Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation
Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus l...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-09-01
|
| Series: | Insects |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-4450/12/9/837 |
| _version_ | 1797518709535801344 |
|---|---|
| author | Muhammad Majid Huang Yuan |
| author_facet | Muhammad Majid Huang Yuan |
| author_sort | Muhammad Majid |
| collection | DOAJ |
| description | Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus <i>Calliptamus</i> diverged from <i>Peripolus</i> around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of <i>Calliptamus barbarus</i>, <i>Calliptamus italicus</i>, and <i>Calliptamus abbreviatus</i>, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus <i>Calliptamus</i> grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were <i>Calliptamus barbarus</i> specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different. |
| first_indexed | 2024-03-10T07:33:33Z |
| format | Article |
| id | doaj.art-1da72cef8ec24f628984c79516137b39 |
| institution | Directory Open Access Journal |
| issn | 2075-4450 |
| language | English |
| last_indexed | 2024-03-10T07:33:33Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Insects |
| spelling | doaj.art-1da72cef8ec24f628984c79516137b392023-11-22T13:37:19ZengMDPI AGInsects2075-44502021-09-0112983710.3390/insects12090837Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size VariationMuhammad Majid0Huang Yuan1College of Life Sciences, Shaanxi Normal University, Xi’an 710100, ChinaCollege of Life Sciences, Shaanxi Normal University, Xi’an 710100, ChinaTransposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus <i>Calliptamus</i> diverged from <i>Peripolus</i> around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of <i>Calliptamus barbarus</i>, <i>Calliptamus italicus</i>, and <i>Calliptamus abbreviatus</i>, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus <i>Calliptamus</i> grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were <i>Calliptamus barbarus</i> specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.https://www.mdpi.com/2075-4450/12/9/837genus <i>Calliptamus</i>repeatome analysissatellitome evolutionrepeat profiling |
| spellingShingle | Muhammad Majid Huang Yuan Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation Insects genus <i>Calliptamus</i> repeatome analysis satellitome evolution repeat profiling |
| title | Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation |
| title_full | Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation |
| title_fullStr | Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation |
| title_full_unstemmed | Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation |
| title_short | Comparative Analysis of Transposable Elements in Genus <i>Calliptamus</i> Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation |
| title_sort | comparative analysis of transposable elements in genus i calliptamus i grasshoppers revealed that satellite dna contributes to genome size variation |
| topic | genus <i>Calliptamus</i> repeatome analysis satellitome evolution repeat profiling |
| url | https://www.mdpi.com/2075-4450/12/9/837 |
| work_keys_str_mv | AT muhammadmajid comparativeanalysisoftransposableelementsingenusicalliptamusigrasshoppersrevealedthatsatellitednacontributestogenomesizevariation AT huangyuan comparativeanalysisoftransposableelementsingenusicalliptamusigrasshoppersrevealedthatsatellitednacontributestogenomesizevariation |