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  1. Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares sign...

    Authors: Patrick J. Monnahan, Jean-Michel Michno, Christine O’Connor, Alex B. Brohammer, Nathan M. Springer, Suzanne E. McGaugh and Candice N. Hirsch

    Citation: BMC Genomics 2020 21:281

    Content type: Methodology article

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  2. The family of NAC proteins (NAM, ATAF1/2, and CUC2) represent a class of large plant-specific transcription factors. However, identification and functional surveys of NAC genes of tomato (Solanum lycopersicum) re...

    Authors: Jian Feng Jin, Zhan Qi Wang, Qi Yu He, Jia Yi Wang, Peng Fei Li, Ji Ming Xu, Shao Jian Zheng, Wei Fan and Jian Li Yang

    Citation: BMC Genomics 2020 21:288

    Content type: Research article

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  3. Recent studies have suggested that the gut microbiota is altered in children with juvenile idiopathic arthritis (JIA). However, age, sex, and body mass index (BMI) were not matched in the previous studies, and...

    Authors: Xubo Qian, Yong-Xin Liu, Xiaohong Ye, Wenjie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wenqin Wang, Weihan Wang, Xianning Zhang and Meiping Lu

    Citation: BMC Genomics 2020 21:286

    Content type: Research article

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  4. Shigella is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans. Shigella invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion Syst...

    Authors: Ramón Cervantes-Rivera, Sophie Tronnet and Andrea Puhar

    Citation: BMC Genomics 2020 21:285

    Content type: Research article

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  5. Ascorbic acid (Vitamin C, AsA) is an antioxidant metabolite involved in plant development and environmental stimuli. AsA biosynthesis has been well studied in plants, and MIOX is a critical enzyme in plants As...

    Authors: Shoaib Munir, Muhammad Ali Mumtaz, John Kojo Ahiakpa, Genzhong Liu, Weifang Chen, Guolin Zhou, Wei Zheng, Zhibiao Ye and Yuyang Zhang

    Citation: BMC Genomics 2020 21:284

    Content type: Research article

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  6. Histological grade (HG) is commonly adopted as a prognostic factor for ER-positive breast cancer patients. However, HG evaluation methods, such as the pathological Nottingham grading system, are highly subject...

    Authors: Jing Li, Wenbin Jiang, Qirui Liang, Guanghao Liu, Yupeng Dai, Hailong Zheng, Jing Yang, Hao Cai and Guo Zheng

    Citation: BMC Genomics 2020 21:283

    Content type: Research article

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  7. Graph-based reference genomes have become popular as they allow read mapping and follow-up analyses in settings where the exact haplotypes underlying a high-throughput sequencing experiment are not precisely k...

    Authors: Ivar Grytten, Knut D. Rand, Alexander J. Nederbragt and Geir K. Sandve

    Citation: BMC Genomics 2020 21:282

    Content type: Methodology Article

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  8. Phytophthora root rot (PRR) caused by Phytophthora sojae (P. sojae) is one of the most serious limitations to soybean production worldwide. The identification of resistance gene(s) and their incorporation into el...

    Authors: Bingzhi Jiang, Yanbo Cheng, Zhandong Cai, Mu Li, Ze Jiang, Ruirui Ma, Yeshan Yuan, Qiuju Xia and Hai Nian

    Citation: BMC Genomics 2020 21:280

    Content type: Research article

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  9. The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parv...

    Authors: Kyle Tretina, Roger Pelle, Joshua Orvis, Hanzel T. Gotia, Olukemi O. Ifeonu, Priti Kumari, Nicholas C. Palmateer, Shaikh B. A. Iqbal, Lindsay M. Fry, Vishvanath M. Nene, Claudia A. Daubenberger, Richard P. Bishop and Joana C. Silva

    Citation: BMC Genomics 2020 21:279

    Content type: Research article

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  10. Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstruc...

    Authors: Wei Yang, Yaorong Wang, Dongneng Jiang, Changxu Tian, Chunhua Zhu, Guangli Li and Huapu Chen

    Citation: BMC Genomics 2020 21:278

    Content type: Research article

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  11. Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allo...

    Authors: Christian D. Powell, Daniel C. Kirchoff, Jason E. DeRouchey and Hunter N. B. Moseley

    Citation: BMC Genomics 2020 21:277

    Content type: Research Article

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  12. DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor famil...

    Authors: Yue Liu, Nannan Liu, Xiong Deng, Dongmiao Liu, Mengfei Li, Dada Cui, Yingkao Hu and Yueming Yan

    Citation: BMC Genomics 2020 21:276

    Content type: Research article

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  13. Phytopathogens secreted effectors during host colonization to suppress or trigger plant immunity. Identification of new effectors is one of the research focuses in recent years. There is only a limited knowled...

