Comparative and evolutionary genomics

Section edited by Igor Rogozin

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. Research article

    An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes

    Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid specie...

    Nora Hohmann and Marcus A. Koch

    BMC Genomics 2017 18:810

    Published on: 23 October 2017

  2. Research article

    Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes

    Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transductio...

    Jiangmei Sun, Leiting Li, Peng Wang, Shaoling Zhang and Juyou Wu

    BMC Genomics 2017 18:763

    Published on: 10 October 2017

  3. Research article

    Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications

    The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) a...

    Jingyin Yu, Sadia Tehrim, Linhai Wang, Komivi Dossa, Xiurong Zhang, Tao Ke and Boshou Liao

    BMC Genomics 2017 18:733

    Published on: 18 September 2017

  4. Research article

    Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

    The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative ...

    Balázs Brankovics, Peter van Dam, Martijn Rep, G. Sybren de Hoog, Theo A. J. van der Lee, Cees Waalwijk and Anne D. van Diepeningen

    BMC Genomics 2017 18:735

    Published on: 18 September 2017

  5. Research article

    Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages

    Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infect...

    Ana Cristina Ferreira, Rogério Tenreiro, Maria Inácia Corrêa de Sá and Ricardo Dias

    BMC Genomics 2017 18:726

    Published on: 12 September 2017

  6. Research article

    Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation

    Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic me...

    Jia Zhou, Renee L. Sears, Xiaoyun Xing, Bo Zhang, Daofeng Li, Nicole B. Rockweiler, Hyo Sik Jang, Mayank N.K. Choudhary, Hyung Joo Lee, Rebecca F. Lowdon, Jason Arand, Brianne Tabers, C. Charles Gu, Theodore J. Cicero and Ting Wang

    BMC Genomics 2017 18:724

    Published on: 12 September 2017

  7. Research Article

    Comparative transcriptome analysis provides clues to molecular mechanisms underlying blue-green eggshell color in the Jinding duck (Anas platyrhynchos)

    In birds, blue-green eggshell color (BGEC) is caused by biliverdin, a bile pigment derived from the degradation of heme and secreted in the eggshell by the shell gland. Functionally, BGEC might promote the pat...

    Zhepeng Wang, Guohua Meng, Yun Bai, Ruifang Liu, Yu Du and Lihong Su

    BMC Genomics 2017 18:725

    Published on: 12 September 2017

  8. Research article

    Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera

    Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very lit...

    Chao Du, Lifang Zhang, Ting Lu, Jingnan Ma, Chenjuan Zeng, Bisong Yue and Xiuyue Zhang

    BMC Genomics 2017 18:698

    Published on: 6 September 2017

  9. Research article

    Patterns of host gene expression associated with harboring a foregut microbial community

    Harboring foregut microbial communities is considered a key innovation that allows herbivorous mammals to colonize new ecological niches. However, the functions of these chambers have only been well studied at...

    Kevin D. Kohl, Kelly F. Oakeson, Diane Dunn, David K. Meyerholz, Colin Dale, Robert B. Weiss and M. Denise Dearing

    BMC Genomics 2017 18:697

    Published on: 6 September 2017

  10. Research article

    Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses

    Parasites can either respond to differences in immune defenses that exist between individual hosts plastically or, alternatively, follow a genetically canalized (“hard wired”) program of infection. Assuming th...

    Totta Ehret, Simone Spork, Christoph Dieterich, Richard Lucius and Emanuel Heitlinger

    BMC Genomics 2017 18:686

    Published on: 5 September 2017

  11. Research article

    A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri

    The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especiall...

    Mario Baumgart, Emanuel Barth, Aurora Savino, Marco Groth, Philipp Koch, Andreas Petzold, Ivan Arisi, Matthias Platzer, Manja Marz and Alessandro Cellerino

    BMC Genomics 2017 18:693

    Published on: 5 September 2017

  12. Research article

    Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing

    Genes encoded in vertebrate mitochondrial DNAs are transcribed as a polycistronic transcript for both strands, which is later processed into individual mRNAs, rRNAs and tRNAs, followed by modifications, such a...

    Yao Sun, Masaki Kurisaki, Yasuyuki Hashiguchi and Yoshinori Kumazawa

    BMC Genomics 2017 18:665

    Published on: 29 August 2017

  13. Research

    Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum)

    Rust fungi constitute the largest group of plant fungal pathogens. However, a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of...

    Si-Qi Tao, Bin Cao, Cheng-Ming Tian and Ying-Mei Liang

    BMC Genomics 2017 18:651

    Published on: 23 August 2017

  14. Research article

    Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping

    Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some t...

    Tingting Wang, Yi-Ping Phoebe Chen, Iona M. MacLeod, Jennie E. Pryce, Michael E. Goddard and Ben J. Hayes

    BMC Genomics 2017 18:618

    Published on: 15 August 2017

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The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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