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  1. Content type: Research article

    In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein,...

    Authors: Moyang Liu, Yongdi Wen, Wenjun Sun, Zhaotang Ma, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2019 20:483

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  2. Content type: Research article

    Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To ...

    Authors: Paul I. Otyama, Andrew Wilkey, Roshan Kulkarni, Teshale Assefa, Ye Chu, Josh Clevenger, Dan J. O’Connor, Graeme C. Wright, Stanley W. Dezern, Gregory E. MacDonald, Noelle L. Anglin, Ethalinda K. S. Cannon, Peggy Ozias-Akins and Steven B. Cannon

    Citation: BMC Genomics 2019 20:481

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  3. Content type: Research article

    Plasmids play an vital role in driving the rapid global spread of antimicrobial resistance and adaptation to changing ambient conditions. It has been suggested that the presence of plasmids can pose tremendous...

    Authors: Dan Long, Lan-lan Zhu, Fang-ling Du, Tian-xin Xiang, La-Gen Wan, Dan-dan Wei, Wei Zhang and Yang Liu

    Citation: BMC Genomics 2019 20:480

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  4. Content type: Research article

    Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and...

    Authors: Huyen-Trang Tran, Hao-Chu Wang, Tsai-Wen Hsu, Rakesh Sarkar, Chao-Li Huang and Tzen-Yuh Chiang

    Citation: BMC Genomics 2019 20:478

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  5. Content type: Research article

    Global RNA sequencing technologies have revealed widespread RNA polymerase II (Pol II) transcription outside of gene promoters. Small 5′-capped RNA sequencing (Start-seq) originally developed for the detection...

    Authors: Adam Scheidegger, Carissa J. Dunn, Ann Samarakkody, Nii Koney-Kwaku Koney, Danielle Perley, Ramendra N. Saha and Sergei Nechaev

    Citation: BMC Genomics 2019 20:477

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  6. Content type: Research article

    Extracellular vesicles (EVs) are small membrane vesicles secreted by the cells that mediate intercellular transfer of molecules and contribute to transduction of various signals. Viral infection and action of ...

    Authors: Andrii Slonchak, Brian Clarke, Jason Mackenzie, Alberto Anastacio Amarilla, Yin Xiang Setoh and Alexander A. Khromykh

    Citation: BMC Genomics 2019 20:474

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  7. Content type: Research article

    Reliable indicators for the onset of flowering are not available for most perennial monocarpic species, representing a drawback for crops such as bamboo, agave and banana. The ability to predict and control th...

    Authors: Emmanuel Avila de Dios, Luis Delaye and June Simpson

    Citation: BMC Genomics 2019 20:473

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  8. Content type: Research article

    Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from ...

    Authors: Sushil Raj Subedi, Nitika Sandhu, Vikas Kumar Singh, Pallavi Sinha, Santosh Kumar, S. P. Singh, Surya Kant Ghimire, Madhav Pandey, Ram Baran Yadaw, Rajeev K. Varshney and Arvind Kumar

    Citation: BMC Genomics 2019 20:471

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  9. Content type: Research article

    A critical goal in biology is to relate the phenotype to the genotype, that is, to find the genetic determinants of various traits. However, while simple monofactorial determinants are relatively easy to ident...

    Authors: George S. Long, Mohammed Hussen, Jonathan Dench and Stéphane Aris-Brosou

    Citation: BMC Genomics 2019 20:470

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  10. Content type: Research article

    The pearl oyster Pinctada fucata martensii (Pfu.), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of a...

    Authors: Meng Xu, Jing Huang, Yu Shi, Hua Zhang and Maoxian He

    Citation: BMC Genomics 2019 20:469

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  11. Content type: Research article

    The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly ...

    Authors: J. Blommaert, S. Riss, B. Hecox-Lea, D. B. Mark Welch and C. P. Stelzer

    Citation: BMC Genomics 2019 20:466

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  12. Content type: Research article

    The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. A...

