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  1. Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare ...

    Authors: Julie E. Hernández-Salmerón and Gabriel Moreno-Hagelsieb

    Citation: BMC Genomics 2020 21:741

    Content type: Methodology article

    Published on:

  2. Understanding the genetic basis of phenotype variations during domestication and breeding is of great interest. Epigenetics and epigenetic modification enzymes (EMEs) may play a role in phenotypic variations; ...

    Authors: Rui Gao, Chun-Lin Li, Xiao-Ling Tong, Min-Jin Han, Kun-Peng Lu, Shu-Bo Liang, Hai Hu, Yue Luan, Bi-Li Zhang, Yan-Yu Liu and Fang-Yin Dai

    Citation: BMC Genomics 2020 21:740

    Content type: Research article

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  3. Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. To map the quantitative trait loci (QTLs) of soybean leaf chlorophyll-content traits,...

    Authors: Liang Wang, Brima Conteh, Linzhi Fang, Qiuju Xia and Hai Nian

    Citation: BMC Genomics 2020 21:739

    Content type: Research article

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  4. The root lesion nematode Pratylenchus penetrans is a migratory plant-parasitic nematode responsible for economically important losses in a wide number of crops. Despite the importance of P. penetrans, the molecul...

    Authors: Paulo Vieira, Jonathan Shao, Paramasivan Vijayapalani, Thomas R. Maier, Clement Pellegrin, Sebastian Eves-van den Akker, Thomas J. Baum and Lev G. Nemchinov

    Citation: BMC Genomics 2020 21:738

    Content type: Research article

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  5. Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from euryt...

    Authors: Lili Liu, Rong Zhang, Xiaowen Wang, Hua Zhu and Zhaohui Tian

    Citation: BMC Genomics 2020 21:737

    Content type: Research article

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  6. TIFY is a plant-specific protein family with a diversity of functions in plant development and responses to stress and hormones, which contains JASMONATE ZIM-domain (JAZ), TIFY, PPD and ZML subfamilies. Despit...

    Authors: Xin He, Yu Kang, Wenqian Li, Wei Liu, Pan Xie, Li Liao, Luyao Huang, Min Yao, Lunwen Qian, Zhongsong Liu, Chunyun Guan, Mei Guan and Wei Hua

    Citation: BMC Genomics 2020 21:736

    Content type: Research article

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  7. Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory ...

    Authors: Mohammad Aslam, Bello Hassan Jakada, Beenish Fakher, Joseph G. Greaves, Xiaoping Niu, Zhenxia Su, Yan Cheng, Shijiang Cao, Xiaomei Wang and Yuan Qin

    Citation: BMC Genomics 2020 21:735

    Content type: Research article

    Published on:

  8. Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transc...

    Authors: Zhaoxi Zhou, Hongmao Gao, Jianhong Ming, Zheli Ding, Xing’e Lin and Rulin Zhan

    Citation: BMC Genomics 2020 21:734

    Content type: Research article

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  9. Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has inc...

    Authors: Lisa Joos, Stien Beirinckx, Annelies Haegeman, Jane Debode, Bart Vandecasteele, Steve Baeyen, Sofie Goormachtig, Lieven Clement and Caroline De Tender

    Citation: BMC Genomics 2020 21:733

    Content type: Research article

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  10. Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mecha...

    Authors: Yi-Ling Chiu, Shinya Shikina, Yuki Yoshioka, Chuya Shinzato and Ching-Fong Chang

    Citation: BMC Genomics 2020 21:732

    Content type: Research article

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  11. Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiologi...

    Authors: Jinwei Xin, Zhixin Chai, Chengfu Zhang, Qiang Zhang, Yong Zhu, Hanwen Cao, Cidan Yangji, Xiaoying Chen, Hui Jiang, Jincheng Zhong and Qiumei Ji

    Citation: BMC Genomics 2020 21:731

    Content type: Research article

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  12. Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in Cali...

    Authors: Peter Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish and Lynn Epstein

    Citation: BMC Genomics 2020 21:730

    Content type: Research article

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  14. The ray floret shapes referred to as petal types on the chrysanthemum (Chrysanthemum × morifolium Ramat.) capitulum is extremely abundant, which is one of the most important ornamental traits of chrysanthemum. Ho...

