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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 1 of 20

  1. Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allo...

    Authors: Christian D. Powell, Daniel C. Kirchoff, Jason E. DeRouchey and Hunter N. B. Moseley

    Citation: BMC Genomics 2020 21:277

    Content type: Research Article

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  2. DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor famil...

    Authors: Yue Liu, Nannan Liu, Xiong Deng, Dongmiao Liu, Mengfei Li, Dada Cui, Yingkao Hu and Yueming Yan

    Citation: BMC Genomics 2020 21:276

    Content type: Research article

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  3. The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes – protists were reported. Giardia lamblia, a protist with ...

    Authors: Jin-Mei Feng, Chun-Lin Yang, Hai-Feng Tian, Jiang-Xin Wang and Jian-Fan Wen

    Citation: BMC Genomics 2020 21:269

    Content type: Research article

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  4. Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and...

    Authors: Tong Wang, Jingjing Hu, Xiao Ma, Chunjin Li, Qihang Yang, Shuyan Feng, Miaomiao Li, Nan Li and Xiaoming Song

    Citation: BMC Genomics 2020 21:264

    Content type: Research article

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  5. Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that contro...

    Authors: Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yui Yamashita, Satoshi Naito, Anna Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima and Hitoshi Onouchi

    Citation: BMC Genomics 2020 21:260

    Content type: Research article

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  6. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a highly diverse group of secondary metabolites (SM) of bacterial and fungal origin. While RiPPs have been intensively studied in ...

    Authors: Gabriel A. Vignolle, Robert L. Mach, Astrid R. Mach-Aigner and Christian Derntl

    Citation: BMC Genomics 2020 21:258

    Content type: Methodology article

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  7. The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic re...

    Authors: Saidi R. Achari, Jatinder Kaur, Quang Dinh, Ross Mann, Tim Sawbridge, Brett A. Summerell and Jacqueline Edwards

    Citation: BMC Genomics 2020 21:248

    Content type: Research article

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  8. Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome no...

    Authors: Sayaka Tanaka, Kentaro Yoshida, Kazuhiro Sato and Shigeo Takumi

    Citation: BMC Genomics 2020 21:246

    Content type: Research article

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  9. Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, ...

    Authors: Maria Luisa Martin Cerezo, Marek Kucka, Karol Zub, Yingguang Frank Chan and Jarosław Bryk

    Citation: BMC Genomics 2020 21:241

    Content type: Research Article

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  10. Barnacles are specialized marine organisms that differ from other crustaceans in possession of a calcareous shell, which is attached to submerged surfaces. Barnacles have a wide distribution, mostly in the int...

    Authors: Zhibin Gan, Jianbo Yuan, Xinming Liu, Dong Dong, Fuhua Li and Xinzheng Li

    Citation: BMC Genomics 2020 21:240

    Content type: Research article

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  11. Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could...

    Authors: Svein-Ole Mikalsen, Marni Tausen and Sunnvør í Kongsstovu

    Citation: BMC Genomics 2020 21:223

    Content type: Research article

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  12. Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically...

    Authors: Meng Chen, Chun-Yang Xu, Xu Wang, Chong-Yang Ren, Jiao Ding and Li Li

    Citation: BMC Genomics 2020 21:217

    Content type: Research article

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  13. Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of...

    Authors: Zeinab Amiri Ghanatsaman, Guo-Dong Wang, Hojjat Asadollahpour Nanaei, Masood Asadi Fozi, Min-Sheng Peng, Ali Esmailizadeh and Ya-Ping Zhang

    Citation: BMC Genomics 2020 21:207

    Content type: Research article

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  14. In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cogn...

    Authors: Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qin Chu, Xiquan Zhang and Xuemei Lu

    Citation: BMC Genomics 2020 21:204

    Content type: Research article

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  15. PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, ...

    Authors: Rongzhi Zhang, Siyuan Huang, Shiming Li, Guoqi Song, Yulian Li, Wei Li, Jihu Li, Jie Gao, Tiantian Gu, Dandan Li, Shujuan Zhang and Genying Li

    Citation: BMC Genomics 2020 21:200

    Content type: Research article

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  16. The H+-PPase (pyrophosphatase) gene family is an important class of proton transporters that play key roles in plant development and stress resistance. Although the physiological and biochemical functions of H+-P...

