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  1. Post-database search is a key procedure in peptide identification with tandem mass spectrometry (MS/MS) strategies for refining peptide-spectrum matches (PSMs) generated by database search engines. Although ma...

    Authors: Xijun Liang, Zhonghang Xia, Ling Jian, Yongxiang Wang, Xinnan Niu and Andrew J. Link

    Citation: BMC Genomics 2020 21:324

    Content type: Methodology Article

    Published on:

  2. Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for op...

    Authors: Linghua Zhou, Zhiqiang Chen, Lars Olsson, Thomas Grahn, Bo Karlsson, Harry X. Wu, Sven-Olof Lundqvist and María Rosario García-Gil

    Citation: BMC Genomics 2020 21:323

    Content type: Research article

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  3. Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition....

    Authors: Jung-Ki Yoon, Taek Soo Kim, Jong-Il Kim and Jae-Joon Yim

    Citation: BMC Genomics 2020 21:322

    Content type: Research article

    Published on:

  4. The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface...

    Authors: Bo Wang, Xiaofei Liang, Mark L. Gleason, Tom Hsiang, Rong Zhang and Guangyu Sun

    Citation: BMC Genomics 2020 21:321

    Content type: Research article

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  5. Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective metho...

    Authors: Min Yao, Mei Guan, Zhenqian Zhang, Qiuping Zhang, Yixin Cui, Hao Chen, Wei Liu, Habib U. Jan, Kai P. Voss-Fels, Christian R. Werner, Xin He, Zhongsong Liu, Chunyun Guan, Rod J. Snowdon, Wei Hua and Lunwen Qian

    Citation: BMC Genomics 2020 21:320

    Content type: Research article

    Published on:

  6. Ashbya gossypii naturally overproduces riboflavin and has been utilized for industrial riboflavin production. To improve riboflavin production, various approaches have been developed. In this study, to investigat...

    Authors: Tatsuya Kato, Junya Azegami, Ami Yokomori, Hideo Dohra, Hesham A. El Enshasy and Enoch Y. Park

    Citation: BMC Genomics 2020 21:319

    Content type: Research article

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  7. Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Benthic communities are the most sensitive parts of the coastal ecosystem to eutrophicati...

    Authors: Hongtao Nie, Huamin Wang, Kunyin Jiang and Xiwu Yan

    Citation: BMC Genomics 2020 21:318

    Content type: Research article

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  8. Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity...

    Authors: Xunhe Huang, Newton O. Otecko, Minsheng Peng, Zhuoxian Weng, Weina Li, Jiebo Chen, Ming Zhong, Fusheng Zhong, Sihua Jin, Zhaoyu Geng, Wei Luo, Danlin He, Cheng Ma, Jianlin Han, Sheila C. Ommeh, Yaping Zhang…

    Citation: BMC Genomics 2020 21:316

    Content type: Research article

    Published on:

  9. Climate change, including higher temperatures (HT) has a detrimental impact on wheat productivity and modeling studies predict more frequent heat waves in the future. Wheat growth can be impaired by high dayti...

    Authors: Sumit Pradhan, Md Ali Babar, Guihua Bai, Jahangir Khan, Dipendra Shahi, Muhsin Avci, Jia Guo, Jordan McBreen, Senthold Asseng, Salvador Gezan, Byung-Kee Baik, Ann Blount, Stephen Harrison, Suraj Sapkota, Paul St. Amand and Sanju Kunwar

    Citation: BMC Genomics 2020 21:315

    Content type: Research article

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  10. Campylobacter jejuni and Campylobacter coli are major global causes of bacterial gastroenteritis. Whilst several individual colonisation and virulence factors have been identified, our understanding of their role...

    Authors: Jai W. Mehat, Roberto M. La Ragione and Arnoud H. M. van Vliet

    Citation: BMC Genomics 2020 21:314

    Content type: Research article

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  11. Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic lin...

    Authors: Xiaoli Huang, Yanxin Jiang, Wanting Zhang, Yingyin Cheng, Yaping Wang, Xiaocui Ma, You Duan, Lei Xia, Yaxin Chen, Nan Wu, Mijuan Shi and Xiao-Qin Xia

    Citation: BMC Genomics 2020 21:313

    Content type: Research article

    Published on:

  12. In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been r...

    Authors: Alemu Takele Assefa, Jo Vandesompele and Olivier Thas

    Citation: BMC Genomics 2020 21:312

    Content type: Research Article

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  13. Puccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals. This halophyte has enormous value...

    Authors: Rui Guo, Long Zhao, Kaijian Zhang, Dan Gao and Chunwu Yang

    Citation: BMC Genomics 2020 21:311

    Content type: Database

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  14. The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of dat...

