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  1. Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basi...

    Authors: Christopher P. Kozakiewicz, Alexandra K. Fraik, Austin H. Patton, Manuel Ruiz-Aravena, David G. Hamilton, Rodrigo Hamede, Hamish McCallum, Paul A. Hohenlohe, Mark J. Margres, Menna E. Jones and Andrew Storfer

    Citation: BMC Genomics 2021 22:698

    Content type: Research

    Published on:

  2. Nitrogen (N) is one of the main factors limiting the wood yield in poplar cultivation. Understanding the molecular mechanism of N utilization could play a guiding role in improving the nitrogen use efficiency ...

    Authors: Cun Chen, Yanguang Chu, Qinjun Huang, Weixi Zhang, Changjun Ding, Jing Zhang, Bo Li, Tengqian Zhang, Zhenghong Li and Xiaohua Su

    Citation: BMC Genomics 2021 22:697

    Content type: Research

    Published on:

  3. Aging and inflammation are important components of Parkinson’s disease (PD) pathogenesis and both are associated with changes in hematopoiesis and blood cell composition. DNA methylation (DNAm) presents a mech...

    Authors: Kimberly C Paul, Alexandra M Binder, Steve Horvath, Cynthia Kusters, Qi Yan, Irish Del Rosario, Yu Yu, Jeff Bronstein and Beate Ritz

    Citation: BMC Genomics 2021 22:696

    Content type: Research article

    Published on:

  4. A coral colony is composed of physiologically integrated polyps. In stony corals, coloniality adopts a wide diversity of forms and involves complex ontogenetic dynamics. However, molecular mechanisms underlyin...

    Authors: Po-Shun Chuang and Satoshi Mitarai

    Citation: BMC Genomics 2021 22:694

    Content type: Research

    Published on:

  5. Previous studies have identified many immune pathways which are consistently altered in humans and model organisms as they age. Dairy cows are often culled at quite young ages due to an inability to cope adequ...

    Authors: Laura Buggiotti, Zhangrui Cheng, Mazdak Salavati and Claire D. Wathes

    Citation: BMC Genomics 2021 22:693

    Content type: Research article

    Published on:

  6. The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accura...

    Authors: Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Antonijo Mrčela, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash and Gregory R. Grant

    Citation: BMC Genomics 2021 22:692

    Content type: Software

    Published on:

  7. Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this specie...

    Authors: Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun and Jianxiong Jiang

    Citation: BMC Genomics 2021 22:690

    Content type: Research article

    Published on:

  8. Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In additio...

    Authors: N. M. Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards and Anelia Horvath

    Citation: BMC Genomics 2021 22:689

    Content type: Methodology article

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  9. Eukaryotic organisms, like the model yeast S. cerevisiae, have linear chromosomes that facilitate organization and protection of nuclear DNA. A recent work described a stepwise break/repair method that enabled fu...

    Authors: Tyler W. Doughty, Rosemary Yu, Lucy Fang-I Chao, Zhongjun Qin, Verena Siewers and Jens Nielsen

    Citation: BMC Genomics 2021 22:688

    Content type: Research article

    Published on:

  10. Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a cold-tolerant plant that is vulnerable to high temperature. This study explored the response mechanism of wucai to low temperature. In this s...

    Authors: Lingyun Yuan, Yushan Zheng, Libing Nie, Liting Zhang, Ying Wu, Shidong Zhu, Jinfeng Hou, Guo Lei Shan, Tong Kun Liu, Guohu Chen, Xiaoyan Tang and Chenggang Wang

    Citation: BMC Genomics 2021 22:687

    Content type: Research

    Published on:

  11. Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooke...

    Authors: Amila S. N. W. Pahalagedara, Ruy Jauregui, Paul Maclean, Eric Altermann, Steve Flint, Jon Palmer, Gale Brightwell and Tanushree Barua Gupta

    Citation: BMC Genomics 2021 22:686

    Content type: Research

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  12. Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate ge...

