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  1. Spike architecture mutants in tetraploid wheat (Triticum turgidum L., 2n = 28, AABB) have a distinct morphology, with parts of the rachis node producing lateral meristems that develop into ramified spikelete (RSs...

    Authors: Shulin Chen, Juan Chen, Fu Hou, Yigao Feng and Ruiqi Zhang
    Citation: BMC Genomics 2018 19:228
    Content type: Research article Published on:

  2. Plant height (PH) is an important agronomic trait and is closely related to yield in soybean [Glycine max (L.) Merr.]. Previous studies have identified many QTLs for PH. Due to the complex genetic background of P...

    Authors: Xiaoli Zhang, Wubin Wang, Na Guo, Youyi Zhang, Yuanpeng Bu, Jinming Zhao and Han Xing
    Citation: BMC Genomics 2018 19:226
    Content type: Research article Published on:

  3. To combat malaria transmission, the Ugandan government has embarked upon an ambitious programme of indoor residual spraying (IRS) with a carbamate class insecticide, bendiocarb. In preparation for this campaig...

    Authors: Alison T. Isaacs, Henry D. Mawejje, Sean Tomlinson, Daniel J. Rigden and Martin J. Donnelly
    Citation: BMC Genomics 2018 19:225
    Content type: Research article Published on:

  4. Tall fescue is a widely used cool season turfgrass and relatively sensitive to high temperature. Chemical compounds like melatonin (MT) and 24-epibrassinolide (EBL) have been reported to improve plant heat str...

    Authors: Mohammad Nur Alam, Lihua Zhang, Li Yang, Md. Rabiul Islam, Yang Liu, Hong Luo, Pingfang Yang, Qingfeng Wang and Zhulong Chan
    Citation: BMC Genomics 2018 19:224
    Content type: Research article Published on:

  5. Understanding the RNA processing of an organism’s transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas ae...

    Authors: Erin E. Gill, Luisa S. Chan, Geoffrey L. Winsor, Neil Dobson, Raymond Lo, Shannan J. Ho Sui, Bhavjinder K. Dhillon, Patrick K. Taylor, Raunak Shrestha, Cory Spencer, Robert E. W. Hancock, Peter J. Unrau and Fiona S. L. Brinkman
    Citation: BMC Genomics 2018 19:223
    Content type: Research article Published on:

  6. Cashmere is a keratinized product derived from the secondary hair follicles (SHFs) of cashmere goat skins. The cashmere fiber stops growing following the transition from the actively proliferating anagen stage...

    Authors: Guangxian Zhou, Danju Kang, Sen Ma, Xingtao Wang, Ye Gao, Yuxin Yang, Xiaolong Wang and Yulin Chen
    Citation: BMC Genomics 2018 19:222
    Content type: Research article Published on:

  7. Doubly uniparental inheritance (DUI) of mitochondrial DNA in bivalves is a fascinating exception to strictly maternal inheritance as practiced by all other animals. Recent work on DUI suggests that there may b...

    Authors: E. E. Chase, B. M. Robicheau, S. Veinot, S. Breton and D. T. Stewart
    Citation: BMC Genomics 2018 19:221
    Content type: Research article Published on:

  8. Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the p...

    Authors: Zhen Zeng, Hui Sun, Eeva J. Vainio, Tommaso Raffaello, Andriy Kovalchuk, Emmanuelle Morin, Sébastien Duplessis and Fred O. Asiegbu
    Citation: BMC Genomics 2018 19:220
    Content type: Research article Published on:

  9. Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The pr...

    Authors: Paul D. N. Hebert, Thomas W. A. Braukmann, Sean W. J. Prosser, Sujeevan Ratnasingham, Jeremy R. deWaard, Natalia V. Ivanova, Daniel H. Janzen, Winnie Hallwachs, Suresh Naik, Jayme E. Sones and Evgeny V. Zakharov
    Citation: BMC Genomics 2018 19:219
    Content type: Methodology article Published on:

  10. With approximately one-third of their genomes consisting of linear and circular plasmids, the Lyme disease agent cluster of species has the most complex genomes among known bacteria. We report here a comparati...