    Authors: Yiming Zhang, Xue Feng, Lihui Wang, Yanping Su, Zhuodong Chu and Yanxiang Sun

    Citation: BMC Genomics 2020 21:195

    Content type: Research article

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  17. Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC

    Authors: Wenjun Tong, Xiangchen Li, Entao Wang, Ying Cao, Weimin Chen, Shiheng Tao and Gehong Wei

    Citation: BMC Genomics 2020 21:186

    Content type: Research article

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  18. The basic helix–loop–helix (bHLH) is the second largest gene family in the plant, some members play important roles in pistil development and response to drought, waterlogging, cold stress and salt stress. The...

    Authors: Liming Miao, Yingying Gao, Kun Zhao, Lijun Kong, Shubo Yu, Rongrong Li, Kaiwen Liu and Xiaolin Yu

    Citation: BMC Genomics 2020 21:178

    Content type: Research article

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  19. Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabol...

    Authors: Yuling Tai, Xiaojuan Hou, Chun Liu, Jiameng Sun, Chunxiao Guo, Ling Su, Wei Jiang, Chengcheng Ling, Chengxiang Wang, Huanhuan Wang, Guifang Pan, Xiongyuan Si and Yi Yuan

    Citation: BMC Genomics 2020 21:169

    Content type: Research article

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  20. The small hive beetle, Aethina tumida, is a rapidly emerging global pest of honey bee colonies. Small hive beetle infestation can be extremely destructive, which may cause honey bees to abscond and render colony ...

    Authors: Frank D. Rinkevich and Lelania Bourgeois

    Citation: BMC Genomics 2020 21:154

    Content type: Research article

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  21. Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular syst...

    Authors: Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Darin R. Rokyta, Mahmood Sasa and Christopher L. Parkinson

    Citation: BMC Genomics 2020 21:147

    Content type: Research Article

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  22. Horseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanism...

    Authors: Yan Zhou, Yuan Liang, Qing Yan, Liang Zhang, Dianbao Chen, Lingwei Ruan, Yuan Kong, Hong Shi, Mingliang Chen and Jianming Chen

    Citation: BMC Genomics 2020 21:137

    Content type: Research article

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  23. Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated ...

    Authors: Mazharul Islam, Kowshika Sarker, Trisha Das, Rezwana Reaz and Md. Shamsuzzoha Bayzid

    Citation: BMC Genomics 2020 21:136

    Content type: Software

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  24. Despite a growing number of investigations on early diverging fungi, the corresponding lineages have not been as extensively characterized as Ascomycota or Basidiomycota ones. The Mucor genus, pertaining to one o...

    Authors: Annie Lebreton, Erwan Corre, Jean-Luc Jany, Loraine Brillet-Guéguen, Carlos Pèrez-Arques, Victoriano Garre, Misharl Monsoor, Robert Debuchy, Christophe Le Meur, Emmanuel Coton, Georges Barbier and Laurence Meslet-Cladière

    Citation: BMC Genomics 2020 21:135

    Content type: Research article

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  25. Listeria monocytogenes Clonal Complexes (CCs) have been epidemiologically associated with foods, especially ready-to-eat (RTE) products for which the most likely source of contamination depends on the occurrence ...

    Authors: Federica Palma, Thomas Brauge, Nicolas Radomski, Ludovic Mallet, Arnaud Felten, Michel-Yves Mistou, Anne Brisabois, Laurent Guillier and Graziella Midelet-Bourdin

    Citation: BMC Genomics 2020 21:130

    Content type: Research article

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  26. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with more than 200 nucleotides in length, which play vital roles in a wide range of biological processes. Powdery mildew disease (PM) has become a ...

    Authors: Chao Gao, Jianlei Sun, Yumei Dong, Chongqi Wang, Shouhua Xiao, Longfei Mo and Zigao Jiao

    Citation: BMC Genomics 2020 21:125

    Content type: Research article

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  27. Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.

    Authors: Hao Duan, Jinbo Guo, Lei Xuan, Ziyang Wang, Mingzhi Li, Yunlong Yin and Ying Yang

    Citation: BMC Genomics 2020 21:114

    Content type: Research article

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  28. Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans a...

    Authors: Simon Bahrndorff, Aritz Ruiz-González, Nadieh de Jonge, Jeppe Lund Nielsen, Henrik Skovgård and Cino Pertoldi

    Citation: BMC Genomics 2020 21:66

    Content type: Research article

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  29. Spirochetal organisms of the Treponema genus are responsible for causing Treponematoses. Pathogenic treponemes is a Gram-negative, motile, spirochete pathogen that causes syphilis in human. Treponema pallidum sub...

