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Evolutionary Genomics

Edited by: Michael Ginger, University of Huddersfield, UK
                 Eugene Koonin, National Center for Biotechnology Information, USA
                 Ferdinand Marlétaz, University College London, UK
                 Yehu Moran, The Hebrew University of Jerusalem, Israel
                 Ben Pascoe, University of Bath, UK
                 Josefin Stiller, University of Copenhagen, Denmark
                 Martina Strömvik, McGill University, Canada
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Developing sequencing technologies and interrogation of ‘big data’ have expanded our capabilities to shed light on the evolution of life, including the genomic substrates for adaptation and evolution of genomes themselves. This Collection in BMC Biology brings together research and methodology articles covering genomic insights into evolution and vice versa, across all taxonomic levels and domains. 

The collection is now closed for submissions.

Our Guest Editors:

Michael Ginger

ginger_head_shouldersDr Ginger holds a BSc and PhD in Biochemistry from the University of Liverpool, UK. Following post-doctoral research at the Universities of Liverpool, Glasgow and Manchester, his independent research career began with tenure as a Royal Society University Research first at the University of Oxford, and subsequently at Lancaster University, UK. Michael moved to the University of Huddersfield in 2016 where he has been Dean of the School of Applied Sciences since 2019. Research within his lab focuses on the evolutionary cell biology and metabolic biochemistry of parasitic and heterotrophic free-living protists.

Eugene Koonin

Koonin smallEugene V. Koonin is the leader of the Evolutionary Genomics Group at the National Center for Biotechnology Information (NCBI). He is a member of the National Academy of Sciences of the USA. The American Academy of Arts and Sciences, American Academy of Microbiology and The European Molecular Biology Organization, and a Foreign Member of the Russian Academy of Sciences. He received his Ph.D. in Molecular Biology in 1983 from Moscow State University, joined the NIH in 1991 and became a Senior Investigator in 1996. His research interests focus on evolutionary genomics of prokaryotes, eukaryotes and viruses, host-parasite coevolution and general theory of the evolution of life. He is the author of about 1000 research papers and the book “The Logic of Chance: On the Nature and Origin of Biological Evolution”.

Ferdinand Marlétaz

FERDINAND MARLETAZMy main research question focuses on the relationship between the diversity of genome organisations, the evolution of gene regulation during development and the establishment of animal body plans. After graduating from the École Normale Supérieure de Lyon, I enrolled for a Phd at the University of Marseille focused on the phylogeny of spiralians and the enigmatic phylum of chaetognaths. During my postdoctoral work, in Oxford, I worked on whole genome duplications and their impact on gene regulation and organismal novelties, particularly using amphioxus as chordate sister group. I pursed on this topic during a stay at the Okinawa Institute of Science & Technology, in Japan, particularly focusing on the evolution of chromosomal architecture among animals. In 2019, I joined the Genetics, Evolution & Environment department at UCL.

Yehu Moran

Yehu MoranYehu Moran studied from 2001-2010 at Tel Aviv University where he obtained a BSc in Life Sciences, MSc in Biochemistry and PhD working on sea anemone toxins. Then he moved to the Department of Molecular Evolution and Development at the University of Vienna to study as postdoctoral fellow supported by EMBO and Marie Curie actions the evolution of post-transcriptional regulation by microRNAs. At January 2014 he was appointed as a senior lecturer at the Department of Ecology, Evolution and Behavior of the Alexander Silberman Institute of Life Sciences of The Hebrew University of Jerusalem and since the academic year 2017-2018 he is an Associate Professor in this department. He is currently a department head and his lab studies the evolution of complexity, focusing on biological systems such as venom and antiviral immunity, using the sea anemone Nematostella vectensis as a model organism.

Ben Pascoe

Ben Pascoe GE picDr Pascoe received a BSc (Hons.) from the University of Hertfordshire and a DPhil in Molecular Biology from the University of Sussex. He gained postdoctoral experience in pathogen genomics at Swansea University Medical School prior to taking up a position managing the core sequencing facility at the University of Bath and the Milner Centre for Evolution. He directs an active research portfolio on bacterial pathogen genomics, with recent work focussed on global differences in pathogen epidemiology, emergence and evolution of multi-drug resistant clones and genome-wide identification of transmission and virulence traits.

