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  1. A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the...

    Authors: Hong-Yan Zhao, Lin Wen, Yu-Feng Miao, Yu Du, Yan Sun, Yin Yin, Chi-Xian Lin, Long-Hui Lin, Xiang Ji and Jian-Fang Gao

    Citation: BMC Genomics 2021 22:520

    Content type: Research article

    Published on:

  2. Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacter...

    Authors: Yang Yang, Yongmao Chai, Jiayi Liu, Jie Zheng, Zhangchen Zhao, Aduragbemi Amo, Chunge Cui, Qiumei Lu, Liang Chen and Yin-Gang Hu

    Citation: BMC Genomics 2021 22:519

    Content type: Research article

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  3. Direct-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications a...

    Authors: Ratanond Koonchanok, Swapna Vidhur Daulatabad, Quoseena Mir, Khairi Reda and Sarath Chandra Janga

    Citation: BMC Genomics 2021 22:513

    Content type: Software

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  4. Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive geneti...

    Authors: Akio Onogi, Toshio Watanabe, Atsushi Ogino, Kazuhito Kurogi and Kenji Togashi

    Citation: BMC Genomics 2021 22:512

    Content type: Research article

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  5. Macrobrachium nipponense is an economically important species of freshwater shrimp in China. Unlike other marine shrimps, the ovaries in adult female M. nipponense can mature rapidly and periodically during the r...

    Authors: Yuning Zhang, Sufei Jiang, Hui Qiao, Yiwei Xiong, Hongtuo Fu, Wenyi Zhang, Yongsheng Gong, Shubo Jin and Yan Wu

    Citation: BMC Genomics 2021 22:510

    Content type: Research

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  6. GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of t...

    Authors: Yu Fan, Jun Yan, Dili Lai, Hao Yang, Guoxing Xue, Ailing He, Tianrong Guo, Long Chen, Xiao-bin Cheng, Da-bing Xiang, Jingjun Ruan and Jianping Cheng

    Citation: BMC Genomics 2021 22:509

    Content type: Research

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  7. Salmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella

    Authors: Xiujuan Zhou, Bin Liu, Yanhong Liu, Chunlei Shi, Pina M. Fratamico, Lida Zhang, Dapeng Wang, Jianhua Zhang, Yan Cui, Ping Xu and Xianming Shi

    Citation: BMC Genomics 2021 22:507

    Content type: Research

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  8. Teleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniof...

    Authors: Laurène Alicia Lecaudey, Pooja Singh, Christian Sturmbauer, Anna Duenser, Wolfgang Gessl and Ehsan Pashay Ahi

    Citation: BMC Genomics 2021 22:506

    Content type: Research

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  9. Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil prope...

    Authors: Alina I. Chernova, Rim F. Gubaev, Anupam Singh, Katrina Sherbina, Svetlana V. Goryunova, Elena U. Martynova, Denis V. Goryunov, Stepan V. Boldyrev, Anna A. Vanyushkina, Nikolay A. Anikanov, Elena A. Stekolshchikova, Ekaterina A. Yushina, Yakov N. Demurin, Zhanna M. Mukhina, Vera A. Gavrilova, Irina N. Anisimova…

    Citation: BMC Genomics 2021 22:505

    Content type: Research article

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  10. Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-co...

    Authors: Guang Yang, Wenqiu Pan, Ruoyu Zhang, Yan Pan, Qifan Guo, Weining Song, Weijun Zheng and Xiaojun Nie

    Citation: BMC Genomics 2021 22:504

    Content type: Research

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  11. The dieback epidemic decimating common ash (Fraxinus excelsior) in Europe is caused by the invasive fungus Hymenoscyphus fraxineus. In this study we analyzed the genomes of H. fraxineus and H. albidus, its native...

