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

    Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

    Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics be...

    J. B. Butler, R. E. Vaillancourt, B. M. Potts, D. J. Lee, G. J. King, A. Baten, M. Shepherd and J. S. Freeman

    BMC Genomics 2017 18:397

    Published on: 22 May 2017

  2. Research article

    Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues

    Cold tolerance is a key determinant of temperate insect distribution and performance. Chill-susceptible insects lose ion and water homeostasis during cold exposure, but prior cold acclimation improves both col...

    Lauren E. Des Marteaux, Alexander H McKinnon, Hiroko Udaka, Jantina Toxopeus and Brent J. Sinclair

    BMC Genomics 2017 18:357

    Published on: 8 May 2017

  3. Research article

    Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages

    Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in whic...

    Deyvid Amgarten, Layla Farage Martins, Karen Cristina Lombardi, Luciana Principal Antunes, Ana Paula Silva de Souza, Gianlucca Gonçalves Nicastro, Elliott Watanabe Kitajima, Ronaldo Bento Quaggio, Chris Upton, João Carlos Setubal and Aline Maria da Silva

    BMC Genomics 2017 18:346

    Published on: 4 May 2017

  4. Research article

    Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python

    Previous studies examining post-feeding organ regeneration in the Burmese python (Python molurus bivittatus) have identified thousands of genes that are significantly differentially regulated during this process....

    Audra L. Andrew, Blair W. Perry, Daren C. Card, Drew R. Schield, Robert P. Ruggiero, Suzanne E. McGaugh, Amit Choudhary, Stephen M. Secor and Todd A. Castoe

    BMC Genomics 2017 18:338

    Published on: 2 May 2017

  5. Research article

    Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates

    Glucose-6-phosphate (G6pc) is a key enzyme involved in the regulation of the glucose homeostasis. The present study aims at revisiting and clarifying the evolutionary history of g6pc genes in vertebrates.

    Lucie Marandel, Stéphane Panserat, Elisabeth Plagnes-Juan, Eva Arbenoits, José Luis Soengas and Julien Bobe

    BMC Genomics 2017 18:342

    Published on: 2 May 2017

  6. Software

    CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

    The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuit...

    Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar and W. Florian Fricke

    BMC Genomics 2017 18:332

    Published on: 27 April 2017

  7. Methodology article

    A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

    Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material.

    Tran Thi Ngoc Dung, Pham Thanh Duy, October M. Sessions, Uma K. Sangumathi, Voong Vinh Phat, Pham Thi Thanh Tam, Nguyen Thi Nguyen To, Tran My Phuc, Tran Thi Hong Chau, Nguyen Ngoc Minh Chau, Ngoc Nguyen Minh, Guy E. Thwaites, Maia A. Rabaa and Stephen Baker

    BMC Genomics 2017 18:324

    Published on: 24 April 2017

  8. Research Article

    Genome-wide identification of genes probably relevant to the adaptation of schizothoracins (Teleostei: Cypriniformes) to the uplift of the Qinghai-Tibet Plateau

    Molecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers. The divergence of the three specialization groups of schizotho...

    Wei Chi, Xufa Ma, Jiangong Niu and Ming Zou

    BMC Genomics 2017 18:310

    Published on: 20 April 2017

  9. Research article

    Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals

    Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received l...

    Xiaotian Feng, Jicai Jiang, Abinash Padhi, Chao Ning, Jinluan Fu, Aiguo Wang, Raphael Mrode and Jian-Feng Liu

    BMC Genomics 2017 18:293

    Published on: 12 April 2017

  10. Research article

    Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

    Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensive roles in transcriptional regulation. In particular, we have reported that promoter-associated ncRNAs (pancRNAs) activa...

    Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima and Takuya Imamura

    BMC Genomics 2017 18:285

    Published on: 7 April 2017

  11. Research article

    Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

    microRNAs (miRNAs) are endogenous small RNAs that play important regulatory functions in plant development. Genetic variations in miRNAs sequences or their target-binding sites (microRNA-target interaction sit...

    Jian Ling, Zhongqin Luo, Feng Liu, Zhenchuan Mao, Yuhong Yang and Bingyan Xie

    BMC Genomics 2017 18:275

    Published on: 4 April 2017

  12. Research article

    Widespread of horizontal gene transfer in the human genome

    A fundamental concept in biology is that heritable material is passed from parents to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene...

    Wenze Huang, Lillian Tsai, Yulong Li, Nan Hua, Chen Sun and Chaochun Wei

    BMC Genomics 2017 18:274

    Published on: 4 April 2017

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