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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.

Page 1 of 30

  1. Content type: Research article

    Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns...

    Authors: Vasudevan Ayyappan, Venkateswara R. Sripathi, Venu ( Kal) Kalavacharla, Malay C. Saha, Jyothi Thimmapuram, Ketaki P. Bhide and Elizabeth Fiedler

    Citation: BMC Genomics 2019 20:667

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  2. Content type: Research article

    Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in L...

    Authors: Haron Salih, Wenfang Gong, Shoupu He, Wang Xia, Magwanga Richard Odongo and Xiongming Du

    Citation: BMC Genomics 2019 20:661

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  3. Content type: Research article

    Wheat is the most important staple crop in Afghanistan and accounts for the main part of cereal production. However, wheat production has been unstable during the last decades and the country depends on seed i...

    Authors: S. Dreisigacker, R. K. Sharma, E. Huttner, A. Karimov, M. Q. Obaidi, P. K. Singh, C. Sansaloni, R. Shrestha, K. Sonder and H.-J. Braun

    Citation: BMC Genomics 2019 20:660

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  4. Content type: Research article

    Inflorescence architecture is denoted by the spatial arrangement of various lateral branches and florets formed on them, which is shaped by a complex of regulators. Unveiling of the regulatory mechanisms under...

    Authors: Qi Wu, Xue Bai, Wei Zhao, Xiaodong Shi, Dabing Xiang, Yan Wan, Xiaoyong Wu, Yanxia Sun, Jianglin Zhao, Lianxin Peng and Gang Zhao

    Citation: BMC Genomics 2019 20:658

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  5. Content type: Research article

    Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly...

    Authors: Siyuan Zhu, Xiaojun Chen, Xia Liu, Jian Zhao and Touming Liu

    Citation: BMC Genomics 2019 20:657

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  6. Content type: Research article

    Argonaute proteins (AGOs) are important players in the regulation of plant development by directing sRNAs to target mRNAs. In maize (Zea mays), AGO18b is a tassel-enriched and grass-specific AGO. Previous studies...

    Authors: Wei Sun, Dong Chen, Yaqiang Xue, Lihong Zhai, Dan Zhang, Zheng Cao, Lei Liu, Chao Cheng, Yi Zhang and Zuxin Zhang

    Citation: BMC Genomics 2019 20:656

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  7. Content type: Research article

    Circular RNAs (circRNAs), a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and developmental processes in eukaryotic cells. However, there have been no related stud...

    Authors: Xingguo Zhang, Xingli Ma, Longlong Ning, Zhongfeng Li, Kunkun Zhao, Ke Li, Jialin He and Dongmei Yin

    Citation: BMC Genomics 2019 20:653

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  8. Content type: Research article

    The efficient detection and initiation of appropriate response to abiotic stresses are important to plants survival. The plant G-protein coupled receptors (GPCRs) are diverse membranous proteins that are respo...

    Authors: Pu Lu, Richard Odongo Magwanga, Joy Nyangasi Kirungu, Qi Dong, Xiaoyan Cai, Zhongli Zhou, Xingxing Wang, Yanchao Xu, Yuqing Hou, Renhai Peng, Kunbo Wang and Fang Liu

    Citation: BMC Genomics 2019 20:651

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  9. Content type: Research article

    Fusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. A putative quantitative trait locus conferring FCR resistance, Qcrs.cpi-1H, had previously been mapped...

    Authors: Shang Gao, Zhi Zheng, Jonathan Powell, Ahsan Habib, Jiri Stiller, Meixue Zhou and Chunji Liu

    Citation: BMC Genomics 2019 20:650

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  10. Content type: Research article

    Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (An...

    Authors: Libin Zhang, Jun Zou, Shisheng Li, Baoshan Wang, Nadia Raboanatahiry and Maoteng Li

    Citation: BMC Genomics 2019 20:649

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  11. Content type: Research article

    The hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types. In this study, a representative sample consisting of 1...

    Authors: Xue Zhao, Hairan Dong, Hong Chang, Jingyun Zhao, Weili Teng, Lijuan Qiu, Wenbin Li and Yingpeng Han

    Citation: BMC Genomics 2019 20:648

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  12. Content type: Research article

    The thermo-sensitive genic male sterility (TGMS) of Brassica napus facilitates reproductive researches and hybrid seed production. Considering the complexity and little information about the molecular mechanism i...

