Genomics and evolution

Section edited by Z Jeffrey Chen

This section considers studies in the evolution of plants as well as comparative genomics in relation to plant biology.

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  1. Research article

    Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

    RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosi...

    Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino and Serena Varotto

    BMC Plant Biology 2017 17:161

    Published on: 12 October 2017

  2. Research article

    Four terpene synthases contribute to the generation of chemotypes in tea tree (Melaleuca alternifolia)

    Terpene rich leaves are a characteristic of Myrtaceae. There is significant qualitative variation in the terpene profile of plants within a single species, which is observable as “chemotypes”. Understanding th...

    Amanda Padovan, Andras Keszei, Yasmin Hassan, Sandra T. Krause, Tobias G. Köllner, Jörg Degenhardt, Jonathan Gershenzon, Carsten Külheim and William J. Foley

    BMC Plant Biology 2017 17:160

    Published on: 4 October 2017

  3. Research article

    B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.)

    The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, t...

    Yunpeng Cao, Yahui Han, Dandan Meng, Dahui Li, Chunyan Jiao, Qing Jin, Yi Lin and Yongping Cai

    BMC Plant Biology 2017 17:156

    Published on: 19 September 2017

  4. Research article

    Identification of a methyltransferase catalyzing the final step of methyl anthranilate synthesis in cultivated strawberry

    Methyl anthranilate (MA) contributes an attractive fruity note to the complex flavor and aroma of strawberry (Fragaria spp.), yet it is rare in modern cultivars. The genetic basis for its biosynthesis has not bee...

    Jeremy Pillet, Alan H. Chambers, Christopher Barbey, Zhilong Bao, Anne Plotto, Jinhe Bai, Michael Schwieterman, Timothy Johnson, Benjamin Harrison, Vance M. Whitaker, Thomas A. Colquhoun and Kevin M. Folta

    BMC Plant Biology 2017 17:147

    Published on: 31 August 2017

  5. Research article

    The core regulatory network of the abscisic acid pathway in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress

    Abscisic acid (ABA) signaling plays a crucial role in developmental and environmental adaptation processes of plants. However, the PYL-PP2C-SnRK2 families that function as the core components of ABA signaling ...

    Wei Hu, Yan Yan, Haitao Shi, Juhua Liu, Hongxia Miao, Weiwei Tie, Zehong Ding, XuPo Ding, Chunlai Wu, Yang Liu, Jiashui Wang, Biyu Xu and Zhiqiang Jin

    BMC Plant Biology 2017 17:145

    Published on: 29 August 2017

  6. Research article

    Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis)

    Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation...

    Shu-Fen Li, Guo-Jun Zhang, Xue-Jin Zhang, Jin-Hong Yuan, Chuan-Liang Deng and Wu-Jun Gao

    BMC Plant Biology 2017 17:143

    Published on: 22 August 2017

  7. Research article

    Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton

    Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, t...

    Yanpeng Li, Tiegang Yang, Dandan Dai, Ying Hu, Xiaoyang Guo and Hongxia Guo

    BMC Plant Biology 2017 17:119

    Published on: 10 July 2017

  8. Research article

    Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses

    WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published co...

    Zhaoen Yang, Qian Gong, Wenqiang Qin, Zuoren Yang, Yuan Cheng, Lili Lu, Xiaoyang Ge, Chaojun Zhang, Zhixia Wu and Fuguang Li

    BMC Plant Biology 2017 17:113

    Published on: 6 July 2017

  9. Research article

    Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F1 hybrids

    Genomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we us...

    Biyue Tan, Dario Grattapaglia, Gustavo Salgado Martins, Karina Zamprogno Ferreira, Björn Sundberg and Pär K. Ingvarsson

    BMC Plant Biology 2017 17:110

    Published on: 29 June 2017

  10. Database

    CottonFGD: an integrated functional genomics database for cotton

    Cotton (Gossypium spp.) is the most important fiber and oil crop in the world. With the emergence of huge -omics data sets, it is essential to have an integrated functional genomics database that allows worldwide...

    Tao Zhu, Chengzhen Liang, Zhigang Meng, Guoqing Sun, Zhaoghong Meng, Sandui Guo and Rui Zhang

    BMC Plant Biology 2017 17:101

    Published on: 8 June 2017

  11. Research article

    Comparative transcriptome profiling and morphology provide insights into endocarp cleaving of apricot cultivar (Prunus armeniaca L.)

    A complete and hardened endocarp is a typical trait of drupe fruits. However, the ‘Liehe’ (LE) apricot cultivar has a thin, soft, cleavable endocarp that represents 60.39% and 63.76% of the thickness and ligni...

    Xiao Zhang, Lijie Zhang, Qiuping Zhang, Jiayu Xu, Weisheng Liu and Wenxuan Dong

    BMC Plant Biology 2017 17:72

    Published on: 11 April 2017

  12. Research article

    Unraveling the complexity of transcriptomic, metabolomic and quality environmental response of tomato fruit

    The environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sens...

    Daniela D’Esposito, Francesca Ferriello, Alessandra Dal Molin, Gianfranco Diretto, Adriana Sacco, Andrea Minio, Amalia Barone, Rossella Di Monaco, Silvana Cavella, Luca Tardella, Giovanni Giuliano, Massimo Delledonne, Luigi Frusciante and Maria Raffaella Ercolano

    BMC Plant Biology 2017 17:66

    Published on: 28 March 2017

  13. Research article

    Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change

    Long non-coding RNA (lncRNA) is a class of non-coding RNA with important regulatory roles in biological process of organisms. The systematic comparison of lncRNAs with protein coding mRNAs in population expres...

    Qin Xu, Zhihong Song, Caiyun Zhu, Chengcheng Tao, Lifang Kang, Wei Liu, Fei He, Juan Yan and Tao Sang

    BMC Plant Biology 2017 17:42

    Published on: 13 February 2017

  14. Research article

    Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives

    Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two w...

    Yingxiao Zhang, Brian J. Iaffaldano, Xiaofeng Zhuang, John Cardina and Katrina Cornish

    BMC Plant Biology 2017 17:34

    Published on: 2 February 2017

  15. Research article

    Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s

    microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, wh...

    Xuyan Li, Xin Xie, Ji Li, Yuhai Cui, Yanming Hou, Lulu Zhai, Xiao Wang, Yanli Fu, Ranran Liu and Shaomin Bian

    BMC Plant Biology 2017 17:32

    Published on: 1 February 2017

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