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Life
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Satellite DNAs: Cell Function and Evolution
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Satellite DNAs: Cell Function and Evolution

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 3797

Special Issue Editor

Dr. Christophe Escudé

E-Mail Website
Guest Editor
Laboratoire Structure et Instabilité des Génomes – INSERM U1154 – CNRS UM7196 – Muséum National d’Histoire Naturelle, 75005 Paris, France
Interests: centromere; repetitive DNA; cytogenetics; chromosome evolution; comparative genomics; genome organization

Special Issue Information

Dear Colleagues,

Satellite DNA represents one of the most intriguing component of eukaryotic genomes. Progress in sequencing technologies, together with new computational and functional approaches, offer new perspectives for understanding the evolutionary dynamics of those peculiar repetitive elements as well as their contribution to important cell functions such as the preservation of genome stability and genome regulatory mechanisms.

This Special Issue of Life aims to compile a timely collection of reviews and research articles covering different aspects of satellite DNA biology, including but not limited to sequence analysis, epigenetic regulations, non-coding RNAs and nuclear organization. Attention will be given to studies aimed at describing how satellite DNA regulate cell proliferation and differentiation and contribute to pathophysiological processes as well as expanding our knowledge on the interplay of satellite DNA and genome evolution.

We hope this Special Issue will help address the challenges raised by satellite DNA and clarify how those sequences impact cell function and evolution. We look forward to receiving your contributions.

Dr. Christophe Escudé
Guest Editor

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. Life 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

  • satellite DNA
  • satellitome
  • satellite DNA evolution
  • satellite DNA transcription
  • satellite DNA function
  • genome evolution
  • genome organization
  • centromere
  • telomere
  • gene regulation
  • tandem repeats
  • heterochromatin

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Published Papers (1 paper)

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Research

18 pages, 7900 KiB  
Article
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda
by Inzamam Ul Haq, Majid Muhammad, Huang Yuan, Shahbaz Ali, Asim Abbasi, Muhammad Asad, Hafiza Javaria Ashraf, Aroosa Khurshid, Kexin Zhang, Qiangyan Zhang and Changzhong Liu
Life 2022, 12(4), 521; https://doi.org/10.3390/life12040521 - 31 Mar 2022
Cited by 11 | Viewed by 3153
Abstract
Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural [...] Read more.
Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. Spodoptera frugiperda’s genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the Spodoptera frugiperda genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of Spodoptera frugiperda, particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1–15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30–35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the Spodoptera frugiperda fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in Spodoptera frugiperda account for a considerable proportion of the genome’s repetitive fraction. The satellite DNA families’ repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of Spodoptera frugiperda. Full article
(This article belongs to the Special Issue Satellite DNAs: Cell Function and Evolution)
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