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Co-evolution of Mobilome and Genome
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Co-evolution of Mobilome and Genome

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 7009

Special Issue Editors

Prof. Dr. Chengyi Song

E-Mail Website
Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou, China
Interests: mobilome; genome; transposable elements; transposon; retrotransposon; evolution; exaptation/domestication; horizontal transfer; gene transfer; gene editing
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Klaus Wimmers

E-Mail Website
Guest Editor
Competence Area Genetics and Genomics, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
Interests: animal genomics; transcriptome; epigenome; animal health; animal welfare
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The mobilome is defined as the set of mobile elements (including DNA transposons and retrotransposons) of a genome. There is growing evidence that the mobilome, which accounts for 30-50% of mammalian genomes, plays an important role in gene and genome evolution in vertebrates and plants, and is the most important factor influencing genome size. Mobile elements have contributed to genome evolution through taming, exaptation and domestication processes, which can lead to evolutionary innovations such as the modification of existing genes, the emergence of new phenotypes or the alteration of cis-regulatory DNA components and transcriptional networks that trigger the evolution of important adaptive traits and possibly speciation. In addition, mobile elements can alter the host genome’s landscape through horizontal transfer between non-mating individuals.

Thus, profiling the co-evolution of the mobilome and genome will help to reveal the process of gene and genome evolution and further develop our understanding of speciation, adaptation and the origin of biodiversity.

This Special Issue focuses on understanding the co-evolution of the mobilome and genome, including the annotation of mobilomes and their evolutionary landscape (distribution, classification, activity, exaptation/domestication and horizontal transfer) and their implications for the evolution of genes and genomes. The study of genome variation and the development of genetic markers based on retrotransposon- and DNA-transposon-insertion polymorphisms are also of interest.

Prof. Dr. Chengyi Song
Prof. Dr. Klaus Wimmers
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • mobilome
  • transposable elements
  • transposon
  • retrotransposon
  • genome
  • evolution
  • exaptation/domestication
  • horizontal transfer

Published Papers (4 papers)