    Authors: Sarika Jaiswal, Samiran Nandi, Mir Asif Iquebal, Rahul Singh Jasrotia, Sunita Patra, Gayatri Mishra, Uday Kumar Udit, Dinesh Kumar Sahu, U. B. Angadi, Prem Kumar Meher, Padmanav Routray, Jitendra Kumar Sundaray, Dhananjay Kumar Verma, Paramananda Das, Pallipuram Jayasankar, Anil Rai…

    Citation: BMC Genomics 2021 22:685

    Content type: Research

    Published on:

  13. The bast fiber crop ramie can be used as high-quality forage resources, especially in tropical or subtropical region where there is lack of high-quality protein feed. Hongxuan No.1 (HX_1) is a unique ramie var...

    Authors: Xinkang Feng, Gang Gao, Chunming Yu, Aiguo Zhu, Jikang Chen, Kunmei Chen, Xiaofei Wang, Aminu Shehu Abubakar and Ping Chen

    Citation: BMC Genomics 2021 22:684

    Content type: Research

    Published on:

  14. As one of “γδ-high” species, chicken is an excellent model for the study of γδ T cells in non-mammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The ...

    Authors: Tongtong Zhang, Qian Li, Xiaoqing Li, Li Kang, Yunliang Jiang and Yi Sun

    Citation: BMC Genomics 2021 22:683

    Content type: Research

    Published on:

  15. BES/BZR family genes have vital roles in plant growth, development, and adaptation to environmental stimuli. However, they have not yet been characterized and systematically analyzed in wheat and foxtail millet.

    Authors: Dan Liu, Yanjiao Cui, Zilong Zhao, Suying Li, Dan Liang, Conglei Wang, Gang Feng, Jianhe Wang and Zhengli Liu

    Citation: BMC Genomics 2021 22:682

    Content type: Research

    Published on:

  16. Freezing temperatures are an abiotic stress that has a serious impact on plant growth and development in temperate regions and even threatens plant survival. The wild apple tree (Malus sieversii) needs to undergo...

    Authors: Ping Zhou, Xiaoshuang Li, Xiaojie Liu, Xuejing Wen, Yan Zhang and Daoyuan Zhang

    Citation: BMC Genomics 2021 22:681

    Content type: Research

    Published on:

  17. Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Its genome was one of the first Aspergillus gen...

    Authors: Valeria Ellena, Sjoerd J. Seekles, Gabriel A. Vignolle, Arthur F. J. Ram and Matthias G. Steiger

    Citation: BMC Genomics 2021 22:679

    Content type: Research

    Published on:

  18. Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with producti...

    Authors: Guoyao Zhao, Yuqiang Liu, Qunhao Niu, Xu Zheng, Tianliu Zhang, Zezhao Wang, Lei Xu, Bo Zhu, Xue Gao, Lupei Zhang, Huijiang Gao, Junya Li and Lingyang Xu

    Citation: BMC Genomics 2021 22:678

    Content type: Research

    Published on:

  19. Candidatus Liberibacter asiaticus (CLas) is one the causative agents of greening disease in citrus, an unccurable, devastating disease of citrus worldwide. CLas is vectored by Diaphorina citri, and the understand...

    Authors: Flavia Moura Manoel Bento, Josiane Cecília Darolt, Bruna Laís Merlin, Leandro Penã, Nelson Arno Wulff and Fernando Luis Cônsoli

    Citation: BMC Genomics 2021 22:677

    Content type: Research

    Published on:

  20. Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour...

    Authors: Darrell Lizamore, Ross Bicknell and Chris Winefield

    Citation: BMC Genomics 2021 22:676

    Content type: Research article

    Published on:

  21. Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolatio...

    Authors: Wenjing Zhang, Yantao Liang, Kaiyang Zheng, Chengxiang Gu, Yundan Liu, Ziyue Wang, Xinran Zhang, Hongbing Shao, Yong Jiang, Cui Guo, Hui He, Hualong Wang, Yeong Yik Sung, Wen Jye Mok, Yuzhong Zhang, Andrew McMinn…

    Citation: BMC Genomics 2021 22:675

    Content type: Research

    Published on:

  22. Plant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant...

    Authors: Jiecuo Duo, Huiyan Xiong, Xiongxiong Wu, Yuan Li, Jianping Si, Chao Zhang and Ruijun Duan

    Citation: BMC Genomics 2021 22:674

    Content type: Research

    Published on:

  23. Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and...

