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  1. Rice (Oryza sativa) is critical for human nutrition worldwide. Due to a growing population, cultivars that produce high yields in high salinity soil are of major importance. Here we describe the discovery and mol...

    Authors: Risheng Chen, Yunfeng Cheng, Suying Han, Ben Van Handel, Ling Dong, Xinmin Li and Xiaoqing Xie
    Citation: BMC Genomics 2017 18:655
    Content type: Research article Published on:

  2. Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can...

    Authors: Keisha D. Carlson, Noe Fernandez-Pozo, Aureliano Bombarely, Rahul Pisupati, Lukas A. Mueller and Andreas Madlung
    Citation: BMC Genomics 2017 18:653
    Content type: Research article Published on:

  3. Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, ...

    Authors: Bidhan Ch. Bera, Nitin Virmani, Naveen Kumar, Taruna Anand, S Pavulraj, Adam Rash, Debra Elton, Nicola Rash, Sandeep Bhatia, Richa Sood, Raj Kumar Singh and Bhupendra Nath Tripathi
    Citation: BMC Genomics 2017 18:652
    Content type: Research Published on:

  4. Rust fungi constitute the largest group of plant fungal pathogens. However, a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of...

    Authors: Si-Qi Tao, Bin Cao, Cheng-Ming Tian and Ying-Mei Liang
    Citation: BMC Genomics 2017 18:651
    Content type: Research Published on:

  5. The vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA s...

    Authors: Luis P. Iñiguez, Mario Ramírez, William B. Barbazuk and Georgina Hernández
    Citation: BMC Genomics 2017 18:650
    Content type: Research article Published on:

  6. Cerasus sachalinensis is widely used in cool regions as a sweet cherry rootstock and is known for its sensitivity to soil waterlogging and waterlogging stress. However, the limited ava...

    Authors: Peng Zhang, Deguo Lyu, Luting Jia, Jiali He and Sijun Qin
    Citation: BMC Genomics 2017 18:649
    Content type: Research article Published on:

  7. Polyploidy is an important phenomenon in plants because of its roles in agricultural and forestry production as well as in plant tolerance to environmental stresses. Tetraploid black locust (Robinia pseudoacacia ...

    Authors: Qiuxiang Luo, Mu Peng, Xiuli Zhang, Pei Lei, Ximei Ji, Wahsoon Chow, Fanjuan Meng and Guanyu Sun
    Citation: BMC Genomics 2017 18:648
    Content type: Research article Published on:

  8. Maturity of intestinal functions is critical for neonatal health and survival, but comprehensive description of mechanisms underlying intestinal maturation that occur during late gestation still remain poorly ...

    Authors: Ying Yao, Valentin Voillet, Maeva Jegou, Magali SanCristobal, Samir Dou, Véronique Romé, Yannick Lippi, Yvon Billon, Marie-Christine Père, Gaëlle Boudry, Laure Gress, Nathalie Iannucelli, Pierre Mormède, Hélène Quesnel, Laurianne Canario, Laurence Liaubet…
    Citation: BMC Genomics 2017 18:647
    Content type: Research article Published on:

  9. Flavor is an important attribute of mandarin (Citrus reticulata Blanco), but flavor improvement via conventional breeding is very challenging largely due to the complexity of the flavor components and traits. Man...

    Authors: Yuan Yu, Jinhe Bai, Chunxian Chen, Anne Plotto, Qibin Yu, Elizabeth A. Baldwin and Frederick G. Gmitter Jr
    Citation: BMC Genomics 2017 18:646
    Content type: Research article Published on:

  10. Small RNAs (sRNAs) constitute an important class of post-transcriptional regulators that control critical cellular processes in bacteria. Recent research using high-throughput transcriptomic approaches has led...

    Authors: Carl Tony Fakhry, Prajna Kulkarni, Ping Chen, Rahul Kulkarni and Kourosh Zarringhalam
    Citation: BMC Genomics 2017 18:645
    Content type: Methodology Article Published on:

  11. Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotat...