    Authors: Ya Pu, He Huang, Xiaohui Wen, Chenfei Lu, Bohan Zhang, Xueqi Gu, Shuai Qi, Guangxun Fan, Wenkui Wang and Silan Dai

    Citation: BMC Genomics 2020 21:728

    Content type: Research article

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  15. Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries an...

    Authors: Zhe Qu, Wenyan Nong, Yifei Yu, Tobias Baril, Ho Yin Yip, Alexander Hayward and Jerome H. L. Hui

    Citation: BMC Genomics 2020 21:726

    Content type: Research article

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  16. Phosphorus (P) is an essential element in maintaining high biomass and yield in crops. Soybean [Glycine max (L.) Merr.] requires a large amount of P during growth and development. Improvement of P efficiency and ...

    Authors: Wenkai Du, Lihua Ning, Yongshun Liu, Shixi Zhang, Yuming Yang, Qing Wang, Shengqian Chao, Hui Yang, Fang Huang, Hao Cheng and Deyue Yu

    Citation: BMC Genomics 2020 21:725

    Content type: Research article

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  17. Infectious bursal disease virus (IBDV) causes acute, highly contagious, immunosuppressive, and lethal infectious disease in young chickens and mainly infects the bursa of Fabricius (BF). To investigate interac...

    Authors: Xuewei Huang, Junyan Zhang, Zengsu Liu, Meng Wang, Xiaolong Fan, Li Wang, Han Zhou, Yanping Jiang, Wen Cui, Xinyuan Qiao, Yigang Xu, Yijing Li and Lijie Tang

    Citation: BMC Genomics 2020 21:724

    Content type: Research article

    Published on:

  18. Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster (Crassostrea gigas) undergoes a major phenotypic chan...

    Authors: Shelly A. Trigg, Kaitlyn R. Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B. Timmins-Schiffman and Steven B. Roberts

    Citation: BMC Genomics 2020 21:723

    Content type: Research article

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  19. The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The A...

    Authors: Nadeem Khan, Frank M. You, Raju Datla, Sridhar Ravichandran, Bosen Jia and Sylvie Cloutier

    Citation: BMC Genomics 2020 21:722

    Content type: Research article

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  20. We previously reported on the interplay between miR156/SPL13 and WD40–1/DFR to improve response to drought stress in alfalfa (Medicago sativa L.). Here we aimed to investigate whether the role of miR156/SPL13 mod...

    Authors: Biruk A. Feyissa, Justin Renaud, Vida Nasrollahi, Susanne E. Kohalmi and Abdelali Hannoufa

    Citation: BMC Genomics 2020 21:721

    Content type: Research article

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  21. Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondria...

    Authors: Jigme Dorji, Christy J. Vander Jagt, Josie B. Garner, Leah C. Marett, Brett A. Mason, Coralie M. Reich, Ruidong Xiang, Emily L. Clark, Benjamin G. Cocks, Amanda J. Chamberlain, Iona M. MacLeod and Hans D. Daetwyler

    Citation: BMC Genomics 2020 21:720

    Content type: Research article

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  22. Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been iso...

    Authors: Juan Chen, Jia-Mei Li, Yan-Jing Tang, Ke Ma, Bing Li, Xu Zeng, Xiao-Bin Liu, Yang Li, Zhu-Liang Yang, Wei-Nan Xu, Bao-Gui Xie, Hong-Wei Liu and Shun-Xing Guo

    Citation: BMC Genomics 2020 21:719

    Content type: Research article

    Published on:

  23. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Somayeh Kordafshari, Pollob Shil, Marc S. Marenda, Olusola M. Olaogun, Barbara Konsak-Ilievski, Jillian Disint and Amir H. Noormohammadi

    Citation: BMC Genomics 2020 21:718

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2020 21:598

  24. RNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic ce...

    Authors: Chatarin Wangsanuwat, Kellie A. Heom, Estella Liu, Michelle A. O’Malley and Siddharth S. Dey

    Citation: BMC Genomics 2020 21:717

    Content type: Methodology article

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  25. To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a sma...

