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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.

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  1. Content type: Research article

    Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi...

    Authors: Ying Wu, Xianfeng Ma, Zhiyong Pan, Shiv D. Kale, Yi Song, Harlan King, Qiong Zhang, Christian Presley, Xiuxin Deng, Cheng-I Wei and Shunyuan Xiao

    Citation: BMC Genomics 2018 19:705

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  2. Content type: Research article

    Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are corallin...

    Authors: Giselle S. Cavalcanti, Priya Shukla, Megan Morris, Bárbara Ribeiro, Mariah Foley, Michael P. Doane, Cristiane C. Thompson, Matthew S. Edwards, Elizabeth A. Dinsdale and Fabiano L. Thompson

    Citation: BMC Genomics 2018 19:701

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  3. Content type: Research article

    Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two is...

    Authors: Bing-Hong Huang, Yuan-Chien Lin, Chih-Wei Huang, Hsin-Pei Lu, Min-Xin Luo and Pei-Chun Liao

    Citation: BMC Genomics 2018 19:692

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  4. Content type: Research article

    The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted i...

    Authors: Rufaida Dhuhai Al-Breiki, Shannon R. Kjeldsen, Hasifa Afzal, Manal Saif Al Hinai, Kyall R. Zenger, Dean R. Jerry, Mohammed Ali Al-Abri and Madjid Delghandi

    Citation: BMC Genomics 2018 19:690

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  5. Content type: Research article

    Sogatella furcifera is a migratory pest that damages rice plants and causes severe economic losses. Due to its ability to annually migrate long distances, S. furcifera has emerged as a major pest of rice in sever...

    Authors: Zhen Zeng, Yating Fu, Dongyang Guo, Yuxuan Wu, Olugbenga Emmanuel Ajayi and Qingfa Wu

    Citation: BMC Genomics 2018 19:688

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  6. Content type: Research article

    In the present study, we sequenced the complete genomes of three novel bacteriophages v_B-Bak1, v_B-Bak6, v_B-Bak10 previously isolated from historical anthrax burial sites in the South Caucasus country of Geo...

    Authors: J. Farlow, D. Bolkvadze, L. Leshkasheli, I. Kusradze, A. Kotorashvili, N. Kotaria, N. Balarjishvili, L. Kvachadze, M. Nikolich and M. Kutateladze

    Citation: BMC Genomics 2018 19:685

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    The Correction to this article has been published in BMC Genomics 2018 19:713

  7. Content type: Research article

    Our previous study found that more than 500 transcripts significantly increased in abundance in the zebrafish and mouse several hours to days postmortem relative to live controls. The current literature sugges...

    Authors: Peter A. Noble and Alexander E. Pozhitkov

    Citation: BMC Genomics 2018 19:675

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  8. Content type: Research article

    Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been...

    Authors: Zhenyi Wang, Kanglu Zhao, Yuxin Pan, Jinpeng Wang, Xiaoming Song, Weina Ge, Min Yuan, Tianyu Lei, Li Wang, Lan Zhang, Yuxian Li, Tao Liu, Wei Chen, Wenjing Meng, Changkai Sun, Xiaobo Cui…

    Citation: BMC Genomics 2018 19:665

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  9. Content type: Research article

    So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by applicati...

    Authors: Francesca Fanelli, Vania Cosma Liuzzi, Antonio Francesco Logrieco and Claudio Altomare

    Citation: BMC Genomics 2018 19:662

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  10. Content type: Research article

    Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium c...

    Authors: Vikas C. Ghattargi, Meghana A. Gaikwad, Bharati S. Meti, Yogesh S. Nimonkar, Kunal Dixit, Om Prakash, Yogesh S. Shouche, Shrikant P. Pawar and Dhiraj P. Dhotre

    Citation: BMC Genomics 2018 19:652

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  11. Content type: Research article

    In the current scenario, the drug-resistant tuberculosis is a significant challenge in the control of tuberculosis worldwide. In order to investigate the in vivo evolution of drug-resistant M. tuberculosis, the p...

    Authors: Yuhui Xu, Fei Liu, Suting Chen, Jiannan Wu, Yongfei Hu, Baoli Zhu and Zhaogang Sun

    Citation: BMC Genomics 2018 19:640

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  12. Content type: Research article

    Canine brucellosis, due to Brucella canis, is a worldwide zoonosis that remains endemic in South America, including Brazil. Implementation of powerful whole-genome sequencing approaches allowed exploring the Bruc...

    Authors: Acácia Ferreira Vicente, Guillaume Girault, Yannick Corde, Mateus Souza Ribeiro Mioni, Lara Borges Keid, Maryne Jay, Jane Megid and Virginie Mick

    Citation: BMC Genomics 2018 19:636

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  13. Content type: Research article

    Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections,...

    Authors: Xavier Argemi, Dorota Matelska, Krzysztof Ginalski, Philippe Riegel, Yves Hansmann, Jochen Bloom, Martine Pestel-Caron, Sandrine Dahyot, Jérémie Lebeurre and Gilles Prévost

    Citation: BMC Genomics 2018 19:621

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  14. Content type: Research article

    Apis mellifera scutellata and A.m. capensis (the Cape honey bee) are western honey bee subspecies indigenous to the Republic of South Africa (RSA). Both bees are important for biological and economic reasons. Fir...

    Authors: Amin Eimanifar, Samantha A. Brooks, Tomas Bustamante and James D. Ellis

    Citation: BMC Genomics 2018 19:615

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  15. Content type: Research article

    It is known that long non-coding RNAs (lncRNAs) play an important role in various biological processes, including cell proliferation, differentiation and apoptosis. However, their functions and profiles in lac...

    Authors: Bing Yang, Beilei Jiao, Wei Ge, Xiaolan Zhang, Shanhe Wang, Hongbo Zhao and Xin Wang

    Citation: BMC Genomics 2018 19:605

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  16. Content type: Research article

    While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads ...

    Authors: Mikhail I. Schelkunov, Aleksey A. Penin and Maria D. Logacheva

    Citation: BMC Genomics 2018 19:602

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  17. Content type: Research article

    Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Bei...

    Authors: Mengmeng Zhang, Wei Han, Hui Tang, Guohui Li, Minjie Zhang, Ran Xu, Yijun Liu, Tao Yang, Wenting Li, Jianmin Zou and Keliang Wu

    Citation: BMC Genomics 2018 19:598

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  18. Content type: Research article

    The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strain...

    Authors: Jon Bohlin, Vegard Eldholm, Ola Brynildsrud, John H.-O. Petterson and Kristian Alfsnes

    Citation: BMC Genomics 2018 19:589

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  19. Content type: Research article

    Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over...

    Authors: Hengfu Yin, Hao-Bo Guo, David J. Weston, Anne M. Borland, Priya Ranjan, Paul E. Abraham, Sara S. Jawdy, James Wachira, Gerald A. Tuskan, Timothy J. Tschaplinski, Stan D. Wullschleger, Hong Guo, Robert L. Hettich, Stephen M. Gross, Zhong Wang, Axel Visel…

    Citation: BMC Genomics 2018 19:588

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    The Correction to this article has been published in BMC Genomics 2019 20:279

  20. Content type: Research article

    Human cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCM...

    Authors: Timokratis Karamitros, Bonnie van Wilgenburg, Mark Wills, Paul Klenerman and Gkikas Magiorkinis

    Citation: BMC Genomics 2018 19:577

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  21. Content type: Short report

    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

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  22. Content type: Research article

    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

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  23. Content type: Methodology article

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Research article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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  36. Content type: Research article

    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

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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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