    Authors: Daniel Gebert, Charlotte Hewel and David Rosenkranz
    Citation: BMC Genomics 2017 18:644
    Content type: Software Published on:

  12. The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current...

    Authors: Harry D. Dawson, Celine Chen, Brady Gaynor, Jonathan Shao and Joseph F. Urban Jr
    Citation: BMC Genomics 2017 18:643
    Content type: Database Published on:

  13. Tuber yield and starch content of the cultivated potato are complex traits of decisive importance for breeding improved varieties. Natural variation of tuber yield and starch content depends on the environment...

    Authors: Elske Maria Schönhals, Jia Ding, Enrique Ritter, Maria João Paulo, Nicolás Cara, Ekhard Tacke, Hans-Reinhard Hofferbert, Jens Lübeck, Josef Strahwald and Christiane Gebhardt
    Citation: BMC Genomics 2017 18:642
    Content type: Research article Published on:

  14. Human hepatitis B virus (HBV) infection is an important public health issue in the Asia-Pacific region and is associated with chronic hepatitis, liver fibrosis, cirrhosis and even liver cancer. However, the un...

    Authors: Fangming Kan, Lei Ye, Tao Yan, Jiaqi Cao, Jianhua Zheng and Wuping Li
    Citation: BMC Genomics 2017 18:641
    Content type: Research article Published on:

  16. The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to o...

    Authors: Sean P. Gilmore, John K. Henske, Jessica A. Sexton, Kevin V. Solomon, Susanna Seppälä, Justin I Yoo, Lauren M. Huyett, Abe Pressman, James Z. Cogan, Veronika Kivenson, Xuefeng Peng, YerPeng Tan, David L. Valentine and Michelle A. O’Malley
    Citation: BMC Genomics 2017 18:639
    Content type: Research article Published on:

  17. Retinal pigment epithelium (RPE) cells transfer oxygen and nutrients from choroid to the neural retina. Reduced oxygen to RPE perturbs development and functions of blood vessels in retina. Previous efforts of ...

    Authors: Zhiwen Jiang, Jiaqi Yang, Aimei Dai, Yuming Wang, Wei Li and Zhi Xie
    Citation: BMC Genomics 2017 18:638
    Content type: Research article Published on:

  18. The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs a...

    Authors: Kevin Cadwell, Sherko S. Niranji, Vanessa L. Armstrong, Catherine A. Mowbray, Richard Bailey, Kellie A Watson and Judith Hall
    Citation: BMC Genomics 2017 18:637
    Content type: Research Published on:

  19. The natural history of type 1 diabetes (T1D) is challenging to investigate, especially as pre-diabetic individuals are difficult to identify. Numerous T1D consortia have been established to collect whole blood...

    Authors: Linda Yip, Rebecca Fuhlbrigge, Mark A. Atkinson and C. Garrison Fathman
    Citation: BMC Genomics 2017 18:636
    Content type: Research article Published on:

  20. Aedes albopictus is a vector of arboviruses that cause severe diseases in humans such as Chikungunya, Dengue and Zika fevers. The vector competence of Ae. albopictus varies depending o...

    Authors: Yoann Saucereau, Claire Valiente Moro, Cindy Dieryckx, Jean-William Dupuy, Florence-Hélène Tran, Vincent Girard, Patrick Potier and Patrick Mavingui
    Citation: BMC Genomics 2017 18:635
    Content type: Research article Published on:

  21. 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...

    Authors: Flavia Mascagni, Tommaso Giordani, Marilena Ceccarelli, Andrea Cavallini and Lucia Natali
    Citation: BMC Genomics 2017 18:634
    Content type: Research article Published on:

  22. Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using...

    Authors: Rediet Oshone, Mariama Ngom, Feixia Chu, Samira Mansour, Mame Ourèye Sy, Antony Champion and Louis S. Tisa
    Citation: BMC Genomics 2017 18:633
    Content type: Research article Published on:

  23. Manipulating maternal nutrition during specific periods of gestation can result in re-programming of fetal and post-natal development. In this experiment we investigated how a feed restriction of 85% compared ...

    Authors: Francois Paradis, Katie M. Wood, Kendall C. Swanson, Stephen P. Miller, Brian W. McBride and Carolyn Fitzsimmons
    Citation: BMC Genomics 2017 18:632
    Content type: Research article Published on:

  24. Fungal pathogens of plants produce diverse repertoires of secondary metabolites, which have functions ranging from iron acquisition, defense against immune perturbation, to toxic assaults on the host. The whea...

