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. Research article

    Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.)

    Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among s...

    Flavia Mascagni, Tommaso Giordani, Marilena Ceccarelli, Andrea Cavallini and Lucia Natali

    BMC Genomics 2017 18:634

    Published on: 18 August 2017

  2. Research article

    A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

    Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increa...

    Maryam Moazzzam Jazi, Seyed Mahdi Seyedi, Esmaeil Ebrahimie, Mansour Ebrahimi, Gianluca De Moro and Christopher Botanga

    BMC Genomics 2017 18:627

    Published on: 17 August 2017

  3. Research article

    Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping

    Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active.

    Lars-Gernot Otto, Prodyut Mondal, Jonathan Brassac, Susanne Preiss, Jörg Degenhardt, Sang He, Jochen Christoph Reif and Timothy Francis Sharbel

    BMC Genomics 2017 18:599

    Published on: 10 August 2017

  4. Research article

    Genome-wide comparative analysis of DNA methylation between soybean cytoplasmic male-sterile line NJCMS5A and its maintainer NJCMS5B

    DNA methylation is an important epigenetic modification. It can regulate the expression of many key genes without changing the primary structure of the genomic DNA, and plays a vital role in the growth and dev...

    Yanwei Li, Xianlong Ding, Xuan Wang, Tingting He, Hao Zhang, Longshu Yang, Tanliu Wang, Linfeng Chen, Junyi Gai and Shouping Yang

    BMC Genomics 2017 18:596

    Published on: 10 August 2017

  5. Research article

    Role of the GRAS transcription factor ATA/RAM1 in the transcriptional reprogramming of arbuscular mycorrhiza in Petunia hybrida

    Development of arbuscular mycorrhiza (AM) requires a fundamental reprogramming of root cells for symbiosis. This involves the induction of hundreds of genes in the host. A recently identified GRAS-type transcr...

    Mélanie K. Rich, Pierre-Emmanuel Courty, Christophe Roux and Didier Reinhardt

    BMC Genomics 2017 18:589

    Published on: 8 August 2017

  6. Research

    Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq

    Blueberries are one of the few horticultural crops adapted to grow in acidic soils. Neutral to basic soil pH is detrimental to all commonly cultivated blueberry species, including Vaccinium corymbosum (VC). In co...

    Miriam Payá-Milans, Gerardo H. Nunez, James W. Olmstead, Timothy A. Rinehart and Margaret Staton

    BMC Genomics 2017 18:580

    Published on: 7 August 2017

  7. Research article

    Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array

    Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to des...

    Geert van Geest, Roeland E Voorrips, Danny Esselink, Aike Post, Richard GF Visser and Paul Arens

    BMC Genomics 2017 18:585

    Published on: 7 August 2017

  8. Research article

    Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula

    Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant g...

    Karen M. Moll, Peng Zhou, Thiruvarangan Ramaraj, Diego Fajardo, Nicholas P. Devitt, Michael J. Sadowsky, Robert M. Stupar, Peter Tiffin, Jason R. Miller, Nevin D. Young, Kevin A. T. Silverstein and Joann Mudge

    BMC Genomics 2017 18:578

    Published on: 4 August 2017

  9. Research

    Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi–SlPH tomato line with reduced fruit acidity and higher pH

    The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, con...

    Shiri Barad, Noa Sela, Amit K. Dubey, Dilip Kumar, Neta Luria, Dana Ment, Shahar Cohen, Arthur A. Schaffer and Dov Prusky

    BMC Genomics 2017 18:579

    Published on: 4 August 2017

  10. Research article

    Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing

    The soybean cyst nematode (SCN), Heterodera glycines, is one of the most devastating diseases limiting soybean production worldwide. It is known that small RNAs, including microRNAs (miRNAs) and small interfering...

    Bin Tian, Shichen Wang, Timothy C. Todd, Charles D. Johnson, Guiliang Tang and Harold N. Trick

    BMC Genomics 2017 18:572

    Published on: 2 August 2017

  11. Methodology article

    Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire

    The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of cr...

    Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D. G. Jones and Matthew D. Clark

    BMC Genomics 2017 18:564

    Published on: 26 July 2017

  12. Research article

    Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles

    Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily ...

    Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, Jill L. Wegrzyn, David B. Neale, J. Bradley St. Clair and Dee R. Denver

    BMC Genomics 2017 18:558

    Published on: 24 July 2017

  13. Research article

    Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims)

    The Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. ed...

    Susan Araya, Alexandre M Martins, Nilton T V Junqueira, Ana Maria Costa, Fábio G Faleiro and Márcio E Ferreira

    BMC Genomics 2017 18:549

    Published on: 21 July 2017

  14. Research article

    Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.)

    The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and i...

    Irina Ćalić, Jennifer Koch, David Carey, Charles Addo-Quaye, John E. Carlson and David B. Neale

    BMC Genomics 2017 18:547

    Published on: 20 July 2017

  15. Research article

    High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying

    Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and qu...

    Jin-Ling Feng, Zhi-Jian Yang, Shi-Pin Chen, Yousry A. El-Kassaby and Hui Chen

    BMC Genomics 2017 18:546

    Published on: 20 July 2017

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