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  1. Gill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoeba Neoparamoeba perurans, is a frequent cause of morbidity. In the abs...

    Authors: Diego Robledo, Alastair Hamilton, Alejandro P. Gutiérrez, James E. Bron and Ross D. Houston
    Citation: BMC Genomics 2020 21:271
    Content type: Research article Published on:

  2. The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes – protists were reported. Giardia lamblia, a protist with ...

    Authors: Jin-Mei Feng, Chun-Lin Yang, Hai-Feng Tian, Jiang-Xin Wang and Jian-Fan Wen
    Citation: BMC Genomics 2020 21:269
    Content type: Research article Published on:

  3. Marine endophytic fungi (MEF) are good sources of structurally unique and biologically active secondary metabolites. Due to the increase in antimicrobial resistance, the secondary metabolites from MEF ought to...

    Authors: Ethel Juliet Blessie, Wasco Wruck, Benaiah Annertey Abbey, Audrey Ncube, Nina Graffmann, Vincent Amarh, Patrick Kobina Arthur and James Adjaye
    Citation: BMC Genomics 2020 21:265
    Content type: Research article Published on:

  4. Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and...

    Authors: Tong Wang, Jingjing Hu, Xiao Ma, Chunjin Li, Qihang Yang, Shuyan Feng, Miaomiao Li, Nan Li and Xiaoming Song
    Citation: BMC Genomics 2020 21:264
    Content type: Research article Published on:

  5. Emergence of antibiotic resistance is a global public health concern. The relationships between antibiotic use, the gut community composition, normal physiology and metabolism, and individual and public health...

    Authors: Lei Xu, Anil Surathu, Isaac Raplee, Ashok Chockalingam, Sharron Stewart, Lacey Walker, Leonard Sacks, Vikram Patel, Zhihua Li and Rodney Rouse
    Citation: BMC Genomics 2020 21:263
    Content type: Research article Published on:

  6. The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on th...

    Authors: Anthony Bayega, Haig Djambazian, Konstantina T. Tsoumani, Maria-Eleni Gregoriou, Efthimia Sagri, Eleni Drosopoulou, Penelope Mavragani-Tsipidou, Kristina Giorda, George Tsiamis, Kostas Bourtzis, Spyridon Oikonomopoulos, Ken Dewar, Deanna M. Church, Alexie Papanicolaou, Kostas D. Mathiopoulos and Jiannis Ragoussis
    Citation: BMC Genomics 2020 21:259
    Content type: Research article Published on:

  7. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a highly diverse group of secondary metabolites (SM) of bacterial and fungal origin. While RiPPs have been intensively studied in ...

    Authors: Gabriel A. Vignolle, Robert L. Mach, Astrid R. Mach-Aigner and Christian Derntl
    Citation: BMC Genomics 2020 21:258
    Content type: Methodology article Published on:

  8. The Brazilian endemic clone Pseudomonas aeruginosa ST277 carries important antibiotic resistance determinants, highlighting the gene coding for SPM-1 carbapenemase. However, the resistance and persistence of this...

    Authors: Melise Chaves Silveira, Cláudio Marcos Rocha-de-Souza, Rodolpho Mattos Albano, Ivson Cassiano de Oliveira Santos and Ana Paula D’Alincourt Carvalho-Assef
    Citation: BMC Genomics 2020 21:255
    Content type: Research article Published on:

  9. The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental period...

    Authors: Zhibin Ji, Tianle Chao, Zhaohua Liu, Lei Hou, Jin Wang, Aili Wang, Jie Zhou, Rong Xuan, Guizhi Wang and Jianmin Wang
    Citation: BMC Genomics 2020 21:254
    Content type: Research article Published on:

  11. The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to ...

    Authors: Andrew S. Lang, Suzanne H. Austin, Rayna M. Harris, Rebecca M. Calisi and Matthew D. MacManes
    Citation: BMC Genomics 2020 21:251
    Content type: Research article Published on:

  12. The Mi-1 gene was the first identified and cloned gene that provides resistance to root-knot nematodes (RKNs) in cultivated tomato. However, owing to its temperature sensitivity, this gene does not meet the need ...