    Authors: Timothy Cairns and Vera Meyer
    Citation: BMC Genomics 2017 18:631
    Content type: Research article Published on:

  25. Microsporidia are highly specialized, parasitic fungi that infect a wide range of eukaryotic hosts from all major taxa. Infections cause a variety of damaging effects on host physiology from increased stress t...

    Authors: Jordan D. Poley, Ben J. G. Sutherland, Mark D. Fast, Ben F. Koop and Simon R. M. Jones
    Citation: BMC Genomics 2017 18:630
    Content type: Research article Published on:

  26. RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the met...

    Authors: Ashwini Kumar, Matti Kankainen, Alun Parsons, Olli Kallioniemi, Pirkko Mattila and Caroline A. Heckman
    Citation: BMC Genomics 2017 18:629
    Content type: Research article Published on:

  27. Type VI secretion systems (T6SS) are widespread among Gram-negative bacteria and have a potential role as essential virulence factors or to maintain symbiotic interactions. Three T6SS gene clusters were identi...

    Authors: Tim Kamber, Joël F. Pothier, Cosima Pelludat, Fabio Rezzonico, Brion Duffy and Theo H. M. Smits
    Citation: BMC Genomics 2017 18:628
    Content type: Research article Published on:

  28. 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...

    Authors: Maryam Moazzzam Jazi, Seyed Mahdi Seyedi, Esmaeil Ebrahimie, Mansour Ebrahimi, Gianluca De Moro and Christopher Botanga
    Citation: BMC Genomics 2017 18:627
    Content type: Research article Published on:

  29. Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today’s broiler (meat-type) chickens. However, this enhanced growth rate was a...

    Authors: C. W. Resnyk, W. Carré, X. Wang, T. E. Porter, J. Simon, E. Le Bihan-Duval, M. J. Duclos, S. E. Aggrey and L. A. Cogburn
    Citation: BMC Genomics 2017 18:626
    Content type: Research article Published on:

  30. Bacteria of the genus Xanthomonas are economically important plant pathogens. Pathogenicity of Xanthomonas spp. depends on the type III-secretion system and additional virulence determinants. The number of sequen...

    Authors: Ulrike Abendroth, Norman Adlung, Andreas Otto, Benjamin Grüneisen, Dörte Becher and Ulla Bonas
    Citation: BMC Genomics 2017 18:625
    Content type: Research article Published on:

  31. Mastitis is the most prevalent disease in dairy sheep with major economic, hygienic and welfare implications. The disease persists in all dairy sheep production systems despite the implementation of improved m...

    Authors: G. Banos, G. Bramis, S. J. Bush, E. L. Clark, M. E.B. McCulloch, J. Smith, G. Schulze, G. Arsenos, D. A. Hume and A. Psifidi
    Citation: BMC Genomics 2017 18:624
    Content type: Research article Published on:

  32. In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful...

    Authors: Sebastian J. Teran Hidalgo, Mengyun Wu and Shuangge Ma
    Citation: BMC Genomics 2017 18:623
    Content type: Methodology Article Published on:

  33. The Norway lobster, Nephrops norvegicus, is economically important in European fisheries and is a key organism in local marine ecosystems. Despite multi-faceted scientific interest in this species, our current kn...

    Authors: Guiomar Rotllant, Tuan Viet Nguyen, Valerio Sbragaglia, Lifat Rahi, Kevin J. Dudley, David Hurwood, Tomer Ventura, Joan B. Company, Vincent Chand, Jacopo Aguzzi and Peter B. Mather
    Citation: BMC Genomics 2017 18:622
    Content type: Research article Published on:

  34. Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a...

    Authors: Yuan Li, Benjamin J. Metcalf, Sopio Chochua, Zhongya Li, Robert E. Gertz Jr, Hollis Walker, Paulina A. Hawkins, Theresa Tran, Lesley McGee and Bernard W. Beall
    Citation: BMC Genomics 2017 18:621
    Content type: Research article Published on:

  37. Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some t...

