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. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Research article

    Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna

    Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal stru...

    Roman A. Volkov, Irina I. Panchuk, Nikolai V. Borisjuk, Marta Hosiawa-Baranska, Jolanta Maluszynska and Vera Hemleben

    BMC Plant Biology 2017 17:21

    Published on: 23 January 2017

  8. Research article

    Comparative analysis of the root transcriptomes of cultivated sweetpotato (Ipomoea batatas [L.] Lam) and its wild ancestor (Ipomoea trifida [Kunth] G. Don)

    The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (

    Sathish K. Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu (Kal) Kalavacharla and Muthusamy Manoharan

    BMC Plant Biology 2017 17:9

    Published on: 13 January 2017

  9. Research article

    Polyploidy and the relationship between leaf structure and function: implications for correlated evolution of anatomy, morphology, and physiology in Brassica

    Polyploidy is well studied from a genetic and genomic perspective, but the morphological, anatomical, and physiological consequences of polyploidy remain relatively uncharacterized. Whether these potential cha...

    Robert L. Baker, Yulia Yarkhunova, Katherine Vidal, Brent E. Ewers and Cynthia Weinig

    BMC Plant Biology 2017 17:3

    Published on: 5 January 2017

  10. Research article

    Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?

    Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these r...

    Oz Barazani, Alexandra Keren-Keiserman, Erik Westberg, Nir Hanin, Arnon Dag, Giora Ben-Ari, Ori Fragman-Sapir, Yizhar Tugendhaft, Zohar Kerem and Joachim W. Kadereit

    BMC Plant Biology 2016 16:261

    Published on: 13 December 2016

  11. Research article

    Characterization of the cytokinin-responsive transcriptome in rice

    Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies o...

    Tracy Raines, Ivory C. Blakley, Yu-Chang Tsai, Jennifer M. Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G. Eric Schaller, Ann E. Loraine and Joseph J. Kieber

    BMC Plant Biology 2016 16:260

    Published on: 8 December 2016

  12. Research article

    Analysis of transcriptional response to heat stress in Rhazya stricta

    Climate change is predicted to be a serious threat to agriculture due to the need for crops to be able to tolerate increased heat stress. Desert plants have already adapted to high levels of heat stress so the...

    Abdullah Y. Obaid, Jamal S. M. Sabir, Ahmed Atef, Xuan Liu, Sherif Edris, Fotouh M. El-Domyati, Mohammed Z. Mutwakil, Nour O. Gadalla, Nahid H. Hajrah, Magdy A. Al-Kordy, Neil Hall, Ahmed Bahieldin and Robert K. Jansen

    BMC Plant Biology 2016 16:252

    Published on: 14 November 2016

  13. Research article

    Range-wide phenotypic and genetic differentiation in wild sunflower

    Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of gro...

    Edward V. McAssey, Jonathan Corbi and John M. Burke

    BMC Plant Biology 2016 16:249

    Published on: 10 November 2016

  14. Research article

    Comparative transcriptome sequencing and de novo analysis of Vaccinium corymbosum during fruit and color development

    Blueberry is an economically important fruit crop in Ericaceae family. The substantial quantities of flavonoids in blueberry have been implicated in a broad range of health benefits. However, the information r...

    Lingli Li, Hehua Zhang, Zhongshuai Liu, Xiaoyue Cui, Tong Zhang, Yanfang Li and Lingyun Zhang

    BMC Plant Biology 2016 16:223

    Published on: 12 October 2016

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