    Authors: Prashant Waiker, Fabiano Carlos Pinto de Abreu, Danielle Luna-Lucena, Flávia Cristina Paula Freitas, Zilá Luz Paulino Simões and Olav Rueppell

    Citation: BMC Genomics 2021 22:673

    Content type: Research

    Published on:

  24. Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has inc...

    Authors: Zhou Hong, Xuezhu Liao, Yuanjun Ye, Ningnan Zhang, Zengjiang Yang, Weidong Zhu, Wei Gao, Joel Sharbrough, Luke R. Tembrock, Daping Xu and Zhiqiang Wu

    Citation: BMC Genomics 2021 22:672

    Content type: Research

    Published on:

  25. Ventilator-induced diaphragm dysfunction (VIDD) is a common complication of life support by mechanical ventilation observed in critical patients in clinical practice and may predispose patients to severe compl...

    Authors: Pengcheng Wang, Xianlong Zhou, Gang Li, Haoli Ma, Ruining Liu and Yan Zhao

    Citation: BMC Genomics 2021 22:671

    Content type: Research article

    Published on:

  26. Isatidis Radix, the root of Isatis indigotica Fort. (Chinese woad) can produce a variety of efficacious compound with medicinal properties. The tetraploid I. indigotica plants exhibit superior phenotypic traits, ...

    Authors: Zixuan Zhang, Mingpu Tan, Yingying Zhang, Yue Jia, Shuxian Zhu, Jiang Wang, Jiajing Zhao, Yueyue Liao and Zengxu Xiang

    Citation: BMC Genomics 2021 22:670

    Content type: Research

    Published on:

  27. From genome-wide association studies, brain-derived neurotrophic factor (BDNF) locus on chromosome 11 was the only SNP associated with both smoking and body mass index (BMI) in European, African and Asian populat...

    Authors: Shan-shan Yang, Yao He, Lin Xu, Yali Jin, Wei-sen Zhang, Chao-qiang Jiang, Kar Keung Cheng and Tai Hing Lam

    Citation: BMC Genomics 2021 22:668

    Content type: Research

    Published on:

  28. The human microbiome is inherently dynamic and its dynamic nature plays a critical role in maintaining health and driving disease. With an increasing number of longitudinal microbiome studies, scientists are e...

    Authors: Chan Wang, Jiyuan Hu, Martin J. Blaser and Huilin Li

    Citation: BMC Genomics 2021 22:667

    Content type: Methodology article

    Published on:

  29. It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvem...

    Authors: Shaohua Li, Gaoping Zhao, Hongmei Han, Yunxia Li, Jun Li, Jinfeng Wang, Guifang Cao and Xihe Li

    Citation: BMC Genomics 2021 22:665

    Content type: Research

    Published on:

  30. Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. ...

    Authors: Lin Liu, Lu-Guang Jiang, Jin-Hong Luo, Ai-Ai Xia, Li-Qun Chen and Yan He

    Citation: BMC Genomics 2021 22:664

    Content type: Research

    Published on:

  31. A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulen...

    Authors: Briallen Lobb, Benjamin Jean-Marie Tremblay, Gabriel Moreno-Hagelsieb and Andrew C. Doxey

    Citation: BMC Genomics 2021 22:663

    Content type: Research

    Published on:

  32. Deer mice (genus Peromyscus) are the most common rodents in North America. Despite the availability of reference genomes for some species, a comprehensive database of polymorphisms, especially in those maintained...

    Authors: Matthew D. Lucius, Hao Ji, Diego Altomare, Robert Doran, Ben Torkian, Amanda Havighorst, Vimala Kaza, Youwen Zhang, Alexander V. Gasparian, Joseph Magagnoli, Vijay Shankar, Michael Shtutman and Hippokratis Kiaris

    Citation: BMC Genomics 2021 22:662

    Content type: Research

    Published on:

  33. Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus Eimeria. The present study a...

    Authors: Arnar K. S. Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lundén, Karin Troell, Staffan G. Svärd and Robert Söderlund

    Citation: BMC Genomics 2021 22:660

    Content type: Research

    Published on:

  34. Zebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic mechanisms of toxicity are still needed. Here, our goal was to identify gen...