    Authors: Xin Tang, You-Jin Hao, Jun-Xing Lu, Geng Lu and Tao Zhang

    Citation: BMC Genomics 2019 20:644

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  13. Content type: Research article

    As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striif...

    Authors: Xueling Ye, Jian Li, Yukun Cheng, Fangjie Yao, Li Long, Yuqi Wang, Yu Wu, Jing Li, Jirui Wang, Qiantao Jiang, Houyang Kang, Wei Li, Pengfei Qi, Xiujin Lan, Jian Ma, Yaxi Liu…

    Citation: BMC Genomics 2019 20:640

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  14. Content type: Research article

    Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. ...

    Authors: Harsh Raman, Rosy Raman, Yu Qiu, Avilash Singh Yadav, Sridevi Sureshkumar, Lauren Borg, Maheswaran Rohan, David Wheeler, Oliver Owen, Ian Menz and Sureshkumar Balasubramanian

    Citation: BMC Genomics 2019 20:636

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  15. Content type: Methodology article

    The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found ...

    Authors: Marc-André Lemay, Davoud Torkamaneh, Guillem Rigaill, Brian Boyle, Adrian O. Stec, Robert M. Stupar and François Belzile

    Citation: BMC Genomics 2019 20:634

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  16. Content type: Research article

    Gypenosides are a group of triterpene saponins from Gynostemma pentaphyllum that are the same as or very similar to ginsenosides from the Panax species. Several enzymes involved in ginsenoside biosynthesis have b...

    Authors: Tongtong Liang, Liqiu Zou, Sijie Sun, Xuejun Kuang, Jianhe Wei, Lizhi Wang, Ying Li and Chao Sun

    Citation: BMC Genomics 2019 20:632

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  17. Content type: Research article

    Free asparagine is the precursor for acrylamide formation during cooking and processing of grains, tubers, beans and other crop products. In wheat grain, free asparagine, free glutamine and total free amino ac...

    Authors: Tanya Y. Curtis, Sarah Raffan, Yongfang Wan, Robert King, Asier Gonzalez-Uriarte and Nigel G. Halford

    Citation: BMC Genomics 2019 20:628

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  18. Content type: Research article

    Low temperature restricts the planting range of all crops, but cold acclimation induces adaption to cold stress in many plants. Camellia sinensis, a perennial evergreen tree that is the source of tea, is mainly g...

    Authors: Yeyun Li, Xuewen Wang, Qiuyan Ban, Xiangxiang Zhu, Changjun Jiang, Chaoling Wei and Jeffrey L. Bennetzen

    Citation: BMC Genomics 2019 20:624

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  20. Content type: Research article

    Heavy metal ATPases (HMAs) are responsible for Cd translocation and play a primary role in Cd detoxification in various plant species. However, the characteristics of HMAs and the regulatory mechanisms between...

    Authors: Min Zhou, Shigang Zheng, Rong Liu, Lu Lu, Chihong Zhang, Lei Zhang, Levi Yant and Yu Wu

    Citation: BMC Genomics 2019 20:615

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  22. Content type: Research article

    Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the ...

    Authors: Matt Hunt, Sagnik Banerjee, Priyanka Surana, Meiling Liu, Greg Fuerst, Sandra Mathioni, Blake C. Meyers, Dan Nettleton and Roger P. Wise

    Citation: BMC Genomics 2019 20:610

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  23. Content type: Research article

    Quercetin is a polyphenol of great interest given its antioxidant activity and involvement in the immune response. Although quercetin has been well studied at the molecular level as a gene regulator and an act...

    Authors: Dana Atrahimovich, Avraham O. Samson, Yifthah Barsheshet, Jacob Vaya, Soliman Khatib and Eli Reuveni

    Citation: BMC Genomics 2019 20:606

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  24. Content type: Research article

    A thorough verification of the ability of genomic selection (GS) to predict estimated breeding values for pea (Pisum sativum L.) grain yield is pending. Prediction for different environments (inter-environment pr...

    Authors: Paolo Annicchiarico, Nelson Nazzicari, Luciano Pecetti, Massimo Romani and Luigi Russi

    Citation: BMC Genomics 2019 20:603

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  25. Content type: Research article

    Long intergenic non-coding RNAs (lincRNAs) can act as regulators of expression of protein-coding genes. Trans-natural antisense transcripts (trans-NATs) are a type of lincRNAs that contain sequence complementary ...