    Authors: Malin Elfstrand, Jun Chen, Michelle Cleary, Sandra Halecker, Katarina Ihrmark, Magnus Karlsson, Kateryna Davydenko, Jan Stenlid, Marc Stadler and Mikael Brandström Durling

    Citation: BMC Genomics 2021 22:503

    Content type: Research

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  12. Dinotefuran (CAS No. 165252–70-0), a neonicotinoid insecticide, has been used to protect various crops against invertebrate pests and has been associated with numerous negative sublethal effects on honey bees....

    Authors: Minjie Huang, Jie Dong, Haikun Guo, Minghui Xiao and Deqian Wang

    Citation: BMC Genomics 2021 22:502

    Content type: Research

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  13. Improving feed efficiency (FE) is an important goal due to its economic and environmental significance for farm animal production. The FE phenotype is complex and based on the measurements of the individual fe...

    Authors: Farouk Messad, Isabelle Louveau, David Renaudeau, Hélène Gilbert and Florence Gondret

    Citation: BMC Genomics 2021 22:501

    Content type: Research article

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  14. Brown adipose tissue (BAT) is specialized to dissipate energy in the form of heat. BAT-mediated heat production in rodents and humans is critical for effective temperature adaptation of newborns to the extraut...

    Authors: Sujoy Ghosh, Chul-Hong Park, Jisu Lee, Nathan Lee, Rui Zhang, Clara Huesing, Dorien Reijnders, Jennifer Sones, Heike Münzberg, Leanne Redman and Ji Suk Chang

    Citation: BMC Genomics 2021 22:500

    Content type: Research article

    Published on:

  15. Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and...

    Authors: Tharvesh M. Liyakat Ali, Annaël Brunet, Philippe Collas and Jonas Paulsen

    Citation: BMC Genomics 2021 22:499

    Content type: Research article

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  16. Virescent mutation broadly exists in plants and is an ideal experimental material to investigate regulatory mechanisms underlying chlorophyll synthesis, photosynthesis and plant growth. Up to date, the molecul...

    Authors: Jin Gao, Yang Shi, Wei Wang, Yong-Hui Wang, Hua Yang, Qing-Hua Shi, Jian-Ping Chen, Yan-Ru Sun and Li-Wang Cai

    Citation: BMC Genomics 2021 22:498

    Content type: Research

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  17. During eye lens development the embryonic vasculature regresses leaving the lens without a direct oxygen source. Both embryonically and throughout adult life, the lens contains a decreasing oxygen gradient fro...

    Authors: Joshua Disatham, Lisa Brennan, Daniel Chauss, Jason Kantorow, Behdad Afzali and Marc Kantorow

    Citation: BMC Genomics 2021 22:497

    Content type: Research

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  18. Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copi...

    Authors: Eldar T. Abdullaev, Iren R. Umarova and Peter F. Arndt

    Citation: BMC Genomics 2021 22:496

    Content type: Research article

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  19. Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem c...

    Authors: Mary Luz Yaya Lancheros, Krishan Mohan Rai, Vimal Kumar Balasubramanian, Lavanya Dampanaboina, Venugopal Mendu and Wilson Terán

    Citation: BMC Genomics 2021 22:494

    Content type: Research article

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  20. The accumulation of carotenoids in adipose tissue leading to yellow fat is, in sheep, a heritable recessive trait that can be attributed to a nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene. Howeve...

    Authors: Matthew Kent, Michel Moser, Inger Anne Boman, Kristine Lindtveit, Mariann Árnyasi, Kristil Kindem Sundsaasen and Dag Inge Våge

    Citation: BMC Genomics 2021 22:492

    Content type: Research article

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  21. Pantothenic acid deficiency (PAD) results in growth depression and intestinal hypofunction of animals. However, the underlying molecular mechanisms remain to be elucidated. Mucosal proteome might reflect dieta...

    Authors: Jing Tang, Yulong Feng, Bo Zhang, Yongbao Wu, Zhanbao Guo, Suyun Liang, Zhengkui Zhou, Ming Xie and Shuisheng Hou

    Citation: BMC Genomics 2021 22:491

    Content type: Research article

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  22. Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection p...

