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Genomics and evolution

Section edited by David Alvarez-Ponce and Z Jeffrey Chen 

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

Page 3 of 7

  1. The mountainous region between the Caucasus and China is considered to be the center of domestication for grapevine. Despite the importance of Central Asia in the history of grape growing, information about th...

    Authors: Summaira Riaz, Gabriella De Lorenzis, Dianne Velasco, Anne Koehmstedt, David Maghradze, Zviad Bobokashvili, Mirza Musayev, Goran Zdunic, Valerie Laucou, M. Andrew Walker, Osvaldo Failla, John E. Preece, Mallikarjuna Aradhya and Rosa Arroyo-Garcia

    Citation: BMC Plant Biology 2018 18:137

    Content type: Research article

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  2. Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to t...

    Authors: Niels Aerts, Suzanne de Bruijn, Hilda van Mourik, Gerco C. Angenent and Aalt D. J. van Dijk

    Citation: BMC Plant Biology 2018 18:131

    Content type: Research article

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  3. Moso bamboo (Phyllostachys edulis) is a well-known bamboo species of high economic value in the textile industry due to its rapid growth. Phytohormones, which are master regulators of growth and development, serv...

    Authors: Hangxiao Zhang, Huihui Wang, Qiang Zhu, Yubang Gao, Huiyuan Wang, Liangzhen Zhao, Yongsheng Wang, Feihu Xi, Wenfei Wang, Yanqiu Yang, Chentao Lin and Lianfeng Gu

    Citation: BMC Plant Biology 2018 18:125

    Content type: Research article

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  4. Rab proteins form the largest family of the Ras superfamily of small GTP-binding proteins and regulate intracellular trafficking pathways. However, the function of the Rab proteins in woody species is still an...

    Authors: Jin Zhang, Yu Li, Bobin Liu, Lijuan Wang, Li Zhang, Jianjun Hu, Jun Chen, Huanquan Zheng and Mengzhu Lu

    Citation: BMC Plant Biology 2018 18:124

    Content type: Research article

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  5. Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative frac...

    Authors: Peng Qi, Davis Gimode, Dipnarayan Saha, Stephan Schröder, Debkanta Chakraborty, Xuewen Wang, Mathews M. Dida, Russell L. Malmberg and Katrien M. Devos

    Citation: BMC Plant Biology 2018 18:117

    Content type: Methodology

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  6. It is known that hexaploid common wheat (Triticum aestivum L.) has stronger adaptability to many stressful environments than its tetraploid wheat progenitor. However, the physiological basis and evolutionary cour...

    Authors: Chunwu Yang, Zongze Yang, Long Zhao, Fasheng Sun and Bao Liu

    Citation: BMC Plant Biology 2018 18:113

    Content type: Research article

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  7. Red algae are economically valuable for food and in industry. However, their genomic information is limited, and the genomic data of only a few species of red algae have been sequenced and deposited recently. In ...

    Authors: Xue Sun, Jun Wu, Guangce Wang, Yani Kang, Hong Sain Ooi, Tingting Shen, Fangjun Wang, Rui Yang, Nianjun Xu and Xiaodong Zhao

    Citation: BMC Plant Biology 2018 18:94

    Content type: Research article

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  8. Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited.

    Authors: Nannan Liu, Jianxiao Liu, Wenqiang Li, Qingchun Pan, Jie Liu, Xiaohong Yang, Jianbing Yan and Yingjie Xiao

    Citation: BMC Plant Biology 2018 18:66

    Content type: Research article

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  9. Pearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production ...

    Authors: Anna Pucher, C. Tom Hash, Jason G. Wallace, Sen Han, Willmar L. Leiser and Bettina I. G. Haussmann

    Citation: BMC Plant Biology 2018 18:65

    Content type: Research article

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  10. The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on h...

    Authors: Murukarthick Jayakodi, Beom-Soon Choi, Sang-Choon Lee, Nam-Hoon Kim, Jee Young Park, Woojong Jang, Meiyappan Lakshmanan, Shobhana V. G. Mohan, Dong-Yup Lee and Tae-Jin Yang

    Citation: BMC Plant Biology 2018 18:62

    Content type: Database

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  11. The ice alga Chlamydomonas sp. ICE-L is the main contributor to primary productivity in Antarctic sea ice ecosystems and is well adapted to the extremely harsh environment. However, the adaptive mechanism of Chla...

    Authors: Zhenhua Zhang, Meiling An, Jinlai Miao, Zhiqiang Gu, Chang Liu and Bojian Zhong

    Citation: BMC Plant Biology 2018 18:53

    Content type: Research article

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  12. In plants, ERF genes participate in a variety of regulatory pathways, such as plant growth and biotic and/or abiotic stress responses. Although the genome of Chinese white pear (‘Dangshansuli’) has been released,...