    Authors: Jules Deforges, Rodrigo S. Reis, Philippe Jacquet, Dominique Jacques Vuarambon and Yves Poirier

    Citation: BMC Genomics 2019 20:601

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  26. Content type: Research article

    Gerbera hybrida is one of the most popular cut flowers in the world; however, stem bending, which always happens when gerbera flower harvested from the field, greatly limits its vase life. To date the molecular m...

    Authors: Yafei Ge, Qixian Lai, Ping Luo, Xiaojing Liu and Wen Chen

    Citation: BMC Genomics 2019 20:600

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  27. Content type: Research article

    Cotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quali...

    Authors: Wenwen Wang, Ying Sun, Peng Yang, Xiaoyan Cai, Le Yang, Junrui Ma, Yuncan Ou, Tianpeng Liu, Iftikhar Ali, Dajun Liu, Jian Zhang, Zhonghua Teng, Kai Guo, Dexin Liu, Fang Liu and Zhengsheng Zhang

    Citation: BMC Genomics 2019 20:599

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  28. Content type: Research article

    Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. P...

    Authors: Sony Kumari, Sandeep Yadav, Debadutta Patra, Sharmila Singh, Ananda K. Sarkar and Kishore C. S. Panigrahi

    Citation: BMC Genomics 2019 20:596

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  29. Content type: Research article

    The allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production. Although its usage grows every year, little is known on this plant’s geno...

    Authors: Matteo Schiavinato, Richard Strasser, Lukas Mach, Juliane C. Dohm and Heinz Himmelbauer

    Citation: BMC Genomics 2019 20:594

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  30. Content type: Research article

    Puccinellia tenuiflora is the most saline-alkali tolerant plant in the Songnen Plain, one of the three largest soda saline-alkali lands worldwide. Here, we investigated the physicochemical properties of saline-al...

    Authors: Xiaoxue Ye, Hao Wang, Xiuling Cao, Xuejiao Jin, Fuqiang Cui, Yuanyuan Bu, Hua Liu, Wenwu Wu, Tetsuo Takano and Shenkui Liu

    Citation: BMC Genomics 2019 20:589

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  31. Content type: Research article

    Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food i...

    Authors: Abdul Fatah A. Samad, Reyhaneh Rahnamaie-Tajadod, Muhammad Sajad, Jaeyres Jani, Abdul Munir Abdul Murad, Normah Mohd Noor and Ismanizan Ismail

    Citation: BMC Genomics 2019 20:586

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    The Correction to this article has been published in BMC Genomics 2019 20:627

  32. Content type: Methodology article

    Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequenc...

    Authors: Sean P. Gordon, Joshua J. Levy and John P. Vogel

    Citation: BMC Genomics 2019 20:580

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  33. Content type: Research article

    Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regul...

    Authors: Ge Bai, He Xie, Heng Yao, Feng Li, Xuejun Chen, Yihan Zhang, Bingguan Xiao, Jun Yang, Yongping Li and Da-Hai Yang

    Citation: BMC Genomics 2019 20:575

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  34. Content type: Research article

    Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expressi...

    Authors: Xiaocong Zhang, Sidi Xie, Jienan Han, Yu Zhou, Chang Liu, Zhiqiang Zhou, Feifei Wang, Zixiang Cheng, Junjie Zhang, Yufeng Hu, Zhuanfang Hao, Mingshun Li, Degui Zhang, Hongjun Yong, Yubi Huang, Jianfeng Weng…

    Citation: BMC Genomics 2019 20:574

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  35. Content type: Research article

    Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increas...

    Authors: Xiao-Qing Huang, Xiao-Hong Lu, Man-Hong Sun, Rong-Jun Guo, Anne D. van Diepeningen and Shi-Dong Li

    Citation: BMC Genomics 2019 20:570

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  36. Content type: Research article

    The bHLH (basic helix-loop-helix) transcription factor is one of the largest families of transcription factors in plants, containing a large number of members with diverse functions. Chinese jujube (Ziziphus juju...

    Authors: Hongtai Li, Weilin Gao, Chaoling Xue, Yao Zhang, Zhiguo Liu, Yu Zhang, Xianwei Meng, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2019 20:568

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  37. Content type: Research article

    Anthocyanins perform diverse biological functions in plants and are beneficial to human health. Leaf color is the most important trait of ornamental kale and the characteristics of changes in leaf color make i...

