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Plant genomics

Section edited by David Lightfoot and Keiichi Mochida

This section covers all aspects of the genome structure and function of plants, including crop species.

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  1. Content type: Research article

    Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to asse...

    Authors: Gina L. Conte, Kathryn A. Hodgins, Sam Yeaman, Jon C. Degner, Sally N. Aitken, Loren H. Rieseberg and Michael C. Whitlock

    Citation: BMC Genomics 2017 18:970

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  2. Content type: Research article

    Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morpholo...

    Authors: Naimat Ullah, Meral Yüce, Z. Neslihan Öztürk Gökçe and Hikmet Budak

    Citation: BMC Genomics 2017 18:969

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  3. Content type: Research article

    Transcriptomic analyses were performed to compare the molecular responses of two potato varieties previously shown to differ in the severity of disease symptoms due to infection by “Candidatus Liberibacter solana...

    Authors: Julien G. Levy, Azucena Mendoza, J. Creighton Miller Jr., Cecilia Tamborindeguy and Elizabeth A. Pierson

    Citation: BMC Genomics 2017 18:960

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  4. Content type: Research article

    Asia minor bluegrass (Polypogon fugax, P. fugax), a weed that is both distributed across China and associated with winter crops, has evolved resistance to acetyl-CoA carboxylase (ACCase) herbicides, but the resis...

    Authors: Fengyan Zhou, Yong Zhang, Wei Tang, Mei Wang and Tongchun Gao

    Citation: BMC Genomics 2017 18:953

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  5. Content type: Research article

    Spinach is a useful source of dietary vitamins and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identificati...

    Authors: Jun Qin, Ainong Shi, Beiquan Mou, Michael A. Grusak, Yuejin Weng, Waltram Ravelombola, Gehendra Bhattarai, Lingdi Dong and Wei Yang

    Citation: BMC Genomics 2017 18:941

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  6. Content type: Research article

    Genomic selection (GS) can offer unprecedented gains, in terms of cost efficiency and generation turnover, to forest tree selective breeding; especially for late expressing and low heritability traits. Here, w...

    Authors: Frances R. Thistlethwaite, Blaise Ratcliffe, Jaroslav Klápště, Ilga Porth, Charles Chen, Michael U. Stoehr and Yousry A. El-Kassaby

    Citation: BMC Genomics 2017 18:930

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  7. Content type: Research article

    MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression of target mRNAs involved in plant growth, development, and abiotic stress. As one of the most important model plants, peach (Prunus persi...

    Authors: Shaoxuan Li, Zhanru Shao, Xiling Fu, Wei Xiao, Ling Li, Ming Chen, Mingyue Sun, Dongmei Li and Dongsheng Gao

    Citation: BMC Genomics 2017 18:938

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  8. Content type: Research article

    The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work ...

    Authors: Zachary N. Harris, Laszlo G. Kovacs and Jason P. Londo

    Citation: BMC Genomics 2017 18:937

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  9. Content type: Research article

    Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molec...

    Authors: Yingchun Xu, Yanjie Wang, Neil Mattson, Liu Yang and Qijiang Jin

    Citation: BMC Genomics 2017 18:926

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  10. Content type: Research article

    Sugarcane is a major crop of the tropics cultivated mainly for its high sucrose content. The crop is genetically less explored due to its complex polyploid genome. Sucrose synthesis and accumulation are comple...

    Authors: Prathima P. Thirugnanasambandam, Nam V. Hoang, Agnelo Furtado, Frederick C. Botha and Robert J. Henry

    Citation: BMC Genomics 2017 18:909

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  11. Content type: Research article

    Cowpea (Vigna unguiculata (L.) Walp.) is the most important food and forage legume in the semi-arid tropics of sub-Saharan Africa where approximately 80% of worldwide production takes place primarily on low-input...

    Authors: Vikram A. Misra, Yu Wang and Michael P. Timko

    Citation: BMC Genomics 2017 18:898

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  12. Content type: Research article

    Lily is an economically important plant, with leaves and bulbs consisting of overlapping scales, large ornamental flowers and a very large genome. Although it is recognized that flowers and bulb scales are mod...

    Authors: Fang Du, Junmiao Fan, Ting Wang, Yun Wu, Donald Grierson, Zhongshan Gao and Yiping Xia

    Citation: BMC Genomics 2017 18:899

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  13. Content type: Research

    Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of...

    Authors: Márcia Carvalho, María Muñoz-Amatriaín, Isaura Castro, Teresa Lino-Neto, Manuela Matos, Marcos Egea-Cortines, Eduardo Rosa, Timothy Close and Valdemar Carnide

    Citation: BMC Genomics 2017 18:891

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  14. Content type: Research

    Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein...

    Authors: Md. Abdul Kayum, Jong-In Park, Ujjal Kumar Nath, Gopal Saha, Manosh Kumar Biswas, Hoy-Taek Kim and Ill-Sup Nou

    Citation: BMC Genomics 2017 18:885

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  15. Content type: Research article

    Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negative...

    Authors: Chandran Nithin, Amal Thomas, Jolly Basak and Ranjit Prasad Bahadur

    Citation: BMC Genomics 2017 18:878

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  16. Content type: Research article

    The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this...

    Authors: Kaleem U. Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A. Almoneafy, Raqeeb Ullah, Xue-liang Ren and Qing-Yao Shu

    Citation: BMC Genomics 2017 18:869

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  17. Content type: Research article

    Soybean is one of most important oilseed crop worldwide, however, its production is often limited by many insect pests. Bean pyralid is one of the major soybean leaf-feeding insects in China. To explore the de...

    Authors: Weiying Zeng, Zudong Sun, Zhaoyan Cai, Huaizhu Chen, Zhenguang Lai, Shouzhen Yang and Xiangmin Tang

    Citation: BMC Genomics 2017 18:871

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  18. Content type: Research article

    Auxin is essential for plant growth and development. Although substantial progress has been made in understanding auxin pathways in model plants such as Arabidopsis and rice, little is known in moso bamboo whi...

    Authors: Wenjia Wang, Lianfeng Gu, Shanwen Ye, Hangxiao Zhang, Changyang Cai, Mengqi Xiang, Yubang Gao, Qin Wang, Chentao Lin and Qiang Zhu

    Citation: BMC Genomics 2017 18:870

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  19. Content type: Research article

    Chinese jujube (Ziziphus jujuba Mill.) is one of the most important members in the Rhamnaceae family. The whole genome sequence and more than 30,000 proteins of Chinese jujube have been obtained in 2014. Mitogen-...

    Authors: Zhiguo Liu, Liman Zhang, Chaoling Xue, Hu Fang, Jin Zhao and Mengjun Liu

    Citation: BMC Genomics 2017 18:855

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  20. Content type: Research article

    Switchgrass is a crop with many desirable traits for bioenergy production. Plant genomes have high DNA methylation levels throughout genes and transposable elements and DNA methylation is known to play a role ...

    Authors: Mollee Dworkin, Shaojun Xie, Malay Saha, Jyothi Thimmapuram and Venu (Kal) Kalavacharla

    Citation: BMC Genomics 2017 18:851

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