    Authors: Prarthana Shankar, Ryan S. McClure, Katrina M. Waters and Robyn L. Tanguay

    Citation: BMC Genomics 2021 22:658

    Content type: Research

    Published on:

  35. Authors: Gen Pan, Zheng Li, Siqi Huang, Jie Tao, Yaliang Shi, Anguo Chen, Jianjun Li, Huijuan Tang, Li Chang, Yong Deng, Defang Li and Lining Zhao

    Citation: BMC Genomics 2021 22:657

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2021 22:595

  36. Authors: Yao Hu, Stephanie A. Bien, Katherine K. Nishimura, Jeffrey Haessler, Chani J. Hodonsky, Antoine R. Baldassari, Heather M. Highland, Zhe Wang, Michael Preuss, Colleen M. Sitlani, Genevieve L. Wojcik, Ran Tao, Mariaelisa Graff, Laura M. Huckins, Quan Sun, Ming-Huei Chen…

    Citation: BMC Genomics 2021 22:656

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2021 22:432

  37. Myxobacteria harbor numerous biosynthetic gene clusters that can produce a diverse range of secondary metabolites. Minicystis rosea DSM 24000T is a soil-dwelling myxobacterium belonging to the suborderSorangiinea...

    Authors: Shilpee Pal, Gaurav Sharma and Srikrishna Subramanian

    Citation: BMC Genomics 2021 22:655

    Content type: Research

    Published on:

  38. The discovery of male sterile materials is of great significance for the development of plant fertility research. Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variety of non-heading Chin...

    Authors: Jian Wang, Yitao Yang, Lei Zhang, Shaoxing Wang, Lingyun Yuan, Guohu Chen, Xiaoyan Tang, Jinfeng Hou, Shidong Zhu and Chenggang Wang

    Citation: BMC Genomics 2021 22:654

    Content type: Research

    Published on:

  39. As non-coding RNA molecules of more than 200 bp in length, long non-coding RNAs (lncRNAs) play a variety of roles in biological processes, including regulating the immune responses to bacterial infections. In ...

    Authors: Qianhui Sun, Jixiu Wang, Guowen Wang, Huanling Wang and Hong Liu

    Citation: BMC Genomics 2021 22:653

    Content type: Research

    Published on:

  40. Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description o...

    Authors: Lucas Palma Perez Braga, Roberta Verciano Pereira, Layla Farage Martins, Livia Maria Silva Moura, Fabio Beltrame Sanchez, José Salvatore Leister Patané, Aline Maria da Silva and João Carlos Setubal

    Citation: BMC Genomics 2021 22:652

    Content type: Research

    Published on:

  41. Heterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively im...

    Authors: Qizhen Xiao, Zekun Huang, Yawei Shen, Yang Gan, Yi Wang, Shihai Gong, Yisha Lu, Xuan Luo, Weiwei You and Caihuan Ke

    Citation: BMC Genomics 2021 22:650

    Content type: Research

    Published on:

  42. Bacillus cereus is a notorious foodborne pathogen, which can grow under anoxic conditions. Anoxic growth is supported by endogenous redox metabolism, for which the thiol redox proteome serves as an interface. Her...

    Authors: Fella Hamitouche, Jean-Charles Gaillard, Philippe Schmitt, Jean Armengaud, Catherine Duport and Luc Dedieu

    Citation: BMC Genomics 2021 22:648

    Content type: Research

    Published on:

  43. Agarwood, generated from the Aquilaria sinensis, has high economic and medicinal value. Although its genome has been sequenced, the ploidy of A. sinensis paleopolyploid remains unclear. Moreover, the expression c...

    Authors: Fanbo Meng, Tianzhe Chu, Qiang Tang and Wei Chen

    Citation: BMC Genomics 2021 22:647

    Content type: Research

    Published on:

  44. Cytoplasmic male sterility (CMS) has been widely used for commercial F1 hybrid seeds production. CMS is primarily caused by chimeric genes in mitochondrial genomes. However, which specific stages of anther dev...

    Authors: Xionghui Zhong, Denghui Chen, Jian Cui, Hailong Li, Yuxin Huang and Jungen Kang

    Citation: BMC Genomics 2021 22:646

    Content type: Research

    Published on:

  45. Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genom...

    Authors: Zhongyu Du, Ke Lu, Kai Zhang, Yiming He, Haitao Wang, Guaiqiang Chai, Jianguo Shi and Yizhong Duan

    Citation: BMC Genomics 2021 22:645

    Content type: Research

    Published on:

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