    Authors: Guilherme C. Baião, Daniela I. Schneider, Wolfgang J. Miller and Lisa Klasson

    Citation: BMC Genomics 2019 20:465

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  13. Content type: Research article

    The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese juj...

    Authors: Chaoling Xue, Hongtai Li, Zhiguo Liu, Lili Wang, Yitong Zhao, Ximeng Wei, Hu Fang, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2019 20:464

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  14. Content type: Research article

    The diamondback moth (DBM), Plutella xylostella (L.), is a major pest of cruciferous crops worldwide. While the species has become a model for genomics, post-transcriptional mechanisms associated with development...

    Authors: Qian Zhao, Weimin Zhong, Weiyi He, Yiying Li, Yaqing Li, Tianpu Li, Liette Vasseur and Minsheng You

    Citation: BMC Genomics 2019 20:463

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  15. Content type: Research article

    Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especiall...

    Authors: Marius Bredon, Benjamin Herran, Baptiste Lheraud, Joanne Bertaux, Pierre Grève, Bouziane Moumen and Didier Bouchon

    Citation: BMC Genomics 2019 20:462

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  16. Content type: Research article

    The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle of pigs divergen...

    Authors: Stafford Vigors, John V. O’Doherty, Kenneth Bryan and Torres Sweeney

    Citation: BMC Genomics 2019 20:461

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  17. Content type: Research article

    Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many s...

    Authors: Alexander Capraro, Denis O’Meally, Shafagh A. Waters, Hardip R. Patel, Arthur Georges and Paul D. Waters

    Citation: BMC Genomics 2019 20:460

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  18. Content type: Research article

    The most widely used human genome reference assembly hg19 harbors minor alleles at 2.18 million positions as revealed by 1000 Genome Phase 3 dataset. Although this is less than 2% of the 89 million variants re...

    Authors: Harsh G. Shukla, Pushpinder Singh Bawa and Subhashini Srinivasan

    Citation: BMC Genomics 2019 20:459

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  19. Content type: Research article

    Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an economically important fruit tree characterized by its juicy fruits rich in antioxidant compounds. Elucidating the genetic basis of the biosynthesis of active a...

    Authors: Haiying Ren, Haiyan Yu, Shuwen Zhang, Senmiao Liang, Xiliang Zheng, Shujian Zhang, Pu Yao, Hongkun Zheng and Xingjiang Qi

    Citation: BMC Genomics 2019 20:458

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  20. Content type: Research article

    Ricinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis...

    Authors: Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xingchu Yan and Xinxin Geng

    Citation: BMC Genomics 2019 20:456

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  21. Content type: Research

    Closing gaps in draft genomes is an important post processing step in genome assembly. It leads to more complete genomes, which benefits downstream genome analysis such as annotation and genotyping. Several to...

    Authors: Chong Chu, Xin Li and Yufeng Wu

    Citation: BMC Genomics 2019 20(Suppl 5):426

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    This article is part of a Supplement: Volume 20 Supplement 5

  22. Content type: Research

    A popular strategy to study alternative splicing in non-model organisms starts from sequencing the entire transcriptome, then assembling the reads by using de novo transcriptome assembly algorithms to obtain p...

    Authors: Shuhua Fu, Peter L. Chang, Maren L. Friesen, Natasha L. Teakle, Aaron M. Tarone and Sing-Hoi Sze

    Citation: BMC Genomics 2019 20(Suppl 5):425

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    This article is part of a Supplement: Volume 20 Supplement 5

  23. Content type: Research

    Motifs are crucial patterns that have numerous applications including the identification of transcription factors and their binding sites, composite regulatory patterns, similarity between families of proteins...

    Authors: Peng Xiao, Martin Schiller and Sanguthevar Rajasekaran

    Citation: BMC Genomics 2019 20(Suppl 5):424

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    This article is part of a Supplement: Volume 20 Supplement 5

  24. Content type: Research

    High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many e...