    Authors: Tingting Wang, Yi-Ping Phoebe Chen, Iona M. MacLeod, Jennie E. Pryce, Michael E. Goddard and Ben J. Hayes
    Citation: BMC Genomics 2017 18:618
    Content type: Research article Published on:

  38. High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poo...

    Authors: Arabinda Mahanty, Gopal Krishna Purohit, Sasmita Mohanty, Nihar Ranjan Nayak and Bimal Prasanna Mohanty
    Citation: BMC Genomics 2017 18:617
    Content type: Research article Published on:

  39. Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in bot...

    Authors: Rabindra K. Mandal, Tieshan Jiang and Young Min Kwon
    Citation: BMC Genomics 2017 18:616
    Content type: Research article Published on:

  40. Nelson Bay orthoreovirus (NBV) is a fusogenic bat borne virus with an unknown zoonotic potential. Previous studies have shown that NBV can infect and replicate in a wide variety of cell types derived from thei...

    Authors: Lawrence Mok, James W. Wynne, Mary Tachedjian, Brian Shiell, Kris Ford, David A. Matthews, Antony Bacic and Wojtek P. Michalski
    Citation: BMC Genomics 2017 18:615
    Content type: Research article Published on:

  41. DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid c...

    Authors: David P. Astling, Ilea E. Heft, Kenneth L. Jones and James M. Sikela
    Citation: BMC Genomics 2017 18:614
    Content type: Methodology article Published on:

  42. The dark sleeper (Odontobutis potamophila) is an important commercial fish species which shows a sexually dimorphic growth pattern. However, the lack of sex transcriptomic data is hindering further research and g...

    Authors: Cheng Zhao, Guosong Zhang, Shaowu Yin, Zecheng Li, Qintao Wang, Shuqiao Chen and Guoqin Zhou
    Citation: BMC Genomics 2017 18:613
    Content type: Research article Published on:

  43. Dimethylsulfoniopropionate (DMSP) is a small sulphur compound which is produced in prodigious amounts in the oceans and plays a pivotal role in the marine sulfur cycle. Until recently, DMSP was believed to be ...

    Authors: Catalina Aguilar, Jean-Baptiste Raina, Cherie A. Motti, Sylvain Fôret, David C. Hayward, Bruno Lapeyre, David G. Bourne and David J. Miller
    Citation: BMC Genomics 2017 18:612
    Content type: Research Published on:

  44. The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of...

    Authors: Maria Stavrianakou, Ricardo Perez, Cheng Wu, Matthew S. Sachs, Rodolfo Aramayo and Mark Harlow
    Citation: BMC Genomics 2017 18:611
    Content type: Research Article Published on:

  46. Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. ...

    Authors: Pamela Wiener, Enrique Sánchez-Molano, Dylan N. Clements, John A. Woolliams, Marie J. Haskell and Sarah C. Blott
    Citation: BMC Genomics 2017 18:609
    Content type: Research article Published on:

  47. Sickle cell anemia causes severe complications and premature death. Five common β-globin gene cluster haplotypes are each associated with characteristic fetal hemoglobin (HbF) levels. As HbF is the major modul...

    Authors: Elmutaz M. Shaikho, John J. Farrell, Abdulrahman Alsultan, Hatem Qutub, Amein K. Al-Ali, Maria Stella Figueiredo, David H.K. Chui, Lindsay A. Farrer, George J. Murphy, Gustavo Mostoslavsky, Paola Sebastiani and Martin H. Steinberg
    Citation: BMC Genomics 2017 18:608
    Content type: Methodology article Published on:

  49. Strict guidelines delimit the use of computational information in the clinical setting, due to the still moderate accuracy of in silico tools. These guidelines indicate that several tools should always be used...

    Authors: Elena Álvarez de la Campa, Natàlia Padilla and Xavier de la Cruz
    Citation: BMC Genomics 2017 18(Suppl 5):569
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

  50. Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease ass...

    Authors: Morena Pappalardo, Francesca Collu, James Macpherson, Martin Michaelis, Franca Fraternali and Mark N. Wass
    Citation: BMC Genomics 2017 18(Suppl 5):566
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

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