    Authors: Gracia Zabala, Anupreet Kour and Lila O. Vodkin

    Citation: BMC Genomics 2020 21:716

    Content type: Research article

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  26. As global warming continues, heat stress (HS) is becoming an increasingly significant factor limiting plant growth and reproduction, especially for cool-season grass species. The objective of this study was to...

    Authors: Qi Yan, Xifang Zong, Fan Wu, Jie Li, Tiantian Ma, Yufeng Zhao, Qian Ma, Penglei Wang, Yanrong Wang and Jiyu Zhang

    Citation: BMC Genomics 2020 21:715

    Content type: Research article

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  27. Amylose accumulation in rice grains is controlled by genetic and environmental factors. Amylose content is a determinant factor of rice quality in terms of cooking and eating. Great variations in amylose conte...

    Authors: Hengdong Zhang, Jiana Chen, Shuanglü Shan, Fangbo Cao, Guanghui Chen, Yingbin Zou, Min Huang and Salah F. Abou-Elwafa

    Citation: BMC Genomics 2020 21:714

    Content type: Research article

    Published on:

  28. Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morpholo...

    Authors: Yiqian Li, Wenyan Nong, Tobias Baril, Ho Yin Yip, Thomas Swale, Alexander Hayward, David E. K. Ferrier and Jerome H. L. Hui

    Citation: BMC Genomics 2020 21:713

    Content type: Research article

    Published on:

  29. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Hye-Seon Kim, Jessica M. Lohmar, Mark Busman, Daren W. Brown, Todd A. Naumann, Hege H. Divon, Erik Lysøe, Silvio Uhlig and Robert H. Proctor

    Citation: BMC Genomics 2020 21:712

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2020 21:510

  30. Genes are regulated by various types of regulators and most of them are still unknown or unobserved. Current gene regulatory networks (GRNs) reverse engineering methods often neglect the unknown regulators and...

    Authors: Ming Shi, Sheng Tan, Xin-Ping Xie, Ao Li, Wulin Yang, Tao Zhu and Hong-Qiang Wang

    Citation: BMC Genomics 2020 21:711

    Content type: Methodology article

    Published on:

  31. In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important ...

    Authors: Jieping Huang, Xue Feng, Ruirui Zhu, Duo Guo, Yutong Wei, Xiaodan Cao, Yun Ma and Deshun Shi

    Citation: BMC Genomics 2020 21:710

    Content type: Research article

    Published on:

  32. The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CL...

    Authors: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi and Bo Zheng

    Citation: BMC Genomics 2020 21:709

    Content type: Methodology article

    Published on:

  33. Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacifi...

    Authors: Marina Athanasouli, Hanh Witte, Christian Weiler, Tobias Loschko, Gabi Eberhardt, Ralf J. Sommer and Christian Rödelsperger

    Citation: BMC Genomics 2020 21:708

    Content type: Research article

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  34. Lotus is an aquatic horticultural crop that is widely cultivated in most regions of China and is used as an important off-season vegetable. The principal root of lotus is degenerated, and adventitious roots (A...

    Authors: Cheng Libao, Han Yuyan, Zhao Minrong, Xu Xiaoyong, Shen Zhiguang, Wang Chunfei, Li Shuyan and Hu Zhubing

    Citation: BMC Genomics 2020 21:707

    Content type: Research article

    Published on:

  35. Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide ...

    Authors: Patrycja Daca-Roszak, Roman Jaksik, Julia Paczkowska, Michał Witt and Ewa Ziętkiewicz

    Citation: BMC Genomics 2020 21:706

    Content type: Research article

    Published on:

  36. Belonging to lineage I of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineag...

    Authors: Zhikang Zhang, Fanbo Meng, Pengchuan Sun, Jiaqing Yuan, Ke Gong, Chao Liu, Weijie Wang and Xiyin Wang

    Citation: BMC Genomics 2020 21:705

    Content type: Research article

    Published on:

  37. The population genetics of U.S. honey bee stocks remain poorly characterized despite the agricultural importance of Apis mellifera as the major crop pollinator. Commercial and research-based breeding programs hav...