Josefin Stiller

New Content ItemJosefin Stiller investigates questions surrounding the evolutionary origins of animal biodiversity. After receiving a BSc from Free University Berlin and a MSc from Humboldt University Berlin, she obtained a PhD in Marine Biology from Scripps Institution of Oceanography at the University of California San Diego. She carried out postdoctoral studies at the University of Copenhagen in biodiversity genomics of birds as part of the Bird 10,000 Genome Project (B10K). With support from a Villum Young Investigator grant, she is now building a research group at University of Copenhagen with projects on phylogenomics, comparative genomics, and phylogeography, with a current focus on the evolution of seahorses, seadragons and pipefishes.

Martina Strömvik
New Content ItemMartina Strömvik earned her Ph.D. in Crop Sciences (plant molecular genetics of soybean) from University of Illinois at Urbana-Champaign (USA), after completing both her B.A. in Theoretical Philosophy and M.Sc. in Biology (tissue culture and transformation in Picea abies) from Stockholm University (Sweden). She carried out postdoctoral studies in Bioinformatics and Computational Genomics at University of Minnesota, Minneapolis (USA) working on plant genomics data. In 2003 she joined McGill University’s Department of Plant Science (Montreal, Canada) where she has served as Department Chair since 2015. She leads an interdisciplinary research group on projects in complex polyploid plant genome analyses, gene regulation and promoter discovery, and adaptation of plants to the Arctic.

  1. A fraction of all genomes is composed of transposable elements (TEs) whose mobility needs to be carefully controlled. In gonads, TE activity is repressed by PIWI-interacting RNAs (piRNAs), a class of small RNA...

    Authors: Amna Asif-Laidin, Karine Casier, Zoheir Ziriat, Antoine Boivin, Elise Viodé, Valérie Delmarre, Stéphane Ronsseray, Clément Carré and Laure Teysset
    Citation: BMC Biology 2023 21:117
  2. Hybrids are chimeric organisms with highly plastic heterozygous genomes that may confer unique traits enabling the adaptation to new environments. However, most evolutionary theory frameworks predict that the ...

    Authors: Verónica Mixão, Juan Carlos Nunez-Rodriguez, Valentina del Olmo, Ewa Ksiezopolska, Ester Saus, Teun Boekhout, Attila Gacser and Toni Gabaldón
    Citation: BMC Biology 2023 21:105
  3. Gene duplication is thought to be a central process in evolution to gain new functions. The factors that dictate gene retention following duplication as well paralog gene divergence in sequence, expression and...

    Authors: Evgeny Fraimovitch and Tzachi Hagai
    Citation: BMC Biology 2023 21:80
  4. With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with ‘low-methan...

    Authors: James G. Volmer, Rochelle M. Soo, Paul N. Evans, Emily C. Hoedt, Ana L. Astorga Alsina, Benjamin J. Woodcroft, Gene W. Tyson, Philip Hugenholtz and Mark Morrison
    Citation: BMC Biology 2023 21:59
  5. Theory suggests that the genetic architecture of traits under divergent natural selection influences how easily reproductive barriers evolve and are maintained between species. Divergently selected traits with...

    Authors: Marta Binaghi, Korinna Esfeld, Therese Mandel, Loreta B. Freitas, Marius Roesti and Cris Kuhlemeier
    Citation: BMC Biology 2023 21:58
  6. Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how geno...

    Authors: Yong Jia, Mingrui Xu, Haifei Hu, Brett Chapman, Calum Watt, B. Buerte, Ning Han, Muyuan Zhu, Hongwu Bian, Chengdao Li and Zhanghui Zeng
    Citation: BMC Biology 2023 21:25
  7. Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and th...

    Authors: Aleena Francis, Srayan Ghosh, Kriti Tyagi, V. Prakasam, Mamta Rani, Nagendra Pratap Singh, Amrita Pradhan, R. M. Sundaram, C. Priyanka, G. S. Laha, C. Kannan, M. S. Prasad, Debasis Chattopadhyay and Gopaljee Jha
    Citation: BMC Biology 2023 21:15
  8. The black cutworm, Agrotis ipsilon, is a serious global underground pest. Its distinct phenotypic traits, especially its polyphagy and ability to migrate long distances, contribute to its widening distribution an...

    Authors: Minghui Jin, Bo Liu, Weigang Zheng, Conghui Liu, Zhenxing Liu, Yuan He, Xiaokang Li, Chao Wu, Ping Wang, Kaiyu Liu, Shigang Wu, Hangwei Liu, Swapan Chakrabarty, Haibin Yuan, Kenneth Wilson, Kongming Wu…
    Citation: BMC Biology 2023 21:2
  9. Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven an...

