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. 2024 Apr 22;25(1):396.