    Authors: Onur Yukselen, Osman Turkyilmaz, Ahmet Rasit Ozturk, Manuel Garber and Alper Kucukural

    Citation: BMC Genomics 2020 21:310

    Content type: Software

    Published on:

  15. Aquaculture is a fast-growing industry and therefore welfare and environmental impact have become of utmost importance. Preventing stress associated to common aquaculture practices and optimizing the fish stre...

    Authors: Cláudia Raposo de Magalhães, Denise Schrama, Ana Paula Farinha, Dominique Revets, Annette Kuehn, Sébastien Planchon, Pedro Miguel Rodrigues and Marco Cerqueira

    Citation: BMC Genomics 2020 21:309

    Content type: Research article

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  16. Göttingen Minipigs (GMP) is the smallest commercially available minipig breed under a controlled breeding scheme and is globally bred in five isolated colonies. The genetic isolation harbors the risk of strati...

    Authors: Christian Reimer, Ngoc-Thuy Ha, Ahmad Reza Sharifi, Johannes Geibel, Lars Friis Mikkelsen, Martin Schlather, Steffen Weigend and Henner Simianer

    Citation: BMC Genomics 2020 21:308

    Content type: Research article

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  17. Hypothyroidism is a common complex endocrinopathy that typically has an autoimmune etiology, and it affects both humans and dogs. Genetic and environmental factors are both known to play important roles in the...

    Authors: Matteo Bianchi, Nima Rafati, Åsa Karlsson, Eva Murén, Carl-Johan Rubin, Katarina Sundberg, Göran Andersson, Olle Kämpe, Åke Hedhammar, Kerstin Lindblad-Toh and Gerli Rosengren Pielberg

    Citation: BMC Genomics 2020 21:307

    Content type: Research article

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  18. The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is fi...

    Authors: Xiaofen Wu, Ting Chen, Da Huo, Zonghe Yu, Yao Ruan, Chuhang Cheng, Xiao Jiang and Chunhua Ren

    Citation: BMC Genomics 2020 21:306

    Content type: Research article

    Published on:

  19. In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogene...

    Authors: Zheng Liu, Xiao-Xia Ge, Xiao-Meng Wu, Qiang Xu, Ross G. Atkinson and Wen-Wu Guo

    Citation: BMC Genomics 2020 21:305

    Content type: Research article

    Published on:

  20. The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorith...

    Authors: Paulina Dziadkiewicz and Norbert Dojer

    Citation: BMC Genomics 2020 21(Suppl 2):274

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  21. Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants.

    Authors: Diego P. Rubert, Fábio V. Martinez, Jens Stoye and Daniel Doerr

    Citation: BMC Genomics 2020 21(Suppl 2):273

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  22. In bacterial genomes, rRNA and tRNA genes are often organized into operons, i.e. segments of closely located genes that share a single promoter and are transcribed as a single unit. Analyzing how these genes a...

    Authors: Tomasz Pawliszak, Meghan Chua, Carson K. Leung and Olivier Tremblay-Savard

    Citation: BMC Genomics 2020 21(Suppl 2):252

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  23. Phylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phy...

    Authors: Vladimir Smirnov and Tandy Warnow

    Citation: BMC Genomics 2020 21(Suppl 2):235

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  24. Multi-locus species phylogeny inference is based on models of sequence evolution on gene trees as well as models of gene tree evolution within the branches of species phylogenies. Almost all statistical method...

    Authors: Hunter Tidwell and Luay Nakhleh

    Citation: BMC Genomics 2020 21(Suppl 2):219

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  25. During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-n...

    Authors: Garance Cordonnier and Manuel Lafond

    Citation: BMC Genomics 2020 21(Suppl 2):198

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 2

  26. The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving > 900 m deep and remaining underwater for more than 60 min...

    Authors: Luca Penso-Dolfin, Wilfried Haerty, Allyson Hindle and Federica Di Palma

    Citation: BMC Genomics 2020 21:303

    Content type: Research article

    Published on:

  27. Piwi-interacting RNAs (piRNAs) have been linked to epigenetic and post-transcriptional gene silencing of retrotransposons in germ line cells, particularly in spermatogenesis. Exosomes are important mediators o...

    Authors: Bo Zhang, Na Zhao, Lei Jia, Jinyuan Che, Xiaoxu He, Kefeng Liu and Baolong Bao

    Citation: BMC Genomics 2020 21:302

    Content type: Research article

    Published on:

  28. Animal coloration is usually an adaptive attribute, under strong local selection pressures and often diversified among species or populations. The strawberry poison frog (Oophaga pumilio) shows an impressive arra...

