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  1. Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus)...

    Authors: Jiazhong Guo, Jie Zhong, George E. Liu, Liu Yang, Li Li, Guangling Chen, Tianzeng Song and Hongping Zhang

    Citation: BMC Genomics 2020 21:840

    Content type: Research article

    Published on:

  2. Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-to...

    Authors: Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen and Wuwei Ye

    Citation: BMC Genomics 2020 21:838

    Content type: Research article

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  3. Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in ...

    Authors: Bianca Büttner, Vera Draba, Klaus Pillen, Günther Schweizer and Andreas Maurer

    Citation: BMC Genomics 2020 21:837

    Content type: Research article

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  4. Insect-killing fungal species, Beauveria bassiana, is as an environment-friendly pest management tool, and many isolates are on the track of industrialization. However, some of B. bassiana isolates show similar m...

    Authors: Sihyeon Kim, Jong Cheol Kim, Se Jin Lee, Mi Rong Lee, So Eun Park, Dongwei Li, Sehyeon Baek, Tae Young Shin and Jae Su Kim

    Citation: BMC Genomics 2020 21:836

    Content type: Research article

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  5. The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in pl...

    Authors: Xiu Feng, Yintao Jia, Ren Zhu, Kemao Li, Zhongzhi Guan and Yifeng Chen

    Citation: BMC Genomics 2020 21:835

    Content type: Research article

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  6. Rhodotorula glutinis is recognized as a biotechnologically important oleaginous red yeast, which synthesizes numerous meritorious compounds with wide industrial usages. One of the most notable properties of R. gl...

    Authors: Chun-Ji Li, Die Zhao, Ping Cheng, Li Zheng and Guo-Hui Yu

    Citation: BMC Genomics 2020 21:834

    Content type: Research article

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  7. Primary hypoadrenocorticism (or Addison’s disease, AD) is an autoimmune disease that results in destruction of the adrenal cortex and consequent adrenal insufficiency. The disease has been described in purebre...

    Authors: Liza C. Gershony, Janelle M. Belanger, Marjo K. Hytönen, Hannes Lohi, Thomas R. Famula and Anita M. Oberbauer

    Citation: BMC Genomics 2020 21:833

    Content type: Research article

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  8. The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a ...

    Authors: Juan F. Guerra Maldonado, Antony T. Vincent, Martin Chenal and Frederic J. Veyrier

    Citation: BMC Genomics 2020 21:832

    Content type: Software

    Published on:

  9. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct...

    Authors: Caroline M. Stott and Louis-Marie Bobay

    Citation: BMC Genomics 2020 21:829

    Content type: Research article

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  10. Long term preservation of living ovarian tissues is a critical approach in human reproductive medicine as well as in the conservation of rare animal genotypes. Compared to single cell preservation, optimizatio...

    Authors: Olga Amelkina and Pierre Comizzoli

    Citation: BMC Genomics 2020 21:828

    Content type: Research article

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  11. Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CC...

    Authors: Meng Zhang, Ji Liu, Qiang Ma, Yuan Qin, Hantao Wang, Pengyun Chen, Liang Ma, Xiaokang Fu, Longfu Zhu, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:825

    Content type: Research article

    Published on:

  12. Periparturient cows release fatty acid reserves from adipose tissue (AT) through lipolysis in response to the negative energy balance induced by physiological changes related to parturition and the onset of la...

    Authors: David Salcedo-Tacuma, Jair Parales-Giron, Crystal Prom, Miguel Chirivi, Juliana Laguna, Adam L. Lock and G. Andres Contreras

    Citation: BMC Genomics 2020 21:824

    Content type: Research article

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  13. Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impac...

    Authors: Xiaofei Yang, Shenghan Gao, Tingjie Wang, Boyu Yang, Ningxin Dang and Kai Ye

    Citation: BMC Genomics 2020 21:823

    Content type: Methodology article

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  14. Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to...

    Authors: Andrew P. Wilkey, Anne V. Brown, Steven B. Cannon and Ethalinda K. S. Cannon

    Citation: BMC Genomics 2020 21:822

    Content type: Software

    Published on:

  15. Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by contro...

    Authors: Vatsala Koul, Divya Srivastava, Pushplata Prasad Singh and Mandira Kochar

    Citation: BMC Genomics 2020 21:821

    Content type: Research article

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  16. Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based ...

    Authors: Pratima Chapagain, Donald Walker, Tim Leeds, Beth M. Cleveland and Mohamed Salem

    Citation: BMC Genomics 2020 21:820

    Content type: Research article

    Published on:

  17. The common cutworm, Spodoptera litura Fabricius is a leaf and fruit feeding generalist insect of the order Lepidoptera and a destructive agriculture pest. The broad host range of the herbivore is due to its abili...

    Authors: Vinod Kumar Prajapati, Mahendra Varma and Jyothilakshmi Vadassery

    Citation: BMC Genomics 2020 21:819

    Content type: Research article

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  18. Actinoplanes sp. SE50/110 is the natural producer of the diabetes mellitus drug acarbose, which is highly produced during the growth phase and ceases during the stationary phase. In previous works, the growth-dep...