    Authors: Atefeh Ghorbani, S. Javad Khataeipour, Monica H. Solbakken, David N. G. Huebert, Minasadat Khoddami, Khalil Eslamloo, Cassandra Collins, Tiago Hori, Sissel Jentoft, Matthew L. Rise and Mani Larijani
    Citation: BMC Biology 2022 20:293
  10. Genes, principal units of genetic information, vary in complexity and evolutionary history. Less-complex genes (e.g., long non-coding RNA (lncRNA) expressing genes) readily emerge de novo from non-genic sequen...

    Authors: Jan Petrzilek, Josef Pasulka, Radek Malik, Filip Horvat, Shubhangini Kataruka, Helena Fulka and Petr Svoboda
    Citation: BMC Biology 2022 20:272
  11. Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathw...

    Authors: Xuanzeng Liu, Muhammad Majid, Hao Yuan, Huihui Chang, Lina Zhao, Yimeng Nie, Lang He, Xiaojing Liu, Xiaoting He and Yuan Huang
    Citation: BMC Biology 2022 20:243
  12. Adaptive laboratory evolution (ALE) is a powerful method for strain optimization towards abiotic stress factors and for identifying adaptation mechanisms. In this study, the green microalga Picochlorum sp. BPE23 ...

    Authors: Robin Barten, Dirk-Jan M. van Workum, Emma de Bakker, Judith Risse, Michelle Kleisman, Sofia Navalho, Sandra Smit, Rene H. Wijffels, Harm Nijveen and Maria J. Barbosa
    Citation: BMC Biology 2022 20:242
  13. In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (...

    Authors: Ryan Gourlie, Megan McDonald, Mohamed Hafez, Rodrigo Ortega-Polo, Kristin E. Low, D. Wade Abbott, Stephen E. Strelkov, Fouad Daayf and Reem Aboukhaddour
    Citation: BMC Biology 2022 20:239
  14. Antarctica harbors the bulk of the species diversity of the dominant teleost fish suborder—Notothenioidei. However, the forces that shape their evolution are still under debate.

    Authors: Ying Lu, Wenhao Li, Yalin Li, Wanying Zhai, Xuming Zhou, Zhichao Wu, Shouwen Jiang, Taigang Liu, Huamin Wang, Ruiqin Hu, Yan Zhou, Jun Zou, Peng Hu, Guijun Guan, Qianghua Xu, Adelino V. M. Canário…
    Citation: BMC Biology 2022 20:231
  15. Cryptophytes are ecologically important algae of interest to evolutionary cell biologists because of the convoluted history of their plastids and nucleomorphs, which are derived from red algal secondary endosy...

    Authors: Jong Im Kim, Goro Tanifuji, Minseok Jeong, Woongghi Shin and John M. Archibald
    Citation: BMC Biology 2022 20:227
  16. Candida glabrata is an opportunistic yeast pathogen thought to have a large genetic and phenotypic diversity and a highly plastic genome. However, the lack of chromosome-level genome assemblies representing this...

    Authors: Marina Marcet-Houben, María Alvarado, Ewa Ksiezopolska, Ester Saus, Piet W. J. de Groot and Toni Gabaldón
    Citation: BMC Biology 2022 20:226
  17. The process of early development varies across the species-rich phylum Arthropoda. Owing to the limited research strategies for dissecting lineage-specific processes of development in arthropods, little is kno...

    Authors: Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda and Hiroki Oda
    Citation: BMC Biology 2022 20:223

    The Publisher Correction to this article has been published in BMC Biology 2022 20:286

  18. Although the wild relatives of pear originated in southwest China, this fruit crop was independently domesticated and improved in Asia and Europe, and there are major phenotypic differences (e.g., maturity and...

    Authors: Bobo Song, Xiaolong Li, Beibei Cao, Mingyue Zhang, Schuyler S. Korban, Li’ang Yu, Wenxi Yang, Kejiao Zhao, Jiaming Li and Jun Wu
    Citation: BMC Biology 2022 20:215
  19. Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction. Anatomical diversity of the olfactory organ suggests that olfaction is differentially i...

    Authors: Maxime Policarpo, Katherine E. Bemis, Patrick Laurenti, Laurent Legendre, Jean-Christophe Sandoz, Sylvie Rétaux and Didier Casane
    Citation: BMC Biology 2022 20:195
  20. Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that h...

