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Comparative and evolutionary genomics

Section edited by Igor Rogozin and Alexei Fedorov

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

Page 5 of 19

  1. Barley is relatively sensitive to Aluminum (Al) toxicity among cereal crops, but shows a wide genotypic difference in Al tolerance. The well-known Al-tolerant mechanism in barley is related to Al exclusion med...

    Authors: Liyuan Wu, Jiahua Yu, Qiufang Shen, Lu Huang, Dezhi Wu and Guoping Zhang

    Citation: BMC Genomics 2018 19:560

    Content type: Short report

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  2. Thraustochytrids are unicellular fungal-like marine protists with ubiquitous existence in marine environments. They are well-known for their ability to produce high-valued omega-3 polyunsaturated fatty acids (...

    Authors: Zhiquan Song, Jason E. Stajich, Yunxuan Xie, Xianhua Liu, Yaodong He, Jinfeng Chen, Glenn R. Hicks and Guangyi Wang

    Citation: BMC Genomics 2018 19:541

    Content type: Research article

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  3. The Zika virus (ZIKV) can cause microcephaly and congenital abnormalities in the foetus. Recent studies have provided insights into the evolution of ZIKV from the current and previous outbreaks, but the types ...

    Authors: Hyeji Lee, Mai Phuong Nguyen, Yunhee Choi and Yong-Hak Kim

    Citation: BMC Genomics 2018 19:535

    Content type: Methodology article

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  4. Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gas...

    Authors: Qiuwen He, Qiangchuan Hou, Yanjie Wang, Jing Li, Weicheng Li, Lai-Yu Kwok, Zhihong Sun, Heping Zhang and Zhi Zhong

    Citation: BMC Genomics 2018 19:527

    Content type: Research article

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  5. Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation...

    Authors: Wuhui Li, Junmei Liu, Hui Tan, Lingling Luo, Jialin Cui, Jie Hu, Shi Wang, Qingfeng Liu, Fangzhou Hu, Chenchen Tang, Li Ren, Conghui Yang, Rurong Zhao, Min Tao, Chun Zhang, Qinbo Qin…

    Citation: BMC Genomics 2018 19:517

    Content type: Research article

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  6. Genomic data from various organisms have been used to study how sexual selection has shaped genetic diversity in reproductive proteins, and in particular, to elucidate how mating systems may have influenced ev...

    Authors: Katrina G. Claw, Renee D. George, Michael J. MacCoss and Willie J. Swanson

    Citation: BMC Genomics 2018 19:488

    Content type: Research article

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  7. Some mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-strande...

    Authors: Yves Quentin, Patricia Siguier, Mick Chandler and Gwennaele Fichant

    Citation: BMC Genomics 2018 19:475

    Content type: Research article

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  8. The availability of the genomes of two archaic humans, Neanderthal and Denisovan, and that of modern humans provides researchers an opportunity to investigate genetic differences between these three subspecies...

    Authors: Matyas F. Cserhati, Mary-Ellen Mooter, Lauren Peterson, Benjamin Wicks, Peng Xiao, Mark Pauley and Chittibabu Guda

    Citation: BMC Genomics 2018 19:472

    Content type: Research article

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  9. Mycorrhizal symbiosis is one of the most fundamental types of mutualistic plant-microbe interaction. Among the many classes of mycorrhizae, the arbuscular mycorrhizae have the most general symbiotic style and ...

    Authors: Yuuki Kobayashi, Taro Maeda, Katsushi Yamaguchi, Hiromu Kameoka, Sachiko Tanaka, Tatsuhiro Ezawa, Shuji Shigenobu and Masayoshi Kawaguchi

    Citation: BMC Genomics 2018 19:465

    Content type: Research article

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  10. The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential componen...

    Authors: Eiichi Shoguchi, Girish Beedessee, Ipputa Tada, Kanako Hisata, Takeshi Kawashima, Takeshi Takeuchi, Nana Arakaki, Manabu Fujie, Ryo Koyanagi, Michael C. Roy, Masanobu Kawachi, Michio Hidaka, Noriyuki Satoh and Chuya Shinzato

    Citation: BMC Genomics 2018 19:458

    Content type: Research article

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  11. Post-transcriptional regulation is crucial for the control of eukaryotic gene expression and might contribute to adaptive divergence. The three prime untranslated regions (3’ UTRs), that are located downstream...

    Authors: Peiwen Xiong, C. Darrin Hulsey, Axel Meyer and Paolo Franchini

    Citation: BMC Genomics 2018 19:433

    Content type: Research article

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  12. Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of...

    Authors: Martina Adamek, Mohammad Alanjary, Helena Sales-Ortells, Michael Goodfellow, Alan T. Bull, Anika Winkler, Daniel Wibberg, Jörn Kalinowski and Nadine Ziemert

    Citation: BMC Genomics 2018 19:426

    Content type: Research article

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  13. Transporter proteins mediate the translocation of substances across the membranes of living cells. Many transport processes are energetically expensive and the cells use 20 to 60% of their energy to power the ...