    Authors: Jia Li, Chao Bian, Yunhai Yi, Hui Yu, Xinxin You and Qiong Shi

    Citation: BMC Genomics 2021 22:490

    Content type: Research article

    Published on:

  23. Preterm birth is the leading cause of neonatal morbidity and mortality, but research efforts in neonatology are complicated due to the unavailability of large volume blood samples. Whole blood assays can be us...

    Authors: Kristin Hieronymus, Benjamin Dorschner, Felix Schulze, Neeta L. Vora, Joel S. Parker, Jennifer Lucia Winkler, Angela Rösen-Wolff and Stefan Winkler

    Citation: BMC Genomics 2021 22:489

    Content type: Methodology article

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  24. The thermal-manipulation (TM) during egg incubation is a cyclic exposure to hot or cold temperatures during embryogenesis that is associated to long-lasting effects on growth performance, physiology, metabolis...

    Authors: Anaïs Vitorino Carvalho, Christelle Hennequet-Antier, Aurélien Brionne, Sabine Crochet, Justine Jimenez, Nathalie Couroussé, Anne Collin and Vincent Coustham

    Citation: BMC Genomics 2021 22:488

    Content type: Research

    Published on:

  25. During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique ...

    Authors: Yan Deng, Shenqiang Hu, Chenglong Luo, Qingyuan Ouyang, Li Li, Jiaming Ma, Zhenping Lin, Junpeng Chen, Hehe Liu, Jiwei Hu, Guohong Chen, Dingming Shu, Yuxuan Pan, Bo Hu, Hua He, Hao Qu…

    Citation: BMC Genomics 2021 22:487

    Content type: Research

    Published on:

  26. Metabolic stress, as negative energy balance on one hand or obesity on the other hand can lead to increased levels of free fatty acids in the plasma and follicular fluid of animals and humans. In an earlier st...

    Authors: Vengala Rao Yenuganti, Dirk Koczan and Jens Vanselow

    Citation: BMC Genomics 2021 22:486

    Content type: Research article

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  27. Calcium (Ca) and phosphorus (P) are essential nutrients that are linked to a large array of biological processes. Disturbances in Ca and P homeostasis in chickens are associated with a decline in growth and eg...

    Authors: Henry Reyer, Michael Oster, Siriluck Ponsuksili, Nares Trakooljul, Adewunmi O. Omotoso, Muhammad A. Iqbal, Eduard Muráni, Vera Sommerfeld, Markus Rodehutscord and Klaus Wimmers

    Citation: BMC Genomics 2021 22:485

    Content type: Research article

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  28. Sex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression ...

    Authors: Yucheng Wang, Eilis Hannon, Olivia A. Grant, Tyler J. Gorrie-Stone, Meena Kumari, Jonathan Mill, Xiaojun Zhai, Klaus D. McDonald-Maier and Leonard C. Schalkwyk

    Citation: BMC Genomics 2021 22:484

    Content type: Methodology article

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  29. Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae subtribe Saccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grass...

    Authors: Nathan Maren, Fangzhou Zhao, Rishi Aryal, Darren Touchell, Wusheng Liu, Thomas Ranney and Hamid Ashrafi

    Citation: BMC Genomics 2021 22:483

    Content type: Research

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  30. Transcription factors (TFs) bind specifically to TF binding sites (TFBSs) at cis-regulatory regions to control transcription. It is critical to locate these TF-DNA interactions to understand transcriptional re...

    Authors: Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime Abraham Castro-Mondragon and Anthony Mathelier

    Citation: BMC Genomics 2021 22:482

    Content type: Research

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  31. Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosom...

    Authors: Satoshi Fujito, Turgut Yigit Akyol, Takuya Mukae, Tadayuki Wako, Ken-ichiro Yamashita, Hikaru Tsukazaki, Hideki Hirakawa, Keisuke Tanaka, Yoko Mine, Shusei Sato and Masayoshi Shigyo

    Citation: BMC Genomics 2021 22:481

    Content type: Research article

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  32. Low conception rate (CR) despite insemination with morphologically normal spermatozoa is a common reproductive restraint that limits buffalo productivity. This accounts for a significant loss to the farmers an...