    Authors: Perot Saelao, Michael Simone-Finstrom, Arian Avalos, Lelania Bilodeau, Robert Danka, Lilia de Guzman, Frank Rinkevich and Philip Tokarz

    Citation: BMC Genomics 2020 21:704

    Content type: Research article

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  38. Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, l...

    Authors: S. Lam, J. Zeidan, F. Miglior, A. Suárez-Vega, I. Gómez-Redondo, P. A. S. Fonseca, L. L. Guan, S. Waters and A. Cánovas

    Citation: BMC Genomics 2020 21:703

    Content type: Research article

    Published on:

  39. Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis, is known to be very com...

    Authors: Noémie S. Becker, Robert E. Rollins, Kateryna Nosenko, Alexander Paulus, Samantha Martin, Stefan Krebs, Ai Takano, Kozue Sato, Sergey Y. Kovalev, Hiroki Kawabata, Volker Fingerle and Gabriele Margos

    Citation: BMC Genomics 2020 21:702

    Content type: Research article

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  40. Intrauterine growth restriction (IUGR) remains a major problem associated with swine production. Thus, understanding the physiological changes of postnatal IUGR piglets would aid in improving growth performanc...

    Authors: Hongmei Gao, Longchao Zhang, Ligang Wang, Xin Liu, Xinhua Hou, Fuping Zhao, Hua Yan and Lixian Wang

    Citation: BMC Genomics 2020 21:701

    Content type: Research article

    Published on:

  41. A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is ...

    Authors: Guosong Zhang, Jie Li, Jiajia Zhang, Xia Liang, Tao Wang and Shaowu Yin

    Citation: BMC Genomics 2020 21:700

    Content type: Research article

    Published on:

  42. Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA cod...

    Authors: Liang Jiang, Yiqian Lu, Lin Zheng, Gaopeng Li, Lianchang Chen, Maona Zhang, Jiazuan Ni, Qiong Liu and Yan Zhang

    Citation: BMC Genomics 2020 21:699

    Content type: Research article

    Published on:

  43. Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This ...

    Authors: Michelle M. Halstead, Colin Kern, Perot Saelao, Ying Wang, Ganrea Chanthavixay, Juan F. Medrano, Alison L. Van Eenennaam, Ian Korf, Christopher K. Tuggle, Catherine W. Ernst, Huaijun Zhou and Pablo J. Ross

    Citation: BMC Genomics 2020 21:698

    Content type: Research article

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  44. Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes mo...

    Authors: Tao Hu, Tao Wang, Huiying Li, Misganaw Wassie, Huawei Xu and Liang Chen

    Citation: BMC Genomics 2020 21:696

    Content type: Research article

    Published on:

  45. The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and ...

    Authors: Cecilie Bækkedal Sonnenberg, Tim Kahlke and Peik Haugen

    Citation: BMC Genomics 2020 21:695

    Content type: Research article

    Published on:

  47. Copepods are fundamental components of pelagic food webs, but reports on how molecular responses link to reproductive success in natural populations are still scarce. We present a de novo transcriptome assembl...

    Authors: Ennio Russo, Chiara Lauritano, Giuliana d’Ippolito, Angelo Fontana, Diana Sarno, Eric von Elert, Adrianna Ianora and Ylenia Carotenuto

    Citation: BMC Genomics 2020 21:693

    Content type: Research article

    Published on:

  48. Head and neck squamous cell carcinoma (HNSCC) is a fatal malignancy owing to the lack of effective tools to predict overall survival (OS). MicroRNAs (miRNAs) play an important role in HNSCC occurrence, develop...

    Authors: Yusheng Huang, Zhiguo Liu, Limei Zhong, Yi Wen, Qixiang Ye, Donglin Cao, Peiwu Li and Yufeng Liu

    Citation: BMC Genomics 2020 21:691

    Content type: Research article

    Published on:

  50. MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different p...

    Authors: Shu-Yun Chen, Mei-Hsiu Su, Karl A. Kremling, Nicholas K. Lepak, M. Cinta Romay, Qi Sun, Peter J. Bradbury, Edward S. Buckler and Hsin-Mei Ku

    Citation: BMC Genomics 2020 21:689

    Content type: Research article

    Published on:

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