    Authors: Shixue Zhao, Bang An, Yanhua Guo, Xingrong Hou, Hongli Luo, Chaozu He and Qiannan Wang

    Citation: BMC Genomics 2020 21:275

    Content type: Research article

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  14. The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hi...

    Authors: Vasanthan Jayakumar, Hiromi Ishii, Misato Seki, Wakako Kumita, Takashi Inoue, Sumitaka Hase, Kengo Sato, Hideyuki Okano, Erika Sasaki and Yasubumi Sakakibara

    Citation: BMC Genomics 2020 21(Suppl 3):243

    Content type: Research

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    This article is part of a Supplement: Volume 21 Supplement 3

  15. DNA methylation is a crucial epigenomic mechanism in various biological processes. Using whole-genome bisulfite sequencing (WGBS) technology, methylated cytosine sites can be revealed at the single nucleotide ...

    Authors: Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao-Yang Chen, Jan-Ming Ho, Shu-Hwa Chen and Chung-Yen Lin

    Citation: BMC Genomics 2020 21(Suppl 3):163

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 3

  16. Most eukaryotic genes produce different transcripts of multiple isoforms by inclusion or exclusion of particular exons. The isoforms of a gene often play diverse functional roles, and thus it is necessary to a...

    Authors: Wei Zhang, Raphael Petegrosso, Jae-Woong Chang, Jiao Sun, Jeongsik Yong, Jeremy Chien and Rui Kuang

    Citation: BMC Genomics 2020 21:272

    Content type: Research Article

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  17. 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

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  18. The C:G > T:A substitution at the CpG dinucleotide contexts is the most frequent substitution type in genome evolution. The mutational process is obviously ongoing in the human germline; however, its impact on...

    Authors: Jeonghwan Youk, Yohan An, Seongyeol Park, June-Koo Lee and Young Seok Ju

    Citation: BMC Genomics 2020 21:270

    Content type: Research article

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  19. 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

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  20. Polydactyly is one of the most common congenital limb dysplasia in many animal species. Although preaxial polydactyly (PPD) has been comprehensively studied in humans as a common abnormality, the genetic varia...

    Authors: Cheng Ma, Saber Khederzadeh, Adeniyi C. Adeola, Xu-Man Han, Hai-Bing Xie and Ya-Ping Zhang

    Citation: BMC Genomics 2020 21:268

    Content type: Research article

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  21. Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play crit...

    Authors: Xian Zou, Tingting Lu, Zhifeng Zhao, Guangbin Liu, Zhiquan Lian, Yongqing Guo, Baoli Sun, Dewu Liu and Yaokun Li

    Citation: BMC Genomics 2020 21:267

    Content type: Research article

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  22. Marmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields. Due to the rapid accumulation of the genetic data in marmots, a highly integ...

    Authors: Baoning Liu, Liang Bai, Qingqing Yu, Fang Hu, Jing Wu, Sihai Zhao, Rong Wang, Weirong Wang, Yuanqing Tao, Jianglin Fan and Enqi Liu

    Citation: BMC Genomics 2020 21:266

    Content type: Database

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  23. 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

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  24. 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

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  25. 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

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  26. The non-climacteric ‘Yellow’ melon (Cucumis melo, inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related p...

    Authors: Michelle Orane Schemberger, Marília Aparecida Stroka, Letícia Reis, Kamila Karoline de Souza Los, Gillize Aparecida Telles de Araujo, Michelle Zibetti Tadra Sfeir, Carolina Weigert Galvão, Rafael Mazer Etto, Amanda Regina Godoy Baptistão and Ricardo Antonio Ayub

    Citation: BMC Genomics 2020 21:262

    Content type: Research article

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  27. The nucleotide second messengers, i.e., guanosine tetraphosphate and pentaphosphate [collectively referred to as (p) ppGpp], trigger the stringent response under nutrient starvation conditions and play an esse...

    Authors: Ho-wen Yang, Menghao Yu, Jae Hoon Lee, Tiyakhon Chatnaparat and Youfu Zhao

    Citation: BMC Genomics 2020 21:261

    Content type: Research article

    Published on:

  28. Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that contro...

    Authors: Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yui Yamashita, Satoshi Naito, Anna Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima and Hitoshi Onouchi

    Citation: BMC Genomics 2020 21:260

    Content type: Research article

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  29. 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

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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:

  35. 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

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  36. 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

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  37. 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:

  38. 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

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  39. 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:

  40. 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

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  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

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