    Authors: Zhudong Liu, Longsheng Xing, Wanlong Huang, Bo Liu, Fanghao Wan, Kenneth F. Raffa, Richard W. Hofstetter, Wanqiang Qian and Jianghua Sun
    Citation: BMC Biology 2022 20:190
  21. The blue-crowned laughingthrush (Garrulax courtoisi) is a critically endangered songbird endemic to Wuyuan, China, with population of ~323 individuals. It has attracted widespread attention, but the lack of a pub...

    Authors: Hao Chen, Min Huang, Daoqiang Liu, Hongbo Tang, Sumei Zheng, Jing Ouyang, Hui Zhang, Luping Wang, Keyi Luo, Yuren Gao, Yongfei Wu, Yan Wu, Yanpeng Xiong, Tao Luo, Yuxuan Huang, Rui Xiong…
    Citation: BMC Biology 2022 20:188
  22. Kisspeptins are neuropeptides that regulate reproductive maturation in mammals via G-protein-coupled receptor-mediated stimulation of gonadotropin-releasing hormone secretion from the hypothalamus. Phylogeneti...

    Authors: Nayeli Escudero Castelán, Dean C. Semmens, Luis Alfonso Yañez Guerra, Meet Zandawala, Mario dos Reis, Susan E. Slade, James H. Scrivens, Cleidiane G. Zampronio, Alexandra M. Jones, Olivier Mirabeau and Maurice R. Elphick
    Citation: BMC Biology 2022 20:187
  23. Hoverflies (Diptera: Syrphidae) including Eupeodes corollae are important insects worldwide that provide dual ecosystem services including pest control and pollination. The larvae are dominant predators of aphids...

    Authors: He Yuan, Bojia Gao, Chao Wu, Lei Zhang, Hui Li, Yutao Xiao and Kongming Wu
    Citation: BMC Biology 2022 20:157
  24. Archaea play fundamental roles in the environment, for example by methane production and consumption, ammonia oxidation, protein degradation, carbon compound turnover, and sulfur compound transformations. Rece...

    Authors: Raphaël Méheust, Cindy J. Castelle, Alexander L. Jaffe and Jillian F. Banfield
    Citation: BMC Biology 2022 20:154
  25. Human babesiosis, caused by parasites of the genus Babesia, is an emerging and re-emerging tick-borne disease that is mainly transmitted by tick bites and infected blood transfusion. Babesia duncani has caused ma...

    Authors: Jinming Wang, Kai Chen, Jifei Yang, Shangdi Zhang, Youquan Li, Guangyuan Liu, Jianxun Luo, Hong Yin, Guangying Wang and Guiquan Guan
    Citation: BMC Biology 2022 20:153
  26. Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including...

    Authors: Erwin Tantoso, Birgit Eisenhaber, Miles Kirsch, Vladimir Shitov, Zhiya Zhao and Frank Eisenhaber
    Citation: BMC Biology 2022 20:146
  27. Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plan...

    Authors: Ke Cao, Zhen Peng, Xing Zhao, Yong Li, Kuozhan Liu, Pere Arus, Weichao Fang, Changwen Chen, Xinwei Wang, Jinlong Wu, Zhangjun Fei and Lirong Wang
    Citation: BMC Biology 2022 20:139
  28. The mammalian X and Y chromosomes originated from a pair of ordinary autosomes. Over the past ~180 million years, the X and Y have become highly differentiated and now only recombine with each other within a s...

    Authors: Jennifer F. Hughes, Helen Skaletsky, Peter K. Nicholls, Alexis Drake, Tatyana Pyntikova, Ting-Jan Cho, Daniel W. Bellott and David C. Page
    Citation: BMC Biology 2022 20:133
  29. The deep-sea may be regarded as a hostile living environment, due to low temperature, high hydrostatic pressure, and limited food and light. Isopods, a species-rich group of crustaceans, are widely distributed...

    Authors: Jianbo Yuan, Xiaojun Zhang, Qi Kou, Yamin Sun, Chengzhang Liu, Shihao Li, Yang Yu, Chengsong Zhang, Songjun Jin, Jianhai Xiang, Xinzheng Li and Fuhua Li
    Citation: BMC Biology 2022 20:113
  30. Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hy...

