American Journal of Botany - 99 (2), 2012

Contents:


        Ashley N. Egan, Jessica Schlueter, and David M. Spooner
    Applications of next-generation sequencing in plant biology
    
        Sarwar Azam, Vivek Thakur, Pradeep Ruperao, Trushar Shah, Jayashree Balaji, BhanuPrakash Amindala, Andrew D. Farmer, David J. Studholme, Gregory D. May, David Edwards, Jonathan D. G. Jones, and Rajeev K. Varshney
    Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
    
        Juan E. Zalapa, Hugo Cuevas, Huayu Zhu, Shawn Steffan, Douglas Senalik, Eric Zeldin, Brent McCown, Rebecca Harbut, and Philipp Simon
    Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
   
        Zhao Lai, Nolan C. Kane, Alex Kozik, Kathryn A. Hodgins, Katrina M. Dlugosch, Michael S. Barker, Marta Matvienko, Qian Yu, Kathryn G. Turner, Stephanie Anne Pearl, Graeme D. M. Bell, Yi Zou, Chris Grassa, Alessia Guggisberg, Keith L. Adams, James V. Anderson, David P. Horvath, Richard V. Kesseli, John M. Burke, Richard W. Michelmore, and Loren H. Rieseberg
    Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression
   
        Alyssa A. Gulledge, April D. Roberts, Hiral Vora, Ketan Patel, and Ann E. Loraine
    Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a
   
        Ruifeng He, Min-Jeong Kim, William Nelson, Tiago S. Balbuena, Ryan Kim, Robin Kramer, John A. Crow, Greg D. May, Jay J. Thelen, Carol A. Soderlund, and David R. Gang
    Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity
    
        Vanessa M. Kvam, Peng Liu, and Yaqing Si
    A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data
   
        Susan R. Strickler, Aureliano Bombarely, and Lukas A. Mueller
    Designing a transcriptome next-generation sequencing project for a nonmodel plant species1
  
        Judson A. Ward, Lalit Ponnala, and Courtney A. Weber
    Strategies for transcriptome analysis in nonmodel plants
    
        Levi Yant
    Genome-wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics
    
        Richard Cronn, Brian J. Knaus, Aaron Liston, Peter J. Maughan, Matthew Parks, John V. Syring, and Joshua Udall
    Targeted enrichment strategies for next-generation plant biology
   
        Corrinne E. Grover, Armel Salmon, and Jonathan F. Wendel
    Targeted sequence capture as a powerful tool for evolutionary analysis1
   
        Nolan Kane, Saemundur Sveinsson, Hannes Dempewolf, Ji Yong Yang, Dapeng Zhang, Johannes M. M. Engels, and Quentin Cronk
    Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA
   
        P. Roxanne Steele, Kate L. Hertweck, Dustin Mayfield, Michael R. McKain, James Leebens-Mack, and J. Chris Pires
    Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae
    
        Shannon C. K. Straub, Matthew Parks, Kevin Weitemier, Mark Fishbein, Richard C. Cronn, and Aaron Liston
    Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics
    
        Paul J. Berkman, Kaitao Lai, Michał T. Lorenc, and David Edwards
    Next-generation sequencing applications for wheat crop improvement
   
        Richard J. A. Buggs, Simon Renny-Byfield, Michael Chester, Ingrid E. Jordon-Thaden, Lyderson Facio Viccini, Srikar Chamala, Andrew R. Leitch, Patrick S. Schnable, W. Bradley Barbazuk, Pamela S. Soltis, and Douglas E. Soltis
    Next-generation sequencing and genome evolution in allopolyploids
   
        Daniel C. Ilut, Jeremy E. Coate, Amelia K. Luciano, Thomas G. Owens, Gregory D. May, Andrew Farmer, and Jeff J. Doyle
    A comparative transcriptomic study of an allotetraploid(s) and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species
  
        Michael R. McKain, Norman Wickett, Yeting Zhang, Saravanaraj Ayyampalayam, W. Richard McCombie, Mark W. Chase, J. Chris Pires, Claude W. dePamphilis, and Jim Leebens-Mack
    Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)
 
        Susan R. McCouch, Kenneth L. McNally, Wen Wang, and Ruaraidh Sackville Hamilton
    Genomics of gene banks: A case study in rice
   
        Na Yuan, Yi Sun, Koh Nakamura, and Ying-Xiong Qiu
    Development of microsatellite markers in heterostylous Hedyotis chrysotricha (Rubiaceae)
    
        Qing-Zhang Du, De-Qiang Zhang, and Bai-Lian Li
    Development of 15 novel microsatellite markers from cellulose synthase genes in Populus tomentosa (Salicaceae)
   
        Cécile Godé, Isabelle Decombeix, Alicja Kostecka, Pawel Wasowicz, Maxime Pauwels, Adeline Courseaux, and Pierre Saumitou-Laprade
    Nuclear microsatellite loci for Arabidopsis halleri (Brassicaceae), a model species to study plant adaptation to heavy metals
    
        Stefan G. Michalski and Walter Durka
    Identification and characterization of microsatellite loci in the rush Juncus effusus (Juncaceae)1
    
        Ari Novy, S. Luke Flory, Joshua A. Honig, Stacy Bonos, and Jean Marie Hartman
    Characterization of polymorphic microsatellites for the invasive grass Microstegium vimineum (Poaceae)
   
        Qiusheng Kong, Guangping Zhang, Wenchao Chen, Zhuqing Zhang, and Xuexiao Zou
    Identification and development of polymorphic EST-SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae)
    
        Yang Liu, Nicholas L. Moskwa, and Bernard Goffinet
    Development of eight mitochondrial markers for Funariaceae (Musci) and their amplification success in other mosses
    
        M. Cristina López-Roberts, Paulo R. M. Almeida, Eddy J. F. Oliveira, and Cássio van den Berg
    Microsatellite marker development for the threatened orchid Masdevallia solomonii (Orchidaceae)
   
        Bin Wu, Zongwen Zhang, Lingyun Chen, and Minggao He
    Isolation and characterization of novel microsatellite markers for Avena sativa (Poaceae) (oat)
  
        Thannya Nascimento Soares, Dayane Borges Melo, Lucileide Vilela Resende, Rosana Pereira Vianello, Lázaro José Chaves, Rosane Garcia Collevatti, and Mariana Pires de Campos Telles
    Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae)
   
        Karol Krak, Inés Álvarez, Petra Caklová, Andrea Costa, Jindrich Chrtek, and Judith Fehrer
    Development of novel low-copy nuclear markers for Hieraciinae (Asteraceae) and their perspective for other tribes
   
        Zuozhou Li, Chuanhua Wang, Yanhong Liu, and Junqing Li
    Microsatellite primers in the Chinese dove tree, Davidia involucrata (Cornaceae), a relic species of the Tertiary
    
        Vinita Gowda, David L. Erickson, and W. John Kress
    Development and characterization of microsatellite loci for two Caribbean Heliconia (Heliconiaceae: H. bihai and H. caribaea)
   
        Kyoko Sugai, Suzuki Setsuko, Kentaro Uchiyama, Noriaki Murakami, Hidetoshi Kato, and Hiroshi Yoshimaru
    Development of EST-SSR markers for Elaeocarpus photiniifolia (Elaeocarpaceae), an endemic taxon of the Bonin Islands
  
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