    Authors: Behrooz Darbani, Douglas B. Kell and Irina Borodina

    Citation: BMC Genomics 2018 19:418

    Content type: Research article

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  14. Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community st...

    Authors: Itai Opatovsky, Diego Santos-Garcia, Zhepu Ruan, Tamar Lahav, Shany Ofaim, Laurence Mouton, Valérie Barbe, Jiandong Jiang, Einat Zchori-Fein and Shiri Freilich

    Citation: BMC Genomics 2018 19:402

    Content type: Research article

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  15. The simplicity of the CRISPR/Cas9 system has enabled its widespread applications in generating animal models, functional genomic screening and in treating genetic and infectious diseases. However, unintended m...

    Authors: Xiaolong Wang, Jing Liu, Yiyuan Niu, Yan Li, Shiwei Zhou, Chao Li, Baohua Ma, Qifang Kou, Bjoern Petersen, Tad Sonstegard, Xingxu Huang, Yu Jiang and Yulin Chen

    Citation: BMC Genomics 2018 19:397

    Content type: Research article

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  16. High hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motil...

    Authors: Yi Lan, Jin Sun, Ting Xu, Chong Chen, Renmao Tian, Jian-Wen Qiu and Pei-Yuan Qian

    Citation: BMC Genomics 2018 19:394

    Content type: Research article

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  17. The emergence of epithelia was the foundation of metazoan expansion. Epithelial tissues are a hallmark of metazoans deeply rooted in the evolution of their complex developmental morphogenesis processes. Howeve...

    Authors: Hassiba Belahbib, Emmanuelle Renard, Sébastien Santini, Cyril Jourda, Jean-Michel Claverie, Carole Borchiellini and André Le Bivic

    Citation: BMC Genomics 2018 19:393

    Content type: Research article

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  18. Mikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species na...

    Authors: Wuxia Guo, Ying Liu, Wei Lun Ng, Pei-Chun Liao, Bing-Hong Huang, Weixi Li, Chunmei Li, Xianggang Shi and Yelin Huang

    Citation: BMC Genomics 2018 19:392

    Content type: Research article

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  19. The sense of smell is unrivaled in terms of molecular complexity of its input channels. Even zebrafish, a model vertebrate system in many research fields including olfaction, possesses several hundred differen...

    Authors: Gaurav Ahuja, Vera Reichel, Daniel Kowatschew, Adnan S. Syed, Aswani Kumar Kotagiri, Yuichiro Oka, Franco Weth and Sigrun I. Korsching

    Citation: BMC Genomics 2018 19:383

    Content type: Research article

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  20. Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chic...

    Authors: Jake A. Lacey, Theodore R. Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas Stent, Xiaoyan Han, Julian I. Rood, Ben Wade, Anthony L. Keyburn, Torsten Seemann, Honglei Chen, Volker Haring, Priscilla A. Johanesen, Dena Lyras and Robert J. Moore

    Citation: BMC Genomics 2018 19:379

    Content type: Research article

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  21. A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological...

    Authors: Fuqiang Ma, Pei Lin, Qingjian Chen, Xuemei Lu, Yong E. Zhang and Chung-I Wu

    Citation: BMC Genomics 2018 19:362

    Content type: Research article

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  22. Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irr...

    Authors: Daria Krefft, Aliaksei Papkov, Maciej Prusinowski, Agnieszka Zylicz-Stachula and Piotr M. Skowron

    Citation: BMC Genomics 2018 19:361

    Content type: Methodology article

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  23. Cryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were still not available. Long non-coding RNAs (lncRNAs) ...

    Authors: Guan-Jing Ren, Xian-Cheng Fan, Ting-Li Liu, Sha-Sha Wang and Guang-Hui Zhao

    Citation: BMC Genomics 2018 19:356

    Content type: Research article

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  24. Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways...

    Authors: Ronald B. Walter, Mikki Boswell, Jordan Chang, William T. Boswell, Yuan Lu, Kaela Navarro, Sean M. Walter, Dylan J. Walter, Raquel Salinas and Markita Savage

    Citation: BMC Genomics 2018 19:355

    Content type: Research article

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  25. Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the com...

    Authors: Lifu Qian, Hui Wang, Jie Yan, Tao Pan, Shanqun Jiang, Dingqi Rao and Baowei Zhang

    Citation: BMC Genomics 2018 19:354

    Content type: Research article

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  26. Brucellosis is a bacterial zoonotic disease. Annually in the world more than 500,000 new cases of brucellosis in humans are registered. In this study, we propose an evolutionary model of the historical distrib...

    Authors: Sergey V. Pisarenko, Dmitry A. Kovalev, Anna S. Volynkina, Dmitry G. Ponomarenko, Diana V. Rusanova, Nina V. Zharinova, Anna A. Khachaturova, Lyudmila E. Tokareva, Irina G. Khvoynova and Alexander N. Kulichenko

    Citation: BMC Genomics 2018 19:353

    Content type: Research article

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  27. Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochond...

