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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

    Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecolo...

    Authors: David Armisén, Rajendhran Rajakumar, Markus Friedrich, Joshua B. Benoit, Hugh M. Robertson, Kristen A. Panfilio, Seung-Joon Ahn, Monica F. Poelchau, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Richard A. Gibbs, Daniel S. T. Hughes, Yi Han, Sandra L. Lee…

    Citation: BMC Genomics 2018 19:832

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  2. Content type: Research article

    Pigeon crop has the unique ability to produce a nutrient rich substance termed pigeon ‘milk’ (PM), which has functional resemblance with the mammalian milk. Previous researches have demonstrated that a large n...

    Authors: Yao Ma, Siyuan Feng, Xun Wang, Izhar Hyder Qazi, Keren Long, Yi Luo, Guojun Li, Chunyou Ning, Yixin Wang, Silu Hu, Juan Xiao, Xiaokai Li, Dan Lan, Yaodong Hu, Qianzi Tang, Jideng Ma…

    Citation: BMC Genomics 2018 19:828

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  3. Content type: Research article

    The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as...

    Authors: Hita Sony Garapati and Krishnaveni Mishra

    Citation: BMC Genomics 2018 19:823

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  4. Content type: Research article

    The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested th...

    Authors: Camille Thomas-Bulle, Mathieu Piednoël, Tifenn Donnart, Jonathan Filée, Didier Jollivet and Éric Bonnivard

    Citation: BMC Genomics 2018 19:821

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  5. Content type: Research article

    Solea senegalensis (Kaup, 1858) is a commercially important flatfish species, belonging to the Pleuronectiformes order. The taxonomy of this group has long been controversial, and the karyotype of the order prese...

    Authors: Aglaya García-Angulo, Manuel A. Merlo, Silvia Portela-Bens, María E. Rodríguez, Emilio García, Ahmed Al-Rikabi, Thomas Liehr and Laureana Rebordinos

    Citation: BMC Genomics 2018 19:818

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  6. Content type: Research article

    The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori ha...

    Authors: Chuan-Zhen Qiu, Qiu-Zhong Zhou, Ting-Ting Liu, Shou-Min Fang, Ya-Wang Wang, Xin Fang, Chun-Li Huang, Quan-You Yu, Chun-Hong Chen and Ze Zhang

    Citation: BMC Genomics 2018 19:788

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  7. Content type: Research article

    Macaca fascicularis (M. fascicularis) is a primate model organism that played important role in studying human health. It is vital to better understand the similarity and differences of gene regulation between M....

    Authors: Tao Tan, Lin Xia, Kailing Tu, Jie Tang, Senlin Yin, Lunzhi Dai, Peng Lei, Biao Dong, Hongbo Hu, Yong Fan, Yang Yu and Dan Xie

    Citation: BMC Genomics 2018 19:787

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  8. Content type: Research article

    The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is pred...

    Authors: Lin-sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-gang Sun, Irfan Ullah and Yin-cang Han

    Citation: BMC Genomics 2018 19:785

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  9. Content type: Methodology article

    Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved o...

    Authors: Zoltán Maróti, Zsolt Boldogkői, Dóra Tombácz, Michael Snyder and Tibor Kalmár

    Citation: BMC Genomics 2018 19:778

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  10. Content type: Research article

    Numerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has ...

    Authors: Dan Zhang, Xiuyu Lou, Hao Yan, Junhang Pan, Haiyan Mao, Hongfeng Tang, Yan Shu, Yun Zhao, Lei Liu, Junping Li, Jiang Chen, Yanjun Zhang and Xuejun Ma

    Citation: BMC Genomics 2018 19:773

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  11. Content type: Research article

    Trypanosoma conorhini and Trypanosoma rangeli, like Trypanosoma cruzi, are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic T. rangeli

    Authors: Katie R Bradwell, Vishal N Koparde, Andrey V Matveyev, Myrna G Serrano, João M P Alves, Hardik Parikh, Bernice Huang, Vladimir Lee, Oneida Espinosa-Alvarez, Paola A Ortiz, André G Costa-Martins, Marta M G Teixeira and Gregory A Buck

    Citation: BMC Genomics 2018 19:770

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  12. Content type: Research article

    Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even th...

    Authors: Atsushi Ogura, Yuki Akizuki, Hiroaki Imoda, Katsuhiko Mineta, Takashi Gojobori and Satoshi Nagai

    Citation: BMC Genomics 2018 19:765

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  13. Content type: Research article

    Ural genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and o...

    Authors: Viacheslav Sinkov, Oleg Ogarkov, Igor Mokrousov, Yuri Bukin, Svetlana Zhdanova and Scott K. Heysell

    Citation: BMC Genomics 2018 19:762

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  14. Content type: Research article

    An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to extern...

    Authors: Gaurav Sharma, Rebecca Parales and Mitchell Singer

    Citation: BMC Genomics 2018 19:757

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  15. Content type: Software

    Previous studies demonstrate the usefulness of using multiple tools and methods for improving the accuracy of motif detection. Over the past years, numerous motif discovery pipelines have been developed. Howev...

    Authors: Ngoc Tam L. Tran and Chun-Hsi Huang

    Citation: BMC Genomics 2018 19:755

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  16. Content type: Research article

    Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops ...

    Authors: S. Zoledowska, A. Motyka-Pomagruk, W. Sledz, A. Mengoni and E. Lojkowska

    Citation: BMC Genomics 2018 19:751

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  17. Content type: Research article

    Studies combining experimental evolution and next-generation sequencing have found that adaptation in sexually reproducing populations is primarily fueled by standing genetic variation. Consequently, the respo...

    Authors: Mark A Phillips, Grant A Rutledge, James N Kezos, Zachary S Greenspan, Andrew Talbott, Sara Matty, Hamid Arain, Laurence D Mueller, Michael R Rose and Parvin Shahrestani

    Citation: BMC Genomics 2018 19:743

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  18. Content type: Research article

    The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute a valuable source of dietary protein. Therefore, they are cultured wor...

    Authors: Oanh T. P. Kim, Phuong T. Nguyen, Eiichi Shoguchi, Kanako Hisata, Thuy T. B. Vo, Jun Inoue, Chuya Shinzato, Binh T. N. Le, Koki Nishitsuji, Miyuki Kanda, Vu H. Nguyen, Hai V. Nong and Noriyuki Satoh

    Citation: BMC Genomics 2018 19:733

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  19. Content type: Research article

    After a short gestation, marsupials give birth to immature neonates with lungs that are not fully developed and in early life the neonate partially relies on gas exchange through the skin. Therefore, significa...

    Authors: Vengamanaidu Modepalli, Amit Kumar, Julie A Sharp, Norman R Saunders, Kevin R Nicholas and Christophe Lefèvre

    Citation: BMC Genomics 2018 19:732

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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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

  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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