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Research

12 pages, 5298 KiB  
Article
A Multi-Tissue Gene Expression Atlas of Water Buffalo (Bubalus bubalis) Reveals Transcriptome Conservation between Buffalo and Cattle
by Jingfang Si, Dongmei Dai, Kun Li, Lingzhao Fang and Yi Zhang
Genes 2023, 14(4), 890; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14040890 - 10 Apr 2023
Viewed by 1593
Abstract
We generated 73 transcriptomic data of water buffalo, which were integrated with publicly available data in this species, yielding a large dataset of 355 samples representing 20 major tissue categories. We established a multi-tissue gene expression atlas of water buffalo. Furthermore, by comparing [...] Read more.
We generated 73 transcriptomic data of water buffalo, which were integrated with publicly available data in this species, yielding a large dataset of 355 samples representing 20 major tissue categories. We established a multi-tissue gene expression atlas of water buffalo. Furthermore, by comparing them with 4866 cattle transcriptomic data from the cattle genotype–tissue expression atlas (CattleGTEx), we found that the transcriptomes of the two species exhibited conservation in their overall gene expression patterns, tissue-specific gene expression and house-keeping gene expression. We further identified conserved and divergent expression genes between the two species, with the largest number of differentially expressed genes found in the skin, which may be related to structural and functional differences in the skin of the two species. This work provides a source of functional annotation of the buffalo genome and lays the foundations for future genetic and evolutionary studies in water buffalo. Full article
(This article belongs to the Special Issue Co-evolution of Mobilome and Genome)
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14 pages, 4421 KiB  
Article
Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species
by Yali Wang, Mengke Guo, Naisu Yang, Zhongxia Guan, Han Wu, Numan Ullah, Emmanuel Asare, Shasha Shi, Bo Gao and Chengyi Song
Genes 2023, 14(2), 523; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14020523 - 19 Feb 2023
Cited by 1 | Viewed by 1943
Abstract
Some families of mobile elements in bacterial genomes encode not only a transposase but also an accessory TnpB gene. This gene has been shown to encode an RNA-guided DNA endonuclease, co-evolving with Y1 transposase and serine recombinase in mobile elements IS605 and IS607 [...] Read more.
Some families of mobile elements in bacterial genomes encode not only a transposase but also an accessory TnpB gene. This gene has been shown to encode an RNA-guided DNA endonuclease, co-evolving with Y1 transposase and serine recombinase in mobile elements IS605 and IS607. In this paper, we reveal the evolutionary relationships among TnpB-containing mobile elements (TCMEs) in well-assembled genomes of six bacterial species: Bacillus cereus, Clostridioides difficile, Deinococcus radiodurans, Escherichia coli, Helicobacter pylori and Salmonella enterica. In total, 9996 TCMEs were identified in 4594 genomes. They belonged to 39 different insertion sequences (ISs). Based on their genetic structures and sequence identities, the 39 TCMEs were classified into three main groups and six subgroups. According to our phylogenetic analysis, TnpBs include two main branches (TnpB-A and TnpB-B) and two minor branches (TnpB-C and TnpB-D). The key TnpB motifs and the associated Y1 and serine recombinases were highly conserved across species, even though their overall sequence identities were low. Substantial variation was observed for the rate of invasion across bacterial species and strains. Over 80% of the genomes of B. cereus, C. difficile, D. radiodurans and E. coli contained TCMEs; however, only 64% of the genomes of H. pylori and 44% of S. enterica genomes contained TCMEs. IS605 showed the largest rate of invasion in these species, while IS607 and IS1341 had a relatively narrow distribution. Co-invasions of IS605, IS607 and IS1341 elements were observed in various genomes. The largest average copy number was observed for IS605b elements in C. difficile. The average copy numbers of most other TCMEs were smaller than four. Our findings have important implications for understanding the co-evolution of TnpB-containing mobile elements and their biological roles in host genome evolution. Full article
(This article belongs to the Special Issue Co-evolution of Mobilome and Genome)
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17 pages, 5660 KiB  
Article
Horizontal Transfer and Evolutionary Profiles of Two Tc1/DD34E Transposons (ZB and SB) in Vertebrates
by Wenzhu Jia, Emmanuel Asare, Tao Liu, Pingjing Zhang, Yali Wang, Saisai Wang, Dan Shen, Csaba Miskey, Bo Gao, Zoltán Ivics, Qijun Qian and Chengyi Song
Genes 2022, 13(12), 2239; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13122239 - 29 Nov 2022
Cited by 4 | Viewed by 1406
Abstract
Both ZeBrafish (ZB), a recently identified DNA transposon in the zebrafish genome, and SB, a reconstructed transposon originally discovered in several fish species, are known to exhibit high transposition activity in vertebrate cells. Although a similar structural organization was observed [...] Read more.
Both ZeBrafish (ZB), a recently identified DNA transposon in the zebrafish genome, and SB, a reconstructed transposon originally discovered in several fish species, are known to exhibit high transposition activity in vertebrate cells. Although a similar structural organization was observed for ZB and SB transposons, the evolutionary profiles of their homologs in various species remain unknown. In the present study, we compared their taxonomic ranges, structural arrangements, sequence identities, evolution dynamics, and horizontal transfer occurrences in vertebrates. In total, 629 ZB and 366 SB homologs were obtained and classified into four distinct clades, named ZB, ZB-like, SB, and SB-like. They displayed narrow taxonomic distributions in eukaryotes, and were mostly found in vertebrates, Actinopterygii in particular tended to be the major reservoir hosts of these transposons. Similar structural features and high sequence identities were observed for transposons and transposase, notably homologous to the SB and ZB elements. The genomic sequences that flank the ZB and SB transposons in the genomes revealed highly conserved integration profiles with strong preferential integration into AT repeats. Both SB and ZB transposons experienced horizontal transfer (HT) events, which were most common in Actinopterygii. Our current study helps to increase our understanding of the evolutionary properties and histories of SB and ZB transposon families in animals. Full article
(This article belongs to the Special Issue Co-evolution of Mobilome and Genome)
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10 pages, 963 KiB  
Article
SINE Insertion May Act as a Repressor to Affect the Expression of Pig LEPROT and Growth Traits
by Xiaoyan Wang, Chengling Chi, Jia He, Zhanyu Du, Yao Zheng, Enrico D’Alessandro, Cai Chen, Ali Shoaib Moawad, Emmanuel Asare and Chengyi Song
Genes 2022, 13(8), 1422; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13081422 - 10 Aug 2022
Cited by 2 | Viewed by 1490
Abstract
Retrotransposon is an important component of the mammalian genome. Previous studies have shown that the expression of protein-coding genes was affected by the insertion of retrotransposon into the proximal genes, and the phenotype variations would be related to the retrotransposon insertion polymorphisms (RIPs). [...] Read more.
Retrotransposon is an important component of the mammalian genome. Previous studies have shown that the expression of protein-coding genes was affected by the insertion of retrotransposon into the proximal genes, and the phenotype variations would be related to the retrotransposon insertion polymorphisms (RIPs). In this study, leptin (LEP), leptin receptor (LEPR), and leptin receptor overlapping transcript (LEPROT), which play important roles in the regulation of fat synthesis and body weight, were screened to search for the RIPs and their effect on phenotype and gene expression, as well as to further study the function of the insertion. The results showed that three RIPs located in intron 1 of LEPROT and intron 2 and 21 of LEPR were identified, and they were all SINEA1, which was one type of retrotransposon. The SINE insertion at the LEPROT was the dominant allele in native pig breeds. The age of 100 kg body weight of SINE+/+ Large White individuals was significantly higher than those of SINE+/− and SINE−/− individuals (p < 0.05). The LEPROT gene expression in the liver and suet of 30-day-old SINE−/− Sujiang piglets were significantly higher than those of SINE+/+ and SINE+/− piglets (p < 0.01). The dual-luciferase reporter gene assay showed that SINE insertion in PK15 and 3T3-L1 cells significantly reduced the promoter activity of the LEPROT gene (p < 0.01). Therefore, SINE insertion can be a repressor to reduce the expression of LEPROT and could be a useful molecular marker for assisted selection of growth traits in pig breeding. Full article
(This article belongs to the Special Issue Co-evolution of Mobilome and Genome)
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