    Authors: Sherwood R. Casjens, Lia Di, Saymon Akther, Emmanuel F. Mongodin, Benjamin J. Luft, Steven E. Schutzer, Claire M. Fraser and Wei-Gang Qiu
    Citation: BMC Genomics 2018 19:218
    Content type: Research article Published on:

  11. Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents i...

    Authors: Alicia Dalongeville, Laura Benestan, David Mouillot, Stephane Lobreaux and Stéphanie Manel
    Citation: BMC Genomics 2018 19:217
    Content type: Research article Published on:

  12. Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to spe...

    Authors: Brian R. Herb, Molly S. Shook, Christopher J. Fields and Gene E. Robinson
    Citation: BMC Genomics 2018 19:216
    Content type: Research article Published on:

  13. Exploring whether and how mutation of silk protein contributes to subsequent re-allocation of nitrogen, and impacts on the timing of silk gland degradation, is important to understand silk gland biology. Rapid...

    Authors: Yong Cui, Yanan Zhu, Yongjian Lin, Lei Chen, Qili Feng, Wen Wang and Hui Xiang
    Citation: BMC Genomics 2018 19:215
    Content type: Research article Published on:

  14. Plant biomass is the most abundant carbon source for many fungal species. In the biobased industry fungi, are used to produce lignocellulolytic enzymes to degrade agricultural waste biomass. Here we evaluated ...

    Authors: Claire Khosravi, Evy Battaglia, Roland S. Kun, Sacha Dalhuijsen, Jaap Visser, María Victoria Aguilar-Pontes, Miaomiao Zhou, Heino M. Heyman, Young-Mo Kim, Scott E. Baker and Ronald P. de Vries
    Citation: BMC Genomics 2018 19:214
    Content type: Research Published on:

  15. Perilla frutescens is well known for its high α-linolenic acid (ALA) accumulation in seeds and medicinal values as well as a source of edible and general-purpose oils. However, the regulatory mechanisms of the bi...

    Authors: BingNan Liao, YouJin Hao, JunXing Lu, HuiYang Bai, Li Guan and Tao Zhang
    Citation: BMC Genomics 2018 19:213
    Content type: Research article Published on:

  16. Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Nex...

    Authors: Georgia Giannoukos, Dawn M. Ciulla, Eugenio Marco, Hayat S. Abdulkerim, Luis A. Barrera, Anne Bothmer, Vidya Dhanapal, Sebastian W. Gloskowski, Hariharan Jayaram, Morgan L. Maeder, Maxwell N. Skor, Tongyao Wang, Vic E. Myer and Christopher J. Wilson
    Citation: BMC Genomics 2018 19:212
    Content type: Methodology article Published on:

  17. Haplotype assembly is the task of reconstructing haplotypes of an individual from a mixture of sequenced chromosome fragments. Haplotype information enables studies of the effects of genetic variations on an o...

    Authors: Abolfazl Hashemi, Banghua Zhu and Haris Vikalo
    Citation: BMC Genomics 2018 19(Suppl 4):191
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  18. Genotype-phenotype association has been one of the long-standing problems in bioinformatics. Identifying both the marginal and epistatic effects among genetic markers, such as Single Nucleotide Polymorphisms (...

    Authors: Easton Li Xu, Xiaoning Qian, Qilian Yu, Han Zhang and Shuguang Cui
    Citation: BMC Genomics 2018 19(Suppl 4):170
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  19. Ranaviruses (family Iridoviridae, nucleocytoplasmic large DNA viruses) have been reported as promiscuous pathogens of cold-blooded vertebrates. Rana grylio virus (RGV, a ranavirus), from diseased frog Rana grylio

    Authors: Fei Ke, Jian-Fang Gui, Zhong-Yuan Chen, Tao Li, Cun-Ke Lei, Zi-Hao Wang and Qi-Ya Zhang
    Citation: BMC Genomics 2018 19:211
    Content type: Research article Published on:

  21. Protein lysine malonylation, a newly discovered post-translational modification (PTM), plays an important role in diverse metabolic processes in both eukaryotes and prokaryotes. Common wheat is a major global ...