    Authors: Ariel Rodríguez, Nicholas I. Mundy, Roberto Ibáñez and Heike Pröhl

    Citation: BMC Genomics 2020 21:301

    Content type: Research article

    Published on:

  29. Low temperatures decrease the capacity for biomass production and lead to growth retardation up to irreversible cellular damage in modern maize cultivars. European flint landraces are an untapped genetic resou...

    Authors: Felix P. Frey, Marion Pitz, Chris-Carolin Schön and Frank Hochholdinger

    Citation: BMC Genomics 2020 21:300

    Content type: Research article

    Published on:

  30. Walnut kernels contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids for humans and have important effects on growth and health. The main ...

    Authors: Kai Liu, Shugang Zhao, Shuang Wang, Hongxia Wang and Zhihua Zhang

    Citation: BMC Genomics 2020 21:299

    Content type: Research article

    Published on:

  31. Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on t...

    Authors: Emelie Berglund, Sami Saarenpää, Anders Jemt, Joel Gruselius, Ludvig Larsson, Ludvig Bergenstråhle, Joakim Lundeberg and Stefania Giacomello

    Citation: BMC Genomics 2020 21:298

    Content type: Methodology article

    Published on:

  32. Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological cha...

    Authors: Zhao Zhang, Daixi Li, Xing Shi, Yao Zhai, Yatao Guo, Yali Zheng, Lili Zhao, Yukun He, Yusheng Chen, Zhanwei Wang, Jianrong Su, Yu Kang and Zhancheng Gao

    Citation: BMC Genomics 2020 21:297

    Content type: Research article

    Published on:

  33. Pseudomonas syringae is an important plant pathogen, which could adapt many different environmental conditions. Under the nutrient-limited and other stress conditions, P. syringae produces nucleotide signal molec...

    Authors: Jun Liu, Menghao Yu, Tiyakhon Chatnaparat, Jae Hoon Lee, Yanli Tian, Baishi Hu and Youfu Zhao

    Citation: BMC Genomics 2020 21:296

    Content type: Research article

    Published on:

  34. Lycium barbarum and L. ruthenicum have been used as traditional medicinal plants in China and other Asian counties for centuries. However, the molecular mechanisms underlying fruit development and ripening, as we...

    Authors: Cuiping Wang, Yan Dong, Lizhen Zhu, Libin Wang, Li Yan, Mengze Wang, Qiang Zhu, Xiongxiong Nan, Yonghua Li and Jian Li

    Citation: BMC Genomics 2020 21:295

    Content type: Research article

    Published on:

  35. Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field tr...

    Authors: Bahman Khahani, Elahe Tavakol, Vahid Shariati and Fabio Fornara

    Citation: BMC Genomics 2020 21:294

    Content type: Research article

    Published on:

  36. Copy number variation is an important class of genomic variation that has been reported in 75% of the human genome. However, it is underreported in African populations. Copy number variants (CNVs) could have i...

    Authors: Oscar A. Nyangiri, Harry Noyes, Julius Mulindwa, Hamidou Ilboudo, Justin Windingoudi Kabore, Bernardin Ahouty, Mathurin Koffi, Olivier Fataki Asina, Dieudonne Mumba, Elvis Ofon, Gustave Simo, Magambo Phillip Kimuda, John Enyaru, Vincent Pius Alibu, Kelita Kamoto, John Chisi…

    Citation: BMC Genomics 2020 21:289

    Content type: Research article

    Published on:

  37. The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed ...

    Authors: Nicolas Scalzitti, Anne Jeannin-Girardon, Pierre Collet, Olivier Poch and Julie D. Thompson

    Citation: BMC Genomics 2020 21:293

    Content type: Research article

    Published on:

  38. Improving feed efficiency is one of the important breeding targets for poultry industry. The aim of current study was to investigate the breast muscle transcriptome data of native chickens divergent for feed e...

    Authors: Lei Yang, Tingting He, Fengliang Xiong, Xianzhen Chen, Xinfeng Fan, Sihua Jin and Zhaoyu Geng

    Citation: BMC Genomics 2020 21:292

    Content type: Research article

    Published on:

  39. Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronom...

    Authors: Fatemeh Maghuly, Tamás Deák, Klemens Vierlinger, Stephan Pabinger, Hakim Tafer and Margit Laimer

    Citation: BMC Genomics 2020 21:290

    Content type: Research article

    Published on:

  40. 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

    Published on:

  41. 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

    Published on:

  42. 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

    Published on:

  43. 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

    Published on:

  44. 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

    Published on:

  45. 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

    Published on:

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