    Authors: Julian Droste, Vera Ortseifen, Lena Schaffert, Marcus Persicke, Susanne Schneiker-Bekel, Alfred Pühler and Jörn Kalinowski

    Citation: BMC Genomics 2020 21:818

    Content type: Research article

    Published on:

  19. The gut microbiome can influence life history traits associated with host fitness such as fecundity and longevity. In most organisms, these two life history traits are traded-off, while they are positively lin...

    Authors: Matteo Antoine Negroni, Francisca H. I. D. Segers, Fanny Vogelweith and Susanne Foitzik

    Citation: BMC Genomics 2020 21:816

    Content type: Research article

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  20. Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and fam...

    Authors: Astrid Tempestini, Gloria Massamba-N’Siala, Fanny Vermandele, Nicholas Beaudreau, Mathieu Mortz, France Dufresne and Piero Calosi

    Citation: BMC Genomics 2020 21:815

    Content type: Research article

    Published on:

  21. Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human sal...

    Authors: Yuanmei Wang, Liying Liu, Min Li, Lili Lin, Pengcheng Su, Hui Tang, Xinzhong Fan and Xianyao Li

    Citation: BMC Genomics 2020 21:814

    Content type: Research article

    Published on:

  22. Amoebozoa is a eukaryotic supergroup composed of unicellular and multicellular amoebic protozoa (e.g. Acanthamoeba, Dictyostelium, and Entamoeba). They are model organisms for studies in cellular and evolutionary...

    Authors: Tetsuro Kawano-Sugaya, Shinji Izumiyama, Yasuaki Yanagawa, Yumiko Saito-Nakano, Koji Watanabe, Seiki Kobayashi, Kumiko Nakada-Tsukui and Tomoyoshi Nozaki

    Citation: BMC Genomics 2020 21:813

    Content type: Research article

    Published on:

  23. Malonylation is a recently discovered post-translational modification that is associated with a variety of diseases such as Type 2 Diabetes Mellitus and different types of cancers. Compared with experimental i...

    Authors: Xin Liu, Liang Wang, Jian Li, Junfeng Hu and Xiao Zhang

    Citation: BMC Genomics 2020 21:812

    Content type: Methodology article

    Published on:

  24. Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids a...

    Authors: Guilherme Gainett, Jesús A. Ballesteros, Charlotte R. Kanzler, Jakob T. Zehms, John M. Zern, Shlomi Aharon, Efrat Gavish-Regev and Prashant P. Sharma

    Citation: BMC Genomics 2020 21:811

    Content type: Research article

    Published on:

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

    Authors: Camilo Breton, Peter M. Clark, Lili Wang, Jenny A. Greig and James M. Wilson

    Citation: BMC Genomics 2020 21:810

    Content type: Correction

    Published on:

    The original article was published in BMC Genomics 2020 21:239

  26. The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’...

    Authors: Manyi Sun, Mingyue Zhang, Jugpreet Singh, Bobo Song, Zikai Tang, Yueyuan Liu, Runze Wang, Mengfan Qin, Jiaming Li, Awais Khan and Jun Wu

    Citation: BMC Genomics 2020 21:809

    Content type: Research article

    Published on:

  27. Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilita...

    Authors: Chia-Chi Hsu, Shu-Yun Chen, Pei-Han Lai, Yu-Yun Hsiao, Wen-Chieh Tsai, Zhong-Jian Liu, Mei-Chu Chung, Olivier Panaud and Hong-Hwa Chen

    Citation: BMC Genomics 2020 21:807

    Content type: Research article

    Published on:

  28. Next-generation sequencing (NGS) is widely used for genome-wide identification and quantification of DNA elements involved in the regulation of gene transcription. Studies that generate multiple high-throughpu...

    Authors: Bronte Wen, Hyun Jun Jung, Lihe Chen, Fahad Saeed and Mark A. Knepper

    Citation: BMC Genomics 2020 21:806

    Content type: Software

    Published on:

  29. With declining wild fish populations, farmed salmon has gained popularity as a source for healthy long-chain highly unsaturated fatty acids (LC-HUFA). However, the introduction of plant oil in farmed salmon fe...

    Authors: Yang Jin, Alex K. Datsomor, Rolf E. Olsen, Jon Olav Vik, Jacob S. Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge and Fabian Grammes

    Citation: BMC Genomics 2020 21:805

    Content type: Research article

    Published on:

  30. The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein transl...

    Authors: Tapan Kumar Mohanta, Awdhesh Kumar Mishra, Abeer Hashem, Elsayed Fathi Abd_Allah, Abdul Latif Khan and Ahmed Al-Harrasi

    Citation: BMC Genomics 2020 21:804

    Content type: Research article

    Published on:

  31. Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale me...

    Authors: Yufei Xiao, Junji Li, Ye Zhang, Xiaoning Zhang, Hailong Liu, Zihai Qin and Bowen Chen

    Citation: BMC Genomics 2020 21:803

    Content type: Research article

    Published on:

  32. The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in li...

    Authors: Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond and Gabriela Lobinska

    Citation: BMC Genomics 2020 21(Suppl 10):779

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  33. The emergence of the third generation sequencing technology, featuring longer read lengths, has demonstrated great advancement compared to the next generation sequencing technology and greatly promoted the bio...