    Authors: Vipul Batra, Vanya Bhushan, Syed Azmal Ali, Parul Sarwalia, Ankit Pal, Seema Karanwal, Subhash Solanki, Arumugam Kumaresan, Rakesh Kumar and Tirtha Kumar Datta

    Citation: BMC Genomics 2021 22:480

    Content type: Research

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  33. Identifying differentially expressed genes between the same or different species is an urgent demand for biological and medical research. For RNA-seq data, systematic technical effects and different sequencing...

    Authors: Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu and Guoliang Tian

    Citation: BMC Genomics 2021 22:479

    Content type: Methodology article

    Published on:

  34. Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant ...

    Authors: Gehendra Bhattarai, Wei Yang, Ainong Shi, Chunda Feng, Braham Dhillon, James C. Correll and Beiquan Mou

    Citation: BMC Genomics 2021 22:478

    Content type: Research article

    Published on:

  35. Glaucoma is a leading cause of visual disability and blindness. Release of iris pigment within the eye, pigment dispersion syndrome (PDS), can lead to one type of glaucoma known as pigmentary glaucoma. PDS has...

    Authors: Carly van der Heide, Wes Goar, Kacie J. Meyer, Wallace L. M. Alward, Erin A. Boese, Nathan C. Sears, Ben R. Roos, Young H. Kwon, Adam P. DeLuca, Owen M. Siggs, Claudia Gonzaga-Jauregui, Val C. Sheffield, Kai Wang, Edwin M. Stone, Robert F. Mullins, Michael G. Anderson…

    Citation: BMC Genomics 2021 22:477

    Content type: Research

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  36. The sequence content of the 3′ UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging.

    Authors: Raeann Goering, Krysta L. Engel, Austin E. Gillen, Nova Fong, David L. Bentley and J. Matthew Taliaferro

    Citation: BMC Genomics 2021 22:476

    Content type: Methodology article

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  37. Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction...

    Authors: Valentine Murigneux, Leah W. Roberts, Brian M. Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam D. Irwin, Patrick N. A. Harris, David L. Paterson, Mark A. Schembri, David M. Whiley and Scott A. Beatson

    Citation: BMC Genomics 2021 22:474

    Content type: Software

    Published on:

  38. Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. Howeve...

    Authors: Jenni Harmoinen, Alina von Thaden, Jouni Aspi, Laura Kvist, Berardino Cocchiararo, Anne Jarausch, Andrea Gazzola, Teodora Sin, Hannes Lohi, Marjo K. Hytönen, Ilpo Kojola, Astrid Vik Stronen, Romolo Caniglia, Federica Mattucci, Marco Galaverni, Raquel Godinho…

    Citation: BMC Genomics 2021 22:473

    Content type: Research article

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  39. Ventilator-induced diaphragmatic dysfunction (VIDD) is associated with weaning difficulties, intensive care unit hospitalization (ICU), infant mortality, and poor long-term clinical outcomes. The expression pa...

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

    Citation: BMC Genomics 2021 22:472

    Content type: Research article

    Published on:

  40. The identification of differentially expressed genes (DEGs) is an important task in many biological studies. The currently widely used methods often calculate a score for each gene by estimating the significan...

    Authors: Bolin Chen, Li Gao and Xuequn Shang

    Citation: BMC Genomics 2021 22(Suppl 1):471

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 1

  41. Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially t...

    Authors: Maria Buerstmayr, Christian Wagner, Tetyana Nosenko, Jimmy Omony, Barbara Steiner, Thomas Nussbaumer, Klaus F. X. Mayer and Hermann Buerstmayr

    Citation: BMC Genomics 2021 22:470

    Content type: Research

    Published on:

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