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Open AccessArticle

Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species

by Qing Xian, Suyin Wang, Yanyan Liu, Shenglong Kan and Wei Zhang

Int. J. Mol. Sci. 2023, 24(9), 7716; https://doi.org/10.3390/ijms24097716 - 23 Apr 2023

Cited by 3 | Viewed by 2351

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 Corydalis 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. Full article

(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)

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16 pages, 1301 KiB

Open AccessArticle

Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution

by Veronika Borůvková, W. Mike Howell, Dominik Matoulek and Radka Symonová

Genes 2021, 12(2), 312; https://doi.org/10.3390/genes12020312 - 22 Feb 2021

Cited by 9 | Viewed by 3524

Abstract

Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates. Full article

(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)

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15 pages, 3747 KiB

Open AccessArticle

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

by Zhitao Niu, Qingyun Xue, Hui Wang, Xuezhu Xie, Shuying Zhu, Wei Liu and Xiaoyu Ding

Int. J. Mol. Sci. 2017, 18(11), 2307; https://doi.org/10.3390/ijms18112307 - 2 Nov 2017

Cited by 48 | Viewed by 5882

Abstract

The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC)—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus. Full article

(This article belongs to the Special Issue Chloroplast)

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