    Authors: Jiaqi Liu, Jiayin Wang, Xiao Xiao, Xin Lai, Daocheng Dai, Xuanping Zhang, Xiaoyan Zhu, Zhongmeng Zhao, Juan Wang and Zhimin Li

    Citation: BMC Genomics 2020 21(Suppl 10):753

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  34. Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people’s health and reinforce vital energy. Despite its prevalence, however...

    Authors: Xueting Wu, Xuetong Li, Wei Wang, Yuanhong Shan, Cuiting Wang, Mulan Zhu, Qiong La, Yang Zhong, Ye Xu, Peng Nan and Xuan Li

    Citation: BMC Genomics 2020 21(Suppl 10):697

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  35. Immense improvements in sequencing technologies enable producing large amounts of high throughput and cost effective next-generation sequencing (NGS) data. This data needs to be processed efficiently for furth...

    Authors: Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars and H. Peter Hofstee

    Citation: BMC Genomics 2020 21(Suppl 10):683

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  36. Single-cell RNA-sequencing (scRNA-seq) is becoming indispensable in the study of cell-specific transcriptomes. However, in scRNA-seq techniques, only a small fraction of the genes are captured due to “dropout”...

    Authors: Xikang Feng, Lingxi Chen, Zishuai Wang and Shuai Cheng Li

    Citation: BMC Genomics 2020 21(Suppl 10):618

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  37. Biological evidence has shown that microRNAs(miRNAs) are greatly implicated in various biological progresses involved in human diseases. The identification of miRNA-disease associations(MDAs) is beneficial to ...

    Authors: Huiran Li, Yin Guo, Menglan Cai and Limin Li

    Citation: BMC Genomics 2020 21(Suppl 10):617

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  38. Regulatory hotspots are genetic variations that may regulate the expression levels of many genes. It has been of great interest to find those hotspots utilizing expression quantitative trait locus (eQTL) analy...

    Authors: Ju Hun Choi, Taegun Kim, Junghyun Jung and Jong Wha J. Joo

    Citation: BMC Genomics 2020 21(Suppl 10):616

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  39. The current computational methods on identifying conserved protein complexes across multiple Protein-Protein Interaction (PPI) networks suffer from the lack of explicit modeling of the desired topological prop...

    Authors: Yijie Wang, Hyundoo Jeong, Byung-Jun Yoon and Xiaoning Qian

    Citation: BMC Genomics 2020 21(Suppl 10):615

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  40. Bivalent promoters marked with both H3K27me3 and H3K4me3 histone modifications are characteristic of poised promoters in embryonic stem (ES) cells. The model of poised promoters postulates that bivalent chroma...

    Authors: Ah-Jung Jeon and Greg Tucker-Kellogg

    Citation: BMC Genomics 2020 21(Suppl 10):614

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  41. Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data.

    Authors: Liandong Yang, Zetan Xu, Honghui Zeng, Ning Sun, Baosheng Wu, Cheng Wang, Jing Bo, Lin Li, Yang Dong and Shunping He

    Citation: BMC Genomics 2020 21:801

    Content type: Database

    Published on:

  42. Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this t...

    Authors: Kunzhe Dong, Min Yang, Jiangang Han, Qing Ma, Jilong Han, Ziyi Song, Cuicheng Luosang, Neena Amatya Gorkhali, Bohui Yang, Xiaohong He, Yuehui Ma and Lin Jiang

    Citation: BMC Genomics 2020 21:800

    Content type: Research article

    Published on:

  43. The archaeal exosome is an exoribonucleolytic multiprotein complex, which degrades single-stranded RNA in 3′ to 5′ direction phosphorolytically. In a reverse reaction, it can add A-rich tails to the 3′-end of ...

    Authors: Jochen Bathke, A. Susann Gauernack, Oliver Rupp, Lennart Weber, Christian Preusser, Marcus Lechner, Oliver Rossbach, Alexander Goesmann, Elena Evguenieva-Hackenberg and Gabriele Klug

    Citation: BMC Genomics 2020 21:797

    Content type: Research article

    Published on:

  44. Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots p...

    Authors: Ainhoa Calleja-Rodriguez, Jin Pan, Tomas Funda, Zhiqiang Chen, John Baison, Fikret Isik, Sara Abrahamsson and Harry X. Wu

    Citation: BMC Genomics 2020 21:796

    Content type: Research article

    Published on:

  45. Valine-glutamine (VQ) motif-containing proteins play important roles in plant growth, development and abiotic stress response. For many plant species, the VQ genes have been identified and their functions have be...

    Authors: Pengyun Chen, Fei wei, Shuaishuai Cheng, Liang Ma, Hantao Wang, Meng Zhang, Guangzhi Mao, Jianhua Lu, Pengbo Hao, Adeel Ahmad, Lijiao Gu, Qiang Ma, Aimin Wu, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:795

    Content type: Research article

    Published on:

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