    Authors: Ning Guo, Shuo Han, Mei Zong, Guixiang Wang, Shuning Zheng and Fan Liu

    Citation: BMC Genomics 2019 20:564

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  38. Content type: Research article

    Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size ...

    Authors: Marco Meola, Etienne Rifa, Noam Shani, Céline Delbès, Hélène Berthoud and Christophe Chassard

    Citation: BMC Genomics 2019 20:560

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  39. Content type: Research article

    Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing...

    Authors: Huiru Sun, Hengling Wei, Hantao Wang, Pengbo Hao, Lijiao Gu, Guoyuan Liu, Liang Ma, Zhengzheng Su and Shuxun Yu

    Citation: BMC Genomics 2019 20:558

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  40. Content type: Research article

    SQUAMOSA Promoter Binding Protein-Likes (SPLs) proteins are plant-specific transcription factors that play many crucial roles in plant growth and development. However, there is little information about SPL family...

    Authors: Hongfeng Wang, Zhichao Lu, Yiteng Xu, Lingcui Kong, Jianjun Shi, Yafei Liu, Chunxiang Fu, Xiaoshan Wang, Zeng-Yu Wang, Chuanen Zhou and Lu Han

    Citation: BMC Genomics 2019 20:552

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  41. Content type: Research article

    Viruses have evolved to create a cellular environment permissive for viral replication in susceptible hosts. Possibly both enabling and resulting from these virus-triggered changes, infected hosts undergo a dr...

    Authors: Mengshi Wu, Xue Ding, Xing Fu and Rosa Lozano-Duran

    Citation: BMC Genomics 2019 20:542

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  42. Content type: Research article

    Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. T...

    Authors: Weixi Li, Dayong Zhang, Guozhong Zhu, Xinyue Mi and Wangzhen Guo

    Citation: BMC Genomics 2019 20:538

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  43. Content type: Research article

    Polycomb group (PcG) proteins play important roles in animal and plant development and stress response. Polycomb repressive complex 1 (PRC1) and PRC2 are the key epigenetic regulators of gene expression, and a...

    Authors: Yong Huang, Ling Jiang, Bo-Yu Liu, Cheng-Fang Tan, Dong-Hong Chen, Wen-Hui Shen and Ying Ruan

    Citation: BMC Genomics 2019 20:533

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  44. Content type: Software

    MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for...

    Authors: Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Sébastien Bini, Delphine Lanselle, Mohcen Benmounah and Hélène Touzet

    Citation: BMC Genomics 2019 20:532

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  45. Content type: Research article

    Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. As...

    Authors: Teshale Assefa, Paul I. Otyama, Anne V. Brown, Scott R. Kalberer, Roshan S. Kulkarni and Steven B. Cannon

    Citation: BMC Genomics 2019 20:527

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  46. Content type: Research article

    Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susc...

    Authors: Nadia Bertazzon, Paolo Bagnaresi, Vally Forte, Elisabetta Mazzucotelli, Luisa Filippin, Davide Guerra, Antonella Zechini, Luigi Cattivelli and Elisa Angelini

    Citation: BMC Genomics 2019 20:526

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  47. Content type: Research article

    Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots...

    Authors: Wenbin Li, Xiaolin Wang, Chunqiang Li, Jianbo Sun, Shuxia Li and Ming Peng

    Citation: BMC Genomics 2019 20:519

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  48. Content type: Research article

    Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are i...

    Authors: Liang Xiao, Xiao-Hong Shang, Sheng Cao, Xiang-Yu Xie, Wen-Dan Zeng, Liu-Ying Lu, Song-Bi Chen and Hua-Bing Yan

    Citation: BMC Genomics 2019 20:514

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  49. Content type: Research article

    DNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modificatio...

    Authors: Mei-Wei Luan, Wei Chen, Jian-Feng Xing, Chuan-Le Xiao, Ying Chen and Shang-Qian Xie

    Citation: BMC Genomics 2019 20:508

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  50. Content type: Research article

    The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultiva...

    Authors: Yasmin A. Mohamoud, Lisa S. Mathew, Maria F. Torres, Shameem Younuskunju, Robert Krueger, Karsten Suhre and Joel A. Malek

    Citation: BMC Genomics 2019 20:498

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