    Authors: Xiaolong Li, Shutian Tao, Shuwei Wei, Meiling Ming, Xiaosan Huang, Shaoling Zhang and Jun Wu

    Citation: BMC Plant Biology 2018 18:46

    Content type: Research article

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  13. The hydroxyproline-rich glycoprotein (HRGP) superfamily, comprising three families (arabinogalactan-proteins, AGPs; extensins, EXTs; proline-rich proteins, PRPs), is a class of proline-rich proteins that exhib...

    Authors: Huijun Jiao, Xing Liu, Shuguang Sun, Peng Wang, Xin Qiao, Jiaming Li, Chao Tang, Juyou Wu, Shaoling Zhang and Shutian Tao

    Citation: BMC Plant Biology 2018 18:36

    Content type: Research article

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  14. The chloroplast genomes (plastome) of most plants are highly conserved in structure, gene content, and gene order. Parasitic plants, including those that are fully photosynthetic, often contain plastome rearra...

    Authors: Daniel C. Frailey, Srinivasa R. Chaluvadi, Justin N. Vaughn, Caroline G. Coatney and Jeffrey L. Bennetzen

    Citation: BMC Plant Biology 2018 18:30

    Content type: Research article

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  15. Common wheat is a typical allohexaploid species (AABBDD) derived from the interspecific crossing between allotetraploid wheat (AABB) and Aegilops tauschii (DD). Wide variation in grain size and shape observed amo...

    Authors: Lei Yan, Zhenshan Liu, Huanwen Xu, Xiaoping Zhang, Aiju Zhao, Fei Liang, Mingming Xin, Huiru Peng, Yingyin Yao, Qixin Sun and Zhongfu Ni

    Citation: BMC Plant Biology 2018 18:28

    Content type: Research article

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  16. There is an urgent need to increase global crop production. Identifying and combining specific genes controlling distinct biological processes holds the potential to enhance crop yields. Transcriptomics is a p...

    Authors: Jemima Brinton, James Simmonds and Cristobal Uauy

    Citation: BMC Plant Biology 2018 18:22

    Content type: Research article

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  17. Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-...

    Authors: Animesh Acharjee, Pierre-Yves Chibon, Bjorn Kloosterman, Twan America, Jenny Renaut, Chris Maliepaard and Richard G. F. Visser

    Citation: BMC Plant Biology 2018 18:20

    Content type: Research article

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  18. Long terminal repeat (LTR) retrotransposons are highly abundant in plant genomes and require transcriptional activity for their proliferative mode of replication. These sequences exist in plant genomes as dive...

    Authors: Fan Qiu and Mark C. Ungerer

    Citation: BMC Plant Biology 2018 18:6

    Content type: Research article

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  19. Alternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tiss...

    Authors: Ying Sun, Han Hou, Hongtao Song, Kui Lin, Zhonghua Zhang, Jinglu Hu and Erli Pang

    Citation: BMC Plant Biology 2018 18:5

    Content type: Research article

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  20. MicroRNAs act as molecular regulator of cell signaling, plant growth and development, and regulate various primary and secondary plant metabolic processes. In the present study, deep sequencing of small RNAs w...

    Authors: Monika Kajal and Kashmir Singh

    Citation: BMC Plant Biology 2017 17:265

    Content type: Research article

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  21. Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their ex...

    Authors: Peng-Fei Ma, Maria S. Vorontsova, Olinirina Prisca Nanjarisoa, Jacqueline Razanatsoa, Zhen-Hua Guo, Thomas Haevermans and De-Zhu Li

    Citation: BMC Plant Biology 2017 17:260

    Content type: Research article

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  22. Microtubules, polymerized from alpha and beta-tubulin monomers, play a fundamental role in plant morphogenesis, determining the cell division plane, the direction of cell expansion and the deposition of cell w...

    Authors: Floriana Gavazzi, Gaia Pigna, Luca Braglia, Silvia Gianì, Diego Breviario and Laura Morello

    Citation: BMC Plant Biology 2017 17:237

    Content type: Research article

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  23. Subtribe Orchidinae (Orchidaceae, Orchidoideae) are a nearly cosmopolitan taxon of terrestrial orchids, comprising about 1800 species in 47 to 60 genera. Although much progress has been made in recent years of...

    Authors: Wei-Tao Jin, André Schuiteman, Mark W. Chase, Jian-Wu Li, Shih-Wen Chung, Tian-Chuan Hsu and Xiao-Hua Jin

    Citation: BMC Plant Biology 2017 17:222

    Content type: Research article

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  24. Elytrigia Desv. is a genus with a varied array of morphology, cytology, ecology, and distribution in Triticeae. Classification and systematic position of Elytrigia remain controversial...