    Authors: Jiabin Liu, Guangyuan Wang, Qi Lin, Wenxing Liang, Zhiqiang Gao, Ping Mu, Guiquan Li and Limin Song
    Citation: BMC Genomics 2018 19:209
    Content type: Research article Published on:

  22. Measures to improve bird performance have been sought due to the imminent phase out of in-feed antibiotics in poultry and continued demand for higher poultry feeding efficiency. Increasing grain particle size ...

    Authors: Sarbast K. Kheravii, Robert A. Swick, Mingan Choct and Shu-Biao Wu
    Citation: BMC Genomics 2018 19:208
    Content type: Research article Published on:

  23. In monogastric animals, phosphorus (P) homeostasis is maintained by regulating intestinal absorption, bone mobilization, and renal excretion. Since P is a non-renewable resource, a shortage is imminent due to ...

    Authors: Franziska Just, Michael Oster, Kirsten Büsing, Luisa Borgelt, Eduard Murani, Siriluck Ponsuksili, Petra Wolf and Klaus Wimmers
    Citation: BMC Genomics 2018 19:207
    Content type: Research article Published on:

  24. The developmental gene regulatory network (GRN) that underlies skeletogenesis in sea urchins and other echinoderms is a paradigm of GRN structure, function, and evolution. This transcriptional network is deplo...

    Authors: Tanvi Shashikant, Jian Ming Khor and Charles A. Ettensohn
    Citation: BMC Genomics 2018 19:206
    Content type: Research article Published on:

  25. Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated t...

    Authors: Ewelina Stefanovic and Olivia McAuliffe
    Citation: BMC Genomics 2018 19:205
    Content type: Research article Published on:

  26. Human herpesvirus-6A and -6B (HHV-6) are betaherpesviruses that reach > 90% seroprevalence in the adult population. Unique among human herpesviruses, HHV-6 can integrate into the subtelomeric regions of human ...

    Authors: Alexander L. Greninger, Giselle M. Knudsen, Pavitra Roychoudhury, Derek J. Hanson, Ruth Hall Sedlak, Hong Xie, Jon Guan, Thuy Nguyen, Vikas Peddu, Michael Boeckh, Meei-Li Huang, Linda Cook, Daniel P. Depledge, Danielle M. Zerr, David M. Koelle, Soren Gantt…
    Citation: BMC Genomics 2018 19:204
    Content type: Research article Published on:

  28. White striping (WS) is an emerging muscular defect occurring on breast and thigh muscles of broiler chickens. It is characterized by the presence of white striations parallel to the muscle fibers and has signi...

    Authors: Eva Pampouille, Cécile Berri, Simon Boitard, Christelle Hennequet-Antier, Stéphane A. Beauclercq, Estelle Godet, Christophe Praud, Yves Jégo and Elisabeth Le Bihan-Duval
    Citation: BMC Genomics 2018 19:202
    Content type: Research article Published on:

  29. The anthocyanins are highly enriched in eggplants (Solanum melongena L.) with purple peel. However, our previous study showed that anthocyanins biosynthesis in eggplant cultivar ‘Lanshan Hexian’ was completely re...

    Authors: Jing Li, Yong-Jun He, Lu Zhou, Yang Liu, Mingmin Jiang, Li Ren and Huoying Chen
    Citation: BMC Genomics 2018 19:201
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:324

  30. Black Aspergilli represent one of the most important fungal resources of primary and secondary metabolites for biotechnological industry. Having several black Aspergilli sequenced genomes should allow targetin...

    Authors: Elodie Choque, Christophe Klopp, Sophie Valiere, José Raynal and Florence Mathieu
    Citation: BMC Genomics 2018 19:200
    Content type: Research article Published on:

  31. Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires ei...

