic Loci, Oryza, Chromosomes, Plant, Evolution, Molecular, Genes, Genome, RNA, Sequence Homology, Nucleic Acid, Genetics, Developmental Biology
Abstract

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

Published
2009

41. Criteria for Annotation of Plant MicroRNAs

Author

Meyers, Blake C., Axtell, Michael J., Bartel, Bonnie, Bartel, David P., Baulcombe, David, Bowman, John L., Cao, Xiaofeng, Carrington, James C., Chen, Xuemei, Green, Pamela J., Griffiths-Jones, Sam, Jacobsen, Steven E., Mallory, Allison C., Martienssen, Robert A., Poethig, R. Scott, Qi, Yijun, Vaucheret, Herve, Voinnet, Olivier, Watanabe, Yuichiro, Weigel, Detlef, and Zhu, Jian-Kang

Published
2008
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