    Authors: Wenpan Dong, Enze Li, Yanlei Liu, Chao Xu, Yushuang Wang, Kangjia Liu, Xingyong Cui, Jiahui Sun, Zhili Suo, Zhixiang Zhang, Jun Wen and Shiliang Zhou
    Citation: BMC Biology 2022 20:92
  31. Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide...

    Authors: Josefin Stiller, Graham Short, Healy Hamilton, Norah Saarman, Sarah Longo, Peter Wainwright, Greg W. Rouse and W. Brian Simison
    Citation: BMC Biology 2022 20:75
  32. Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservati...

    Authors: Hala Al Adhami, Anaïs Flore Bardet, Michael Dumas, Elouan Cleroux, Sylvain Guibert, Patricia Fauque, Hervé Acloque and Michael Weber
    Citation: BMC Biology 2022 20:70
  33. The plastid genomes of the green algal order Chlamydomonadales tend to expand their non-coding regions, but this phenomenon is poorly understood. Here we shed new light on organellar genome evolution in Chlamy...

    Authors: Tomáš Pánek, Dovilė Barcytė, Sebastian C. Treitli, Kristína Záhonová, Martin Sokol, Tereza Ševčíková, Eliška Zadrobílková, Karin Jaške, Naoji Yubuki, Ivan Čepička and Marek Eliáš
    Citation: BMC Biology 2022 20:66
  34. Mitochondria and peroxisomes are the two organelles that are most affected during adaptation to microoxic or anoxic environments. Mitochondria are known to transform into anaerobic mitochondria, hydrogenosomes...

    Authors: Kristína Záhonová, Sebastian Cristian Treitli, Tien Le, Ingrid Škodová-Sveráková, Pavla Hanousková, Ivan Čepička, Jan Tachezy and Vladimír Hampl
    Citation: BMC Biology 2022 20:56
  35. Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology ...

    Authors: Sergio E. Palma-Vera, Henry Reyer, Martina Langhammer, Norbert Reinsch, Lorena Derezanin, Joerns Fickel, Saber Qanbari, Joachim M. Weitzel, Soeren Franzenburg, Georg Hemmrich-Stanisak and Jennifer Schoen
    Citation: BMC Biology 2022 20:52

    The Correction to this article has been published in BMC Biology 2022 20:238

  36. Parasite evolution has been conceptualized as a process of genetic loss and simplification. Contrary to this model, there is evidence of expansion and conservation of gene families related to essential functio...

    Authors: Qingxiang Guo, Stephen D. Atkinson, Bin Xiao, Yanhua Zhai, Jerri L. Bartholomew and Zemao Gu
    Citation: BMC Biology 2022 20:51
  37. The morning glories (Convolvulaceae) are distributed worldwide and produce economically important crops, medicinal herbs, and ornamentals. Members of this family are diverse in morphological characteristics an...

    Authors: Yanxiang Lin, Pan Li, Yuchan Zhang, Delara Akhter, Ronghui Pan, Zhixi Fu, Mingqing Huang, Xiaobo Li and Yanlei Feng
    Citation: BMC Biology 2022 20:49
  38. The full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evol...

    Authors: Juan Pedro M. Camacho, Josefa Cabrero, María Dolores López-León, María Martín-Peciña, Francisco Perfectti, Manuel A. Garrido-Ramos and Francisco J. Ruiz-Ruano
    Citation: BMC Biology 2022 20:36

    The Correction to this article has been published in BMC Biology 2022 20:69

  39. A single circular mitochondrial (mt) genome is a common feature across most metazoans. The mt-genome includes protein-coding genes involved in oxidative phosphorylation, as well as RNAs necessary for translati...

    Authors: Shiqian Feng, Andrea Pozzi, Vaclav Stejskal, George Opit, Qianqian Yang, Renfu Shao, Damian K. Dowling and Zhihong Li
    Citation: BMC Biology 2022 20:7
  40. The explosive radiation and diversification of the advanced snakes (superfamily Colubroidea) was associated with changes in all aspects of the shared venom system. Morphological changes included the partitioni...

    Authors: Bing Xie, Daniel Dashevsky, Darin Rokyta, Parviz Ghezellou, Behzad Fathinia, Qiong Shi, Michael K. Richardson and Bryan G. Fry
    Citation: BMC Biology 2022 20:4
  41. Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spr...

    Authors: Dongseok Kim, JunMo Lee, Chung Hyun Cho, Eun Jeung Kim, Debashish Bhattacharya and Hwan Su Yoon
    Citation: BMC Biology 2022 20:2