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  1. 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:

  2. 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

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  3. 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:

  4. 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

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  5. 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

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  6. 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

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  7. 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

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  8. 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:

  9. 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:

  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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:

  18. 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

  19. Pathway analysis is one of the later stage data analysis steps essential in interpreting high-throughput gene expression data. We propose a set of algorithms which given gene expression data can recognize whic...

    Authors: Yue Zhao, Stephanie Piekos, Tham H. Hoang and Dong-Guk Shin

    Citation: BMC Genomics 2020 21(Suppl 1):834

    Content type: Methodology

    Published on:

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

  20. 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

  21. 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

  22. 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

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  23. 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

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  24. 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

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  25. Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully expl...

    Authors: Ali Ali, Rafet Al-Tobasei, Daniela Lourenco, Tim Leeds, Brett Kenney and Mohamed Salem

    Citation: BMC Genomics 2020 21:209

    Content type: Research article

    Published on:

  26. 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

  27. Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic nove...

    Authors: Gur Sevillya, Orit Adato and Sagi Snir

    Citation: BMC Genomics 2020 21(Suppl 1):106

    Content type: Research

    Published on:

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

  28. Postpartum developmental delay has been proposed as an important phenotype of human evolution which contributes to many human-specific features including the increase in brain size and the advanced human-speci...

    Authors: Hui Tang, Ying Tang, Tao Zeng and Luonan Chen

    Citation: BMC Genomics 2020 21(Suppl 1):74

    Content type: Research

    Published on:

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

  29. Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-estab...

    Authors: Hoi Man Ng, Jeff Cheuk Hin Ho, Wenyan Nong, Jerome Ho Lam Hui, Keng Po Lai and Chris Kong Chu Wong

    Citation: BMC Genomics 2020 21:208

    Content type: Research article

    Published on:

  30. Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of...

    Authors: Zeinab Amiri Ghanatsaman, Guo-Dong Wang, Hojjat Asadollahpour Nanaei, Masood Asadi Fozi, Min-Sheng Peng, Ali Esmailizadeh and Ya-Ping Zhang

    Citation: BMC Genomics 2020 21:207

    Content type: Research article

    Published on:

  31. Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will fac...

    Authors: Guohao Han, Shiyu Liu, Yuli Jin, Mengshu Jia, Pengtao Ma, Hong Liu, Jing Wang and Diaoguo An

    Citation: BMC Genomics 2020 21:206

    Content type: Research article

    Published on:

  32. The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. T...

    Authors: Pierce Rafter, Isobel Claire Gormley, Andrew C. Parnell, John Francis Kearney and Donagh P. Berry

    Citation: BMC Genomics 2020 21:205

    Content type: Research article

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  33. In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cogn...

    Authors: Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qin Chu, Xiquan Zhang and Xuemei Lu

    Citation: BMC Genomics 2020 21:204

    Content type: Research article

    Published on:

  34. Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS...

    Authors: Anthony Bernard, Annarita Marrano, Armel Donkpegan, Patrick J. Brown, Charles A. Leslie, David B. Neale, Fabrice Lheureux and Elisabeth Dirlewanger

    Citation: BMC Genomics 2020 21:203

    Content type: Research article

    Published on:

  35. Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated fr...

    Authors: Eleonora Mastrorilli, Sara Petrin, Massimiliano Orsini, Alessandra Longo, Debora Cozza, Ida Luzzi, Antonia Ricci, Lisa Barco and Carmen Losasso

    Citation: BMC Genomics 2020 21:202

    Content type: Research article

    Published on:

  36. The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population ...

    Authors: Yu Wang, Haoyang Cai, Xiaolin Luo, Yi Ai, Mingfeng Jiang and Yongli Wen

    Citation: BMC Genomics 2020 21:201

    Content type: Research article

    Published on:

  37. PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, ...

    Authors: Rongzhi Zhang, Siyuan Huang, Shiming Li, Guoqi Song, Yulian Li, Wei Li, Jihu Li, Jie Gao, Tiantian Gu, Dandan Li, Shujuan Zhang and Genying Li

    Citation: BMC Genomics 2020 21:200

    Content type: Research article

    Published on:

  38. Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at ...

    Authors: Katie O’Connor, Ben Hayes, Craig Hardner, Catherine Nock, Abdul Baten, Mobashwer Alam, Robert Henry and Bruce Topp

    Citation: BMC Genomics 2020 21:199

    Content type: Research article

    Published on:

  39. Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt str...

    Authors: Mohamed Hamed Arisha, Hesham Aboelnasr, Muhammad Qadir Ahmad, Yaju Liu, Wei Tang, Runfei Gao, Hui Yan, Meng Kou, Xin Wang, Yungang Zhang and Qiang Li

    Citation: BMC Genomics 2020 21:197

    Content type: Research article

    Published on:

  40. Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred t...

    Authors: If H. A. Barnes, Ximena Ibarra-Soria, Stephen Fitzgerald, Jose M. Gonzalez, Claire Davidson, Matthew P. Hardy, Deepa Manthravadi, Laura Van Gerven, Mark Jorissen, Zhen Zeng, Mona Khan, Peter Mombaerts, Jennifer Harrow, Darren W. Logan and Adam Frankish

    Citation: BMC Genomics 2020 21:196

    Content type: Research article

    Published on:

  41. Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly “full-length” ones, provide read coverage of many individua...

    Authors: Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda and Itoshi Nikaido

    Citation: BMC Genomics 2020 21:177

    Content type: Software

    Published on:

  42. The H+-PPase (pyrophosphatase) gene family is an important class of proton transporters that play key roles in plant development and stress resistance. Although the physiological and biochemical functions of H+-P...

    Authors: Yiming Zhang, Xue Feng, Lihui Wang, Yanping Su, Zhuodong Chu and Yanxiang Sun

    Citation: BMC Genomics 2020 21:195

    Content type: Research article

    Published on:

  43. Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic div...

    Authors: Nancy Manchanda, John L. Portwood II, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence-Dill, Carson M. Andorf and Matthew B. Hufford

    Citation: BMC Genomics 2020 21:193

    Content type: Software

    Published on:

  44. Cyclic nucleotide gated channels (CNGCs) play multifaceted roles in plant physiological processes, especially with respect to signalling processes, plant development, and responses to environmental stresses. H...

    Authors: Lixin Wang, Min Li, Zhiguo Liu, Li Dai, Mengling Zhang, Lili Wang, Jin Zhao and Mengjun Liu

    Citation: BMC Genomics 2020 21:191

    Content type: Research article

    Published on:

  45. The AIG (avrRpt2-induced gene) family of GTPases, characterized by the presence of a distinctive AIG1 domain, is mysterious in having a peculiar phylogenetic distribution, a predilection for undergoing expansi...

    Authors: Lijun Lu, Eric S. Loker, Si-Ming Zhang, Sarah K. Buddenborg and Lijing Bu

    Citation: BMC Genomics 2020 21:190

    Content type: Research article

    Published on:

  46. Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool ...

    Authors: Ranran Zhao, Nan Liu, Fuhui Han, Hegang Li, Jifeng Liu, Lanlan Li, Guoyi Wang and Jianning He

    Citation: BMC Genomics 2020 21:187

    Content type: Research article

    Published on:

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