    Authors: Chong Du, Jingbin Jiang, He Zhang, Tingting Zhao, Huanhuan Yang, Dongye Zhang, Zhentong Zhao, Xiangyang Xu and Jingfu Li
    Citation: BMC Genomics 2020 21:250
    Content type: Research article Published on:

  14. The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic re...

    Authors: Saidi R. Achari, Jatinder Kaur, Quang Dinh, Ross Mann, Tim Sawbridge, Brett A. Summerell and Jacqueline Edwards
    Citation: BMC Genomics 2020 21:248
    Content type: Research article Published on:

  15. The stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), threats world wheat production. Resistance to Pst is often overcome by pathogen virulence changes, but the mechanisms of variation are not clea...

    Authors: Yuxiang Li, Chongjing Xia, Meinan Wang, Chuntao Yin and Xianming Chen
    Citation: BMC Genomics 2020 21:247
    Content type: Research article Published on:

  16. Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome no...

    Authors: Sayaka Tanaka, Kentaro Yoshida, Kazuhiro Sato and Shigeo Takumi
    Citation: BMC Genomics 2020 21:246
    Content type: Research article Published on:

  17. Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular bree...

    Authors: Wei Shi, Shao-Lu Zhao, Kai Liu, Yi-Biao Sun, Zheng-Bin Ni, Gui-Yun Zhang, Hong-Sheng Tang, Jing-Wen Zhu, Bai-Jie Wan, Hong-Qin Sun, Jin-Ying Dai, Ming-Fa Sun, Guo-Hong Yan, Ai-Min Wang and Guo-Yong Zhu
    Citation: BMC Genomics 2020 21:245
    Content type: Research article Published on:

  18. Conogethes pinicolalis (Lepidoptera: Crambidae), is similar to Conogethes punctiferalis (yellow peach moth) and its host plant is gymnosperms, especially for masson pine. So far, less literature was reported on t...

    Authors: Dapeng Jing, Tiantao Zhang, Shuxiong Bai, Kanglai He, Sivaprasath Prabu, Junbo Luan and Zhenying Wang
    Citation: BMC Genomics 2020 21:244
    Content type: Research article Published on:

  19. The fall webworm Hyphantria cunea is an invasive and polyphagous defoliator pest that feeds on nearly any type of deciduous tree worldwide. The silk web of H. cunea aids its aggregating behavior, provides thermal...

    Authors: Qi Chen, Hanbo Zhao, Ming Wen, Jiaxin Li, Haifeng Zhou, Jiatong Wang, Yuxin Zhou, Yulin Liu, Lixin Du, Hui Kang, Jian Zhang, Rui Cao, Xiaoming Xu, Jing-Jiang Zhou, Bingzhong Ren and Yinliang Wang
    Citation: BMC Genomics 2020 21:242
    Content type: Research article Published on:

  20. Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, ...

    Authors: Maria Luisa Martin Cerezo, Marek Kucka, Karol Zub, Yingguang Frank Chan and Jarosław Bryk
    Citation: BMC Genomics 2020 21:241
    Content type: Research Article Published on:

  21. Barnacles are specialized marine organisms that differ from other crustaceans in possession of a calcareous shell, which is attached to submerged surfaces. Barnacles have a wide distribution, mostly in the int...

    Authors: Zhibin Gan, Jianbo Yuan, Xinming Liu, Dong Dong, Fuhua Li and Xinzheng Li
    Citation: BMC Genomics 2020 21:240
    Content type: Research article Published on:

  22. Identifying nuclease-induced double-stranded breaks in DNA on a genome-wide scale is critical for assessing the safety and efficacy of genome editing therapies. We previously demonstrated that after administer...

    Authors: Camilo Breton, Peter M. Clark, Lili Wang, Jenny A. Greig and James M. Wilson
    Citation: BMC Genomics 2020 21:239
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Genomics 2020 21:810

  23. Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new varieties of glyphosate-tolerant crops is a research focus of seed companies and researchers. The glyphosate...

    Authors: Rongrong Zhai, Shenghai Ye, Guofu Zhu, Yanting Lu, Jing Ye, Faming Yu, Qiren Chu and Xiaoming Zhang
    Citation: BMC Genomics 2020 21:238
    Content type: Research article Published on:

  24. Plant genomes are rich in repetitive sequences, and transposable elements (TEs) are the most accumulated of them. This mobile fraction can be distinguished as Class I (retrotransposons) and Class II (transposo...

    Authors: Rafael de Assis, Viviane Yumi Baba, Leonardo Adabo Cintra, Leandro Simões Azeredo Gonçalves, Rosana Rodrigues and André Luís Laforga Vanzela
    Citation: BMC Genomics 2020 21:237
    Content type: Research article Published on:

  26. Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the...