    Authors: Nathan LaPierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C. Wu, David Koslicki and Eleazar Eskin

    Citation: BMC Genomics 2019 20(Suppl 5):423

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    This article is part of a Supplement: Volume 20 Supplement 5

  25. Content type: Research

    Ribo-seq is a popular technique for studying translation and its regulation. A Ribo-seq experiment produces a snap-shot of the location and abundance of actively translating ribosomes within a cell’s transcrip...

    Authors: Patrick Perkins, Serina Mazzoni-Putman, Anna Stepanova, Jose Alonso and Steffen Heber

    Citation: BMC Genomics 2019 20(Suppl 5):422

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    This article is part of a Supplement: Volume 20 Supplement 5

  26. Content type: Research article

    Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. An improved understanding of the genetic diversity of C. b...

    Authors: Claudia M. Hemsley, Paul A. O’Neill, Angela Essex-Lopresti, Isobel H. Norville, Tim P. Atkins and Richard W. Titball

    Citation: BMC Genomics 2019 20:441

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  27. Content type: Research article

    Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg., which is nat...

    Authors: Camila Campos Mantello, Lucas Boatwright, Carla Cristina da Silva, Erivaldo Jose Scaloppi Jr, Paulo de Souza Goncalves, W. Brad Barbazuk and Anete Pereira de Souza

    Citation: BMC Genomics 2019 20:455

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  28. Content type: Research article

    Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes in diseases such as cancer, although the functions of most remain poorly understood. To address this, here we apply a nov...

    Authors: Kevin Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, Daniel W. Lambert, Stephen Brown and James R. Bradford

    Citation: BMC Genomics 2019 20:454

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  29. Content type: Research article

    Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted...

    Authors: Belinda Wright, Katherine A. Farquharson, Elspeth A. McLennan, Katherine Belov, Carolyn J. Hogg and Catherine E. Grueber

    Citation: BMC Genomics 2019 20:453

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  30. Content type: Research article

    Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification ag...

    Authors: A. C. Picornell, I. Echavarria, E. Alvarez, S. López-Tarruella, Y. Jerez, K. Hoadley, J. S. Parker, M. del Monte-Millán, R. Ramos-Medina, J. Gayarre, I. Ocaña, M. Cebollero, T. Massarrah, F. Moreno, J. A. García Saenz, H. Gómez Moreno…

    Citation: BMC Genomics 2019 20:452

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  31. Content type: Research article

    Herpetospermum pedunculosum (Ser.) Baill is annual scandent herbs. They are used in the treatment of piles, inflammation of the stomach and the intestines. It can survive the extreme environment of the Tibetan Pl...

    Authors: Yong Zhao, Fuling Xu, Jia Liu, Fachun Guan, Hong Quan and Fanjuan Meng

    Citation: BMC Genomics 2019 20:451

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  32. Content type: Research article

    Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be ident...

    Authors: Octávio Augusto Costa Almeida, Gabriel Costa Monteiro Moreira, Fernanda Marcondes Rezende, Clarissa Boschiero, Jane de Oliveira Peixoto, Adriana Mercia Guaratini Ibelli, Mônica Corrêa Ledur, Francisco José de Novais and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2019 20:449

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  33. Content type: Research article

    The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although a...

    Authors: Maria José Gonzalo, Aurora Díaz, Narinder P. S. Dhillon, Umesh K. Reddy, Belén Picó and Antonio J. Monforte

    Citation: BMC Genomics 2019 20:448

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  34. Content type: Research article

    Under caged conditions, birds are affected more severely by environmental stressors such as dietary structure, activity space, human disturbances, and pathogens, which may be reflected in the gene expression i...

    Authors: Yu Wang, Jinxin Guo, Lin Wang, Hengjiu Tian and Jinling Sui

    Citation: BMC Genomics 2019 20:447

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  35. Content type: Research article

    Circulating microRNAs (miRNAs) are attractive non-invasive biomarkers for a variety of conditions due to their stability and altered pathophysiological expression levels. Reliable detection of global expressio...