    Authors: Arun Kumar Jaiswal, Sandeep Tiwari, Syed Babar Jamal, Letícia de Castro Oliveira, Leandro Gomes Alves, Vasco Azevedo, Preetam Ghosh, Carlo Jose Freira Oliveira and Siomar C. Soares

    Citation: BMC Genomics 2020 21:33

    Content type: Research article

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  30. Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are kn...

    Authors: Sivasubramanian Rajarammohan, Kumar Paritosh, Deepak Pental and Jagreet Kaur

    Citation: BMC Genomics 2019 20:1036

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:82

  31. In 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant “priority pathogens” that are posing the greatest threats to human health. Six of these dreaded pathogens a...

    Authors: Tungadri Bose, K. V. Venkatesh and Sharmila S. Mande

    Citation: BMC Genomics 2019 20:1022

    Content type: Research article

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  32. Genomic studies demonstrate that components of virulence mechanisms in filamentous eukaryotic pathogens (FEPs, fungi and oomycetes) of plants are often highly conserved, or found in gene families that include ...

    Authors: Eswari PJ Pandaranayaka, Omer Frenkel, Yigal Elad, Dov Prusky and Arye Harel

    Citation: BMC Genomics 2019 20:1020

    Content type: Research article

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  33. Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, on...

    Authors: Robert Bücking, Murray P Cox, Georgi Hudjashov, Lauri Saag, Herawati Sudoyo and Mark Stoneking

    Citation: BMC Genomics 2019 20:1017

    Content type: Research Article

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    The Correction to this article has been published in BMC Genomics 2020 21:55

  34. White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies...

    Authors: A. Zumaquero, S. Kanematsu, H. Nakayashiki, A. Matas, E. Martínez-Ferri, A. Barceló-Muñóz, F. Pliego-Alfaro, C. López-Herrera, F. M. Cazorla and C. Pliego

    Citation: BMC Genomics 2019 20:1016

    Content type: Research article

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  35. Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food pr...

    Authors: Yan Wang, Lijuan Luo, Qun Li, Hong Wang, Yiqian Wang, Hui Sun, Jianguo Xu, Ruiting Lan and Changyun Ye

    Citation: BMC Genomics 2019 20:1014

    Content type: Research article

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  36. Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake dive...

    Authors: Kevin Schneider, Colin E. Adams and Kathryn R. Elmer

    Citation: BMC Genomics 2019 20:1010

    Content type: Research article

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  37. Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific g...

    Authors: Ruijie Liu, Wai Yee Low, Rick Tearle, Sergey Koren, Jay Ghurye, Arang Rhie, Adam M. Phillippy, Benjamin D. Rosen, Derek M. Bickhart, Timothy P. L. Smith, Stefan Hiendleder and John L. Williams

    Citation: BMC Genomics 2019 20:1000

    Content type: Research article

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  38. The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in so...

    Authors: Jean F. Challacombe, Cedar N. Hesse, Lisa M. Bramer, Lee Ann McCue, Mary Lipton, Samuel Purvine, Carrie Nicora, La Verne Gallegos-Graves, Andrea Porras-Alfaro and Cheryl R. Kuske

    Citation: BMC Genomics 2019 20:976

    Content type: Research article

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  39. During infection by intracellular pathogens, a highly complex interplay occurs between the infected cell trying to degrade the invader and the pathogen which actively manipulates the host cell to enable surviv...

    Authors: Jonas Kjellin, Maria Pränting, Frauke Bach, Roshan Vaid, Bart Edelbroek, Zhiru Li, Marc P. Hoeppner, Manfred Grabherr, Ralph R. Isberg, Monica Hagedorn and Fredrik Söderbom

    Citation: BMC Genomics 2019 20:961

    Content type: Research article

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  40. After the extensive implementation of genomic selection (GS), the choice of the statistical model and data used to estimate variance components (VCs) remains unclear. A primary concern is that VCs estimated fr...

    Authors: Hongding Gao, Per Madsen, Gert Pedersen Aamand, Jørn Rind Thomasen, Anders Christian Sørensen and Just Jensen

    Citation: BMC Genomics 2019 20:956

    Content type: Research article

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