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Genomics and evolution

Section edited by Z Jeffrey Chen and Jim Leebens-Mack

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

Page 1 of 6

  1. Content type: Research article

    Great advances have been achieved in our understanding of flower development and evolution since the establishment of the ABC model. However, it remains a challenge to define the exact context of organ identit...

    Authors: Jing Liu, Chao-Qun Li, Yang Dong, Xia Yang and Yin-Zheng Wang

    Citation: BMC Plant Biology 2018 18:341

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  2. Content type: Research article

    The auxin response factor (ARF) gene family is involved in plant development and hormone regulation. Although the ARF gene family has been studied in some plant species, its structural features, molecular evoluti...

    Authors: Nannan Liu, Liwei Dong, Xiong Deng, Dongmiao Liu, Yue Liu, Mengfei Li, Yingkao Hu and Yueming Yan

    Citation: BMC Plant Biology 2018 18:336

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  3. Content type: Research article

    Soybean is a paleopolyploid that has undergone two whole genome duplication events. Gene duplication is a type of genomic change that can lead to novel functions of pre-existing genes. Chalcone synthase (CHS) ...

    Authors: Arun Kumaran Anguraj Vadivel, Kevin Krysiak, Gang Tian and Sangeeta Dhaubhadel

    Citation: BMC Plant Biology 2018 18:325

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  4. Content type: Research article

    Comparative analyses of chloroplast and mitochondrial genomes have shown that organelle genomes in bryophytes evolve slowly. However, in contrast to seed plants, the organellar genomes are yet poorly explored ...

    Authors: Kamil Myszczyński, Piotr Górski, Monika Ślipiko and Jakub Sawicki

    Citation: BMC Plant Biology 2018 18:321

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  5. Content type: Research article

    Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion...

    Authors: Susanne Gramlich, Natascha Dorothea Wagner and Elvira Hörandl

    Citation: BMC Plant Biology 2018 18:317

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  6. Content type: Research article

    Fruits of persimmon plants are traditional healthy food in China, Korea and Japan. However, due to the shortage of morphological and DNA markers, the development of persimmon industry has been heavily inhibited.

    Authors: Wenqing Li, Yanlei Liu, Yong Yang, Xiaoman Xie, Yizeng Lu, Zhirong Yang, Xiaobai Jin, Wenpan Dong and Zhili Suo

    Citation: BMC Plant Biology 2018 18:210

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  7. Content type: Database

    The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-...

    Authors: Andrew J. Robinson, Muluneh Tamiru, Rachel Salby, Clayton Bolitho, Andrew Williams, Simon Huggard, Eva Fisch, Kathryn Unsworth, James Whelan and Mathew G. Lewsey

    Citation: BMC Plant Biology 2018 18:200

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  8. Content type: Research article

    Crassulacean acid metabolism (CAM) plants use water 20–80% more efficiently by shifting stomata opening and primary CO2 uptake and fixation to the nighttime. Protein kinases (PKs) play pivotal roles in this biolo...

    Authors: Kaikai Zhu, Hui Liu, Xinlu Chen, Qunkang Cheng and Zong-Ming (Max) Cheng

    Citation: BMC Plant Biology 2018 18:199

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  9. Content type: Research article

    Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crys...

    Authors: Chih-Kai Yang, Bing-Hong Huang, Shao-Wei Ho, Meng-Yuan Huang, Jenn-Che Wang, Jian Gao and Pei-Chun Liao

    Citation: BMC Plant Biology 2018 18:196

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  10. Content type: Research article

    Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With th...

    Authors: Wei Wu, Wei-Lun Ng, Jun-Xin Yang, Wei-Ming Li and Xue-Jun Ge

    Citation: BMC Plant Biology 2018 18:194

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  11. Content type: Research article

    As one of the largest subfamilies of the receptor-like protein kinases (RLKs) in plants, Leucine Rich Repeats-RLKs (LRR-RLKs) are involved in many critical biological processes including growth, development an...

    Authors: Ning Yuan, Krishan Mohan Rai, Vimal Kumar Balasubramanian, Santosh Kumar Upadhyay, Hong Luo and Venugopal Mendu

    Citation: BMC Plant Biology 2018 18:185

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  12. Content type: Research article

    Sweetpotato (Ipomoea batatas (L.) Lam.) is one of the most important crops from the family of Convolvulaceae. It is widely reported that cultivated sweetpotato was originated from Ipomoea trifida. However, diploi...

    Authors: J. Y. Feng, M. Li, S. Zhao, C. Zhang, S. T. Yang, S. Qiao, W. F. Tan, H. J. Qu, D. Y. Wang and Z. G. Pu

    Citation: BMC Plant Biology 2018 18:181

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  13. Content type: Research article

    Nectar gain and loss are important flower transitions observed in angiosperms, and are particularly common in orchids. To understand such transitions, the availability of detailed anatomical data and species-l...

    Authors: Poliana Cardoso-Gustavson, Mariana Naomi Saka, Edlley Max Pessoa, Clarisse Palma-Silva and Fabio Pinheiro

    Citation: BMC Plant Biology 2018 18:179

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  14. Content type: Research article

    MADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development. Bamboo is an important non-timber forest product worldwide, but previous studies on th...

    Authors: Yuting Zhang, Dingqin Tang, Xinchun Lin, Mingquan Ding and Zaikang Tong

    Citation: BMC Plant Biology 2018 18:176

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  15. Content type: Research article

    Histone methylation and acetylation regulate biological processes in plants through various histone modifications (HMs) gene families. However, knowledge of HMs genes is limited in horticultural deciduous trees, ...

    Authors: Sheng Fan, Jue Wang, Chao Lei, Cai Gao, Yang Yang, Youmei Li, Na An, Dong Zhang and Mingyu Han

    Citation: BMC Plant Biology 2018 18:173

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  16. Content type: Research article

    Wood basic density (WBD), the biomass of plant cell walls per unit volume, is an important trait for elite tree selection in kraft pulp production. Here, we investigated the correlation between WBD and wood vo...

    Authors: Katsuhiko Nakahama, Nobuaki Urata, Tomotaka Shinya, Kazunori Hayashi, Kazuya Nanto, Antonio C. Rosa and Akiyoshi Kawaoka

    Citation: BMC Plant Biology 2018 18:156

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  17. Content type: Research article

    The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation S...

    Authors: Sean V. Burke, Mark C. Ungerer and Melvin R. Duvall

    Citation: BMC Plant Biology 2018 18:152

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  18. Content type: Research article

    Switchgrass breeders need to improve the rates of genetic gain in many bioenergy-related traits in order to create improved cultivars that are higher yielding and have optimal biomass composition. One way to a...

    Authors: Jason D. Fiedler, Christina Lanzatella, Serge J. Edmé, Nathan A. Palmer, Gautam Sarath, Rob Mitchell and Christian M. Tobias

    Citation: BMC Plant Biology 2018 18:142

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Methodology

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Database

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Research article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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  36. Content type: Research article

    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

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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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  39. Content type: Research article

    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

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  40. Content type: Research article

    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

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  41. Content type: Research article

    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

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  42. Content type: Research

    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

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  43. Content type: Research article

    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

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  44. Content type: Research article

    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

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