    Authors: Ryan K.Y. Wong, Meabh MacMahon, Jayne V. Woodside and David A. Simpson

    Citation: BMC Genomics 2019 20:446

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  36. Content type: Methodology article

    Directed DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relat...

    Authors: Zach K. O’Brown, Konstantinos Boulias, Jie Wang, Simon Yuan Wang, Natasha M. O’Brown, Ziyang Hao, Hiroki Shibuya, Paul-Enguerrand Fady, Yang Shi, Chuan He, Sean G. Megason, Tao Liu and Eric L. Greer

    Citation: BMC Genomics 2019 20:445

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  37. Content type: Research article

    Host genetic backgrounds affect gene functions. The genetic backgrounds of genetically engineered organisms must be identified to confirm their genetic backgrounds identity with those of recipients. Marker-ass...

    Authors: Tiantian Li, Zhiwei Fang, Hai Peng, Junfei Zhou, Pengcheng Liu, Yanyan Wang, Wenhui Zhu, Lun Li, Quanfang Zhang, Lihong Chen, Lili Li, Zhihao Liu, Weixiong Zhang, Wenxue Zhai, Long Lu and Lifen Gao

    Citation: BMC Genomics 2019 20:444

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  38. Content type: Database

    Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred g...

    Authors: Qingchun Pan, Junfeng Wei, Feng Guo, Suiyong Huang, Yong Gong, Hao Liu, Jianxiao Liu and Lin Li

    Citation: BMC Genomics 2019 20:443

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  39. Content type: Research article

    Alternative splicing (AS) is a regulatory mechanism used to create many forms of mature messengers RNAs (mRNAs) from the same gene. Sequencing of RNA (RNA-Seq) is an advanced technology, which has been utilized b...

    Authors: Vishwas Sharma, Amrita Nandan, Harpreet Singh, Suyash Agarwal, Richa Tripathi, Dhirendra Narain Sinha and Ravi Mehrotra

    Citation: BMC Genomics 2019 20:442

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  40. Content type: Research article

    Cytochrome P450-dependent monooxygenases (P450s), constituting one of the largest and oldest gene superfamilies found in many organisms from bacteria to humans, play a vital role in the detoxification and inac...

    Authors: Binu Antony, Jibin Johny, Mahmoud M. Abdelazim, Jernej Jakše, Mohammed Ali Al-Saleh and Arnab Pain

    Citation: BMC Genomics 2019 20:440

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  41. Content type: Research article

    Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environm...

    Authors: Xian Zhang, Xueduan Liu, Liangzhi Li, Guanyun Wei, Danli Zhang, Yili Liang and Bo Miao

    Citation: BMC Genomics 2019 20:438

    Published on:

  42. Content type: Research article

    For spring-type Chinese cabbage production, premature bolting refers to the excessive elongation of dwarf stems before harvesting. Although quantitative trait loci (QTL) mapping for bolting-related traits have...

    Authors: Shuantao Liu, Ronghua Wang, Zhigang Zhang, Qiaoyun Li, Lihua Wang, Yongqiang Wang and Zhizhong Zhao

    Citation: BMC Genomics 2019 20:437

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  43. Content type: Research article

    Bacillus cereus sensu lato s.l.) is a group of bacteria displaying close phylogenetic relationships but a high ecological diversity. The three most studied species are Bacillus anthracis, Bacillus cereus sensu st...

    Authors: Nancy Fayad, Mireille Kallassy Awad and Jacques Mahillon

    Citation: BMC Genomics 2019 20:436

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  44. Content type: Correction

    He authors reported that one of the authors’ names was typeset incorrectly in the authorship list.

    Authors: Camus Nimmo, Liam P. Shaw, Ronan Doyle, Rachel Williams, Kayleen Brien, Carrie Burgess, Judith Breuer, Francois Balloux and Alexander S. Pym

    Citation: BMC Genomics 2019 20:433

    Published on:

    The original article was published in BMC Genomics 2019 20:389

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