    Authors: Zachary T. Herbert, Jamie P. Kershner, Vincent L. Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O. Alekseyev, Jun Fan, Jessica W. Podnar, Edward Wilcox, Jenny Gipson, Allison Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc…
    Citation: BMC Genomics 2018 19:199
    Content type: Methodology article Published on:

  32. Omics profiling is now a routine component of biomedical studies. In the analysis of omics data, clustering is an essential step and serves multiple purposes including for example revealing the unknown functio...

    Authors: Sebastian J. Teran Hidalgo and Shuangge Ma
    Citation: BMC Genomics 2018 19:198
    Content type: Methodology article Published on:

  33. Aneuploidy, or abnormal chromosome numbers, severely alters cell physiology and is widespread in cancers and other pathologies. Using model cell lines engineered to carry one or more extra chromosomes, it has ...

    Authors: Milena Dürrbaum, Christine Kruse, K. Julia Nieken, Bianca Habermann and Zuzana Storchová
    Citation: BMC Genomics 2018 19:197
    Content type: Research article Published on:

  34. Bulbs of the ornamental flower Lilium pumilum enter a period of dormancy after flowering in spring, and require exposure to cold for a period of time in order to release dormancy. Previous studies focused mainly ...

    Authors: Wang Wang, Xiaoxia Su, Zhongping Tian, Yu Liu, Yunwei Zhou and Miao He
    Citation: BMC Genomics 2018 19:196
    Content type: Research article Published on:

  35. Understanding variation in genome structure is essential to understand phenotypic differences within populations and the evolutionary history of species. A promising form of this structural variation is copy n...

    Authors: Vinicius H. da Silva, Veronika N. Laine, Mirte Bosse, Kees van Oers, Bert Dibbits, Marcel E. Visser, Richard P. M. A. Crooijmans and Martien A. M. Groenen
    Citation: BMC Genomics 2018 19:195
    Content type: Research article Published on:

  36. The murine discs large homolog 2 (DLG2; post synaptic density 93 (PSD-93); Chapsyn-110) is a member of the membrane-associated guanylate kinase (MAGUK) protein family involved in receptor assembly and associat...

    Authors: Shafaqat Ali, Alexander Hoven, Regine J. Dress, Heiner Schaal, Judith Alferink and Stefanie Scheu
    Citation: BMC Genomics 2018 19:194
    Content type: Research article Published on:

  37. SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, le...

    Authors: Qin Zhou, Sisi Zhang, Feng Chen, Baojun Liu, Lan Wu, Fei Li, Jiaqi Zhang, Manzhu Bao and Guofeng Liu
    Citation: BMC Genomics 2018 19:193
    Content type: Research article Published on:

  38. Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture fish species and cause high lethality and economic loss. Current methods of controlling ...

    Authors: Ruanni Chen, Yong Mao, Jun Wang, Min Liu, Ying Qiao, Libing Zheng, Yongquan Su, Qiaozhen Ke and Weiqiang Zheng
    Citation: BMC Genomics 2018 19:192
    Content type: Research article Published on:

  39. Bamboo is an important member of the family Poaceae and has many inflorescence and flowering features rarely observed in other plant groups. It retains an unusual form of perennialism by having a long vegetati...

    Authors: Smritikana Dutta, Prasun Biswas, Sukanya Chakraborty, Devrani Mitra, Amita Pal and Malay Das
    Citation: BMC Genomics 2018 19:190
    Content type: Research article Published on:

  40. Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. ...

    Authors: Geromy G. Moore, Brian M. Mack, Shannon B. Beltz and Olivier Puel
    Citation: BMC Genomics 2018 19:189
    Content type: Research article Published on:

  41. Noninvasive biomarkers are urgently needed for patients with nonalcoholic steatohepatitis (NASH) to assist in diagnosis, monitoring disease progression and assessing treatment response. Recently several explor...