    Authors: Yan Yang, Xing Fan, Long Wang, Hai-Qin Zhang, Li-Na Sha, Yi Wang, Hou-Yang Kang, Jian Zeng, Xiao-Fang Yu and Yong-Hong Zhou

    Citation: BMC Plant Biology 2017 17:207

    Content type: Research

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  25. While floral symmetry has traditionally been assessed qualitatively, recent advances in geometric morphometrics have opened up new avenues to specifically quantify flower shape and size using robust multivaria...

    Authors: Brent A. Berger, Vincent A. Ricigliano, Yoland Savriama, Aedric Lim, Veronica Thompson and Dianella G. Howarth

    Citation: BMC Plant Biology 2017 17:205

    Content type: Research article

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  26. Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identif...

    Authors: Haitao Li, Bo Wang, Qinghua Zhang, Jing Wang, Graham J. King and Kede Liu

    Citation: BMC Plant Biology 2017 17:204

    Content type: Research article

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  27. Pennycress [Thlaspi arvense L (Brassicaceae)] is being domesticated as a renewable biodiesel feedstock that also provides crucial ecosystems services, including as a nutritional resource for pollinators. However,...

    Authors: Jason B. Thomas, Marshall E. Hampton, Kevin M. Dorn, M. David Marks and Clay J. Carter

    Citation: BMC Plant Biology 2017 17:201

    Content type: Research article

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  28. Hemicelluloses are a diverse group of complex, non-cellulosic polysaccharides, which constitute approximately one-third of the plant cell wall and find use as dietary fibres, food additives and raw materials f...

    Authors: Simerjeet Kaur, Kanwarpal S. Dhugga, Robin Beech and Jaswinder Singh

    Citation: BMC Plant Biology 2017 17:193

    Content type: Research article

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  29. Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make ...

    Authors: Katherine Domb, Danielle Keidar, Beery Yaakov, Vadim Khasdan and Khalil Kashkush

    Citation: BMC Plant Biology 2017 17:175

    Content type: Research article

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  30. 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...

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

    Citation: BMC Plant Biology 2017 17:161

    Content type: Research article

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  31. 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...

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

    Citation: BMC Plant Biology 2017 17:160

    Content type: Research article

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  32. 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...

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

    Citation: BMC Plant Biology 2017 17:156

    Content type: Research article

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  33. 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...

    Authors: 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

    Citation: BMC Plant Biology 2017 17:147

    Content type: Research article

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  34. 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 ...

    Authors: 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

    Citation: BMC Plant Biology 2017 17:145

    Content type: Research article

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  35. 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...

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

    Citation: BMC Plant Biology 2017 17:143

    Content type: Research article

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  36. The mechanism of winter survival for perennials involves multiple levels of gene regulation, especially cold resistance. Agropyron mongolicum is one important perennial grass species, but there is little informat...

    Authors: Jiancai Du, Xiaoquan Li, Tingting Li, Dongyang Yu and Bing Han

    Citation: BMC Plant Biology 2017 17:138

    Content type: Research article

    Published on:

  37. The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a com...

    Authors: Shisong Ma, Zehong Ding and Pinghua Li

    Citation: BMC Plant Biology 2017 17:131

    Content type: Research article

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  38. 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...

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

    Citation: BMC Plant Biology 2017 17:119

    Content type: Research article

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  39. 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...

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

    Citation: BMC Plant Biology 2017 17:113

    Content type: Research article

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  40. 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...

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

    Citation: BMC Plant Biology 2017 17:110

    Content type: Research article

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  41. Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and...

    Authors: Liming Wang, Yuexia Zheng, Shihui Ding, Qing Zhang, Youqiang Chen and Jisen Zhang

    Citation: BMC Plant Biology 2017 17:109

    Content type: Research article

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  42. 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...

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

    Citation: BMC Plant Biology 2017 17:101

    Content type: Database

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  43. 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...

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

    Citation: BMC Plant Biology 2017 17:72

    Content type: Research article

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  44. 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...

    Authors: 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

    Citation: BMC Plant Biology 2017 17:66

    Content type: Research article

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  45. 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...

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

    Citation: BMC Plant Biology 2017 17:42

    Content type: Research article

    Published on:

  46. Ca2+ ion is a versatile second messenger that operate in a wide ranges of cellular processes that impact nearly every aspect of life. Ca2+ regulates gene expression and biotic and abiotic stress responses in orga...

    Authors: Tapan Kumar Mohanta, Pradeep Kumar and Hanhong Bae

    Citation: BMC Plant Biology 2017 17:38

    Content type: Research article

    Published on:

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