Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> Species
Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 wa...
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MDPI AG
2023-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/9/7716 |
| _version_ | 1797602589976559616 |
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| author | Qing Xian Suyin Wang Yanyan Liu Shenglong Kan Wei Zhang |
| author_facet | Qing Xian Suyin Wang Yanyan Liu Shenglong Kan Wei Zhang |
| author_sort | Qing Xian |
| collection | DOAJ |
| description | Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 was high-throughput sequenced from 29 <i>Corydalis</i> species, and their GC contents were comparatively investigated in the context of ITS2’s characteristic secondary structure and concerted evolution. Our results showed that the GC contents of ITS2 were 131% higher than those of their adjacent 5.8S regions, suggesting that ITS2 underwent GC-biased evolution. These GCs were distributed in a heterogeneous manner in the ITS2 secondary structure, with the paired regions being 130% larger than the unpaired regions, indicating that GC is chosen for thermodynamic stability. In addition, species with homogeneous ITS2 sequences were always GC-rich, supporting GC-biased gene conversion (gBGC), which occurred with ITS2’s concerted evolution. The RNA substitution model inferred also showed a GC preference among base pair transformations, which again supports gBGC. Overall, structurally based GC investigation reveals that ITS2 evolves under structural stability and gBGC selection, significantly increasing its GC content. |
| first_indexed | 2024-03-11T04:18:44Z |
| format | Article |
| id | doaj.art-ee50c7193de54ec49e0ce500889f3558 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T04:18:44Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ee50c7193de54ec49e0ce500889f35582023-11-17T22:59:36ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-04-01249771610.3390/ijms24097716Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> SpeciesQing Xian0Suyin Wang1Yanyan Liu2Shenglong Kan3Wei Zhang4Marine College, Shandong University, Weihai 264209, ChinaMarine College, Shandong University, Weihai 264209, ChinaCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, ChinaMarine College, Shandong University, Weihai 264209, ChinaGuanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 was high-throughput sequenced from 29 <i>Corydalis</i> species, and their GC contents were comparatively investigated in the context of ITS2’s characteristic secondary structure and concerted evolution. Our results showed that the GC contents of ITS2 were 131% higher than those of their adjacent 5.8S regions, suggesting that ITS2 underwent GC-biased evolution. These GCs were distributed in a heterogeneous manner in the ITS2 secondary structure, with the paired regions being 130% larger than the unpaired regions, indicating that GC is chosen for thermodynamic stability. In addition, species with homogeneous ITS2 sequences were always GC-rich, supporting GC-biased gene conversion (gBGC), which occurred with ITS2’s concerted evolution. The RNA substitution model inferred also showed a GC preference among base pair transformations, which again supports gBGC. Overall, structurally based GC investigation reveals that ITS2 evolves under structural stability and gBGC selection, significantly increasing its GC content.https://www.mdpi.com/1422-0067/24/9/7716internal transcribed spacer 2GC-biased evolutionGC contentsecondary structureconcerted evolution |
| spellingShingle | Qing Xian Suyin Wang Yanyan Liu Shenglong Kan Wei Zhang Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> Species International Journal of Molecular Sciences internal transcribed spacer 2 GC-biased evolution GC content secondary structure concerted evolution |
| title | Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> Species |
| title_full | Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> Species |
| title_fullStr | Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> Species |
| title_full_unstemmed | Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> Species |
| title_short | Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in <i>Corydalis</i> Species |
| title_sort | structure based gc investigation sheds new light on its2 evolution in i corydalis i species |
| topic | internal transcribed spacer 2 GC-biased evolution GC content secondary structure concerted evolution |
| url | https://www.mdpi.com/1422-0067/24/9/7716 |
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