    Authors: Jie Liu, Yue Xiao, Xikun Wu, Lichun Jiang, Shurong Yang, Zhiming Ding, Zhuo Fang, Haiqing Hua, Mark Stephen Kirby and Jianyong Shou
    Citation: BMC Genomics 2018 19:188
    Content type: Research article Published on:

  42. Because the cost of cereals is unstable and represents a large part of production charges for meat-type chicken, there is an urge to formulate alternative diets from more cost-effective feedstuff. We have rece...

    Authors: C. Desert, E. Baéza, M. Aite, M. Boutin, A. Le Cam, J. Montfort, M. Houee-Bigot, Y. Blum, P. F. Roux, C. Hennequet-Antier, C. Berri, S. Metayer-Coustard, A. Collin, S. Allais, E. Le Bihan, D. Causeur…
    Citation: BMC Genomics 2018 19:187
    Content type: Research article Published on:

  43. The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are fou...

    Authors: Kai K. Lie, Ole K. Tørresen, Monica Hongrø Solbakken, Ivar Rønnestad, Ave Tooming-Klunderud, Alexander J. Nederbragt, Sissel Jentoft and Øystein Sæle
    Citation: BMC Genomics 2018 19:186
    Content type: Research article Published on:

  44. Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover...

    Authors: Yuanting Jin, Yubin Wo, Haojie Tong, Sen Song, Lixun Zhang and Richard P. Brown
    Citation: BMC Genomics 2018 19:185
    Content type: Research article Published on:

  45. Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming seque...

    Authors: Viktor Tokan, Janka Puterova, Matej Lexa and Eduard Kejnovsky
    Citation: BMC Genomics 2018 19:184
    Content type: Research article Published on:

  46. The generation of induced pluripotent stem cells (iPSCs) has underdefined mechanisms. In addition, leukemia inhibitory factor (LIF) activated Janus kinase/signal transducer and activator of transcription 3 (JA...

    Authors: Ling Wang, Zongliang Jiang, Delun Huang, Jingyue Duan, Chang Huang, Shannon Sullivan, Kaneha Vali, Yexuan Yin, Ming Zhang, Jill Wegrzyn, Xiuchun ( Cindy) Tian and Young Tang
    Citation: BMC Genomics 2018 19:183
    Content type: Research article Published on:

  47. The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of who...

    Authors: Casey L. Dagnall, Lindsay M. Morton, Belynda D. Hicks, Shengchao Li, Weiyin Zhou, Eric Karlins, Kedest Teshome, Salma Chowdhury, Kerrie S. Lashley, Joshua N. Sampson, Leslie L. Robison, Gregory T. Armstrong, Smita Bhatia, Gretchen A. Radloff, Stella M. Davies, Margaret A. Tucker…
    Citation: BMC Genomics 2018 19:182
    Content type: Methodology article Published on:

  48. Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. H...

    Authors: Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Sougat Misra, Carsten O. Daub, Juha Kere and Peter Swoboda
    Citation: BMC Genomics 2018 19:181
    Content type: Research article Published on:

  49. The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measuremen...

    Authors: P. Scott Pine, Steven P. Lund, Jerod R. Parsons, Lindsay K. Vang, Ashish A. Mahabal, Luca Cinquini, Sean C. Kelly, Heather Kincaid, Daniel J. Crichton, Avrum Spira, Gang Liu, Adam C. Gower, Harvey I. Pass, Chandra Goparaju, Steven M. Dubinett, Kostyantyn Krysan…
    Citation: BMC Genomics 2018 19:180
    Content type: Methodology article Published on:

  50. The mitogen-activated protein kinase (MAPK) family is involved in signal transduction networks that underpin many different biological processes in plants, ranging from development to biotic and abiotic stress...

    Authors: Ravinder K. Goyal, Dan Tulpan, Nora Chomistek, Dianevys González-Peña Fundora, Connor West, Brian E. Ellis, Michele Frick, André Laroche and Nora A. Foroud
    Citation: BMC Genomics 2018 19:178
    Content type: Research article Published on:

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BMC Genomics

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