    Authors: Matthew T. Oetjens, Axel Martin, Krishna R. Veeramah and Jeffrey M. Kidd

    Citation: BMC Genomics 2018 19:350

    Content type: Research article

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  28. Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions ...

    Authors: Erica S. Nielsen, Romina Henriques, Robert J. Toonen, Ingrid S. S. Knapp, Baocheng Guo and Sophie von der Heyden

    Citation: BMC Genomics 2018 19:347

    Content type: Research article

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  29. The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehe...

    Authors: Xiaoming Song, Xiao Ma, Chunjin Li, Jingjing Hu, Qihang Yang, Tong Wang, Li Wang, Jinpeng Wang, Di Guo, Weina Ge, Zhenyi Wang, Miaomiao Li, Qiumei Wang, Tianzeng Ren, Shuyan Feng, Lixia Wang…

    Citation: BMC Genomics 2018 19:346

    Content type: Research article

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  30. Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impa...

    Authors: Adam B. Burkholder, Scott A. Lujan, Christopher A. Lavender, Sara A. Grimm, Thomas A. Kunkel and David C. Fargo

    Citation: BMC Genomics 2018 19:345

    Content type: Methodology article

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  31. Valine-glutamine (VQ) motif containing proteins play important roles in abiotic and biotic stress responses in plants. However, little is known about the origin and evolution as well as comprehensive expressio...

    Authors: Shu-Ye Jiang, Mayalagu Sevugan and Srinivasan Ramachandran

    Citation: BMC Genomics 2018 19:342

    Content type: Research article

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  32. Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Ga...

    Authors: G. P. Tiley, R. T. Kimball, E. L. Braun and J. G. Burleigh

    Citation: BMC Genomics 2018 19:336

    Content type: Research article

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  33. Xylella fastidiosa (Xf) is a gram negative bacterium inhabiting the plant vascular system. In most species this bacterium lives as a benign symbiote, but in several agriculturally important plants (e.g. coffee, c...

    Authors: Gregory A. Gambetta, Mark A. Matthews and Michael Syvanen

    Citation: BMC Genomics 2018 19:329

    Content type: Research article

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  34. Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. ...

    Authors: Frederick Johannes Clasen, Rian Ewald Pierneef, Bernard Slippers and Oleg Reva

    Citation: BMC Genomics 2018 19:323

    Content type: Software

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  35. The renewed interest in epigenetics has led to the understanding that both the environment and individual lifestyle can directly interact with the epigenome to influence its dynamics. Epigenetic phenomena are ...

    Authors: Loris Pratx, Corinne Rancurel, Martine Da Rocha, Etienne G. J. Danchin, Philippe Castagnone-Sereno, Pierre Abad and Laetitia Perfus-Barbeoch

    Citation: BMC Genomics 2018 19:321

    Content type: Research article

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  36. Temperature adaptation of biological molecules is fundamental in evolutionary studies but remains unsolved. Fishes living in cold water are adapted to low temperatures through adaptive modification of their bi...

    Authors: Dongsheng Zhang, Peng Hu, Taigang Liu, Jian Wang, Shouwen Jiang, Qianghua Xu and Liangbiao Chen

    Citation: BMC Genomics 2018 19:315

    Content type: Research article

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  37. Plasmodium falciparum is the most virulent malaria parasite capable of parasitizing human erythrocytes. The identification of genes related to this capability can enhance our understanding of the molecular mechan...

    Authors: Xuewu Liu, Yuanyuan Wang, Jiao Liang, Luojun Wang, Na Qin, Ya Zhao and Gang Zhao

    Citation: BMC Genomics 2018 19:312

    Content type: Methodology article

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  38. Both calcium signals and protein phosphorylation responses are universal signals in eukaryotic cell signaling. Currently three pathways have been characterized in different eukaryotes converting the Ca2+ signals ...

    Authors: Fei Chen, Liangsheng Zhang, Zhenguo Lin and Zong-Ming Max Cheng

    Citation: BMC Genomics 2018 19:306

    Content type: Research article

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  39. At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as ...

    Authors: Nora Hohmann, Eva M. Wolf, Philippe Rigault, Wenbin Zhou, Markus Kiefer, Yunpeng Zhao, Cheng-Xin Fu and Marcus A. Koch

    Citation: BMC Genomics 2018 19:299

    Content type: Research article

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  40. Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial...

    Authors: Daniel R. Bogema, Melinda L. Micallef, Michael Liu, Matthew P. Padula, Steven P. Djordjevic, Aaron E. Darling and Cheryl Jenkins

    Citation: BMC Genomics 2018 19:298

    Content type: Research article

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  41. Chagas disease is a parasitic infection caused by Trypanosoma cruzi. It is an important public health problem affecting around seven to eight million people in the Americas. A large number of hematophagous triato...

    Authors: Jesús Martínez-Barnetche, Andrés Lavore, Melina Beliera, Juan Téllez-Sosa, Federico A. Zumaya-Estrada, Victorio Palacio, Ernestina Godoy-Lozano, Rolando Rivera-Pomar and Mario Henry Rodríguez

    Citation: BMC Genomics 2018 19:296

    Content type: Research article

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