    Authors: Xiao-Yong Zhang, Jie-Ya Qiu, Qiu-Ling Hui, Yuan-Yuan Xu, Yi-Zhong He, Liang-Zhi Peng and Xing-Zheng Fu
    Citation: BMC Genomics 2020 21:233
    Content type: Research article Published on:

  27. Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, dev...

    Authors: Hui Xia, Shunwu Yu, Deyan Kong, Jie Xiong, Xiaosong Ma, Liang Chen and Lijun Luo
    Citation: BMC Genomics 2020 21:232
    Content type: Research article Published on:

  28. Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF...

    Authors: Jeky Chanwala, Suresh Satpati, Anshuman Dixit, Ajay Parida, Mrunmay Kumar Giri and Nrisingha Dey
    Citation: BMC Genomics 2020 21:231
    Content type: Research article Published on:

  29. DNA sequencing is at the core of many molecular biology laboratories. Despite its long history, there is a lack of user-friendly Sanger sequencing data analysis tools that can be run interactively as a web app...

    Authors: Tobias Rausch, Markus Hsi-Yang Fritz, Andreas Untergasser and Vladimir Benes
    Citation: BMC Genomics 2020 21:230
    Content type: Software Published on:

  30. Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals.

    Authors: Tinghua Huang, Min Yang, Kaihui Dong, Mingjiang Xu, Jinhui Liu, Zhi Chen, Shijia Zhu, Wang Chen, Jun Yin, Kai Jin, Yu Deng, Zhou Guan, Xiali Huang, Jun Yang, Rongxun Han and Min Yao
    Citation: BMC Genomics 2020 21:229
    Content type: Research article Published on:

  31. Quantitative red blood cell (RBC) traits are highly polygenic clinically relevant traits, with approximately 500 reported GWAS loci. The majority of RBC trait GWAS have been performed in European- or East Asia...

    Authors: Chani J. Hodonsky, Antoine R. Baldassari, Stephanie A. Bien, Laura M. Raffield, Heather M. Highland, Colleen M. Sitlani, Genevieve L. Wojcik, Ran Tao, Marielisa Graff, Weihong Tang, Bharat Thyagarajan, Steve Buyske, Myriam Fornage, Lucia A. Hindorff, Yun Li, Danyu Lin…
    Citation: BMC Genomics 2020 21:228
    Content type: Research article Published on:

  32. Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in hum...

    Authors: Michael E. Sparks, Raman Bansal, Joshua B. Benoit, Michael B. Blackburn, Hsu Chao, Mengyao Chen, Sammy Cheng, Christopher Childers, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Elena N. Elpidina, David W. Farrow, Markus Friedrich, Richard A. Gibbs, Brantley Hall…
    Citation: BMC Genomics 2020 21:227
    Content type: Research article Published on:

  33. Cope’s gray treefrog, Dryophytes chrysoscelis, withstands the physiological challenges of corporeal freezing, partly by accumulating cryoprotective compounds of hepatic origin, including glycerol, urea, and gluco...

    Authors: M. Clara F. do Amaral, James Frisbie, Raphael J. Crum, David L. Goldstein and Carissa M. Krane
    Citation: BMC Genomics 2020 21:226
    Content type: Research article Published on:

  34. Hi-C is a molecular biology technique to understand the genome spatial structure. However, data obtained from Hi-C experiments is biased. Therefore, several methods have been developed to model Hi-C data and i...

    Authors: Saman Khakmardan, Mohsen Rezvani, Ali Akbar Pouyan, Mansoor Fateh and Hamid Alinejad-Rokny
    Citation: BMC Genomics 2020 21:225
    Content type: Software Published on:

  35. The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene...

    Authors: Huan Li, Shiyao Zhang, Wenxiang Zhang, Siyu Chen, Anjara Rabearivony, Yujie Shi, Jie Liu, Christopher J. Corton and Chang Liu
    Citation: BMC Genomics 2020 21:224
    Content type: Research article Published on:

  36. Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could...

    Authors: Svein-Ole Mikalsen, Marni Tausen and Sunnvør í Kongsstovu
    Citation: BMC Genomics 2020 21:223
    Content type: Research article Published on:

  37. The creation of arrays of yeast strains each encoding a different protein with constant tags is a powerful method for understanding how genes and their proteins control cell function. As genetic tools become m...

    Authors: Lisa K. Berry, Grace Heredge Thomas and Peter H. Thorpe
    Citation: BMC Genomics 2020 21:221
    Content type: Methodology article Published on:

  38. Circular RNA (circRNA) is produced during the splicing of mRNA (in addition to linear splicing) and is part of the gene regulatory network. The temporal expression patterns the different developmental stages w...

    Authors: Yinghui Ling, Qi Zheng, Lu Zhu, Lina Xu, Menghua Sui, Yunhai Zhang, Ya Liu, Fugui Fang, Mingxing Chu, Yuehui Ma and Xiaorong Zhang
    Citation: BMC Genomics 2020 21:220
    Content type: Research article Published on:

  39. Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically...

    Authors: Meng Chen, Chun-Yang Xu, Xu Wang, Chong-Yang Ren, Jiao Ding and Li Li
    Citation: BMC Genomics 2020 21:217
    Content type: Research article Published on:

  40. All retroviruses, including human immunodeficiency virus (HIV), must integrate a DNA copy of their genomes into the genome of the infected host cell to replicate. Although integrated retroviral DNA, known as a...

    Authors: Daria W. Wells, Shuang Guo, Wei Shao, Michael J. Bale, John M. Coffin, Stephen H. Hughes and Xiaolin Wu
    Citation: BMC Genomics 2020 21:216
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Genomics 2020 21:517

  41. In recent years, interest in Bacillus velezensis has increased significantly due to its role in many industrial water bioremediation processes. In this study, we isolated and assessed the transcriptome of Bacillu...

    Authors: Guangxin Liu, Sarath Babu Vijayaraman, Yanjun Dong, Xinfeng Li, Binda Tembeng Andongmaa, Lijuan Zhao, Jiagang Tu, Jin He and Li Lin
    Citation: BMC Genomics 2020 21:215
    Content type: Research article Published on:

  42. Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is h...

    Authors: Agnieszka Klonowska, Lionel Moulin, Julie Kaye Ardley, Florence Braun, Margaret Mary Gollagher, Jaco Daniel Zandberg, Dora Vasileva Marinova, Marcel Huntemann, T. B. K. Reddy, Neha Jacob Varghese, Tanja Woyke, Natalia Ivanova, Rekha Seshadri, Nikos Kyrpides and Wayne Gerald Reeve
    Citation: BMC Genomics 2020 21:214
    Content type: Research article Published on:

  43. The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefo...

    Authors: Xuke Lu, Na Shu, Delong Wang, Junjuan Wang, Xiugui Chen, Binglei Zhang, Shuai Wang, Lixue Guo, Chao Chen and Wuwei Ye
    Citation: BMC Genomics 2020 21:213
    Content type: Research article Published on:

  44. The Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function anal...

    Authors: Yingbo Cui, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang and Canqun Yang
    Citation: BMC Genomics 2020 21(Suppl 1):872
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  45. Circular RNA is a type of non-coding RNA, which has a circular structure. Many circular RNAs are stable and contain exons, but are not translated into proteins. Circular RNA has important functions in gene reg...

    Authors: Xin Li and Yufeng Wu
    Citation: BMC Genomics 2020 21(Suppl 1):749
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  46. Methylation of cytosine bases in DNA is a critical epigenetic mark in many eukaryotes and has also been implicated in the development and progression of normal and diseased cells. Therefore, profiling DNA meth...

    Authors: Ximei Luo, Fang Wang, Guohua Wang and Yuming Zhao
    Citation: BMC Genomics 2020 21(Suppl 1):672
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  47. Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been cha...

    Authors: Lili Fu, Zehong Ding, Deguan Tan, Bingying Han, Xuepiao Sun and Jiaming Zhang
    Citation: BMC Genomics 2020 21:212
    Content type: Research article Published on:

  48. Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular...

    Authors: Fengdan Guo, Junjie Ma, Lei Hou, Suhua Shi, Jinbo Sun, Guanghui Li, Chuanzhi Zhao, Han Xia, Shuzhen Zhao, Xingjun Wang and Yanxiu Zhao
    Citation: BMC Genomics 2020 21:211
    Content type: Research article Published on:

  49. The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive....

    Authors: Carlos S. Casimiro-Soriguer, Alejandro Rubio, Juan Jimenez and Antonio J. Pérez-Pulido
    Citation: BMC Genomics 2020 21:210
    Content type: Research article Published on:

  50. Genomic inversion is one type of structural variations (SVs) and is known to play an important biological role. An established problem in sequence data analysis is calling inversions from high-throughput seque...

    Authors: Zhongjia Wu, Yufeng Wu and Jingyang Gao
    Citation: BMC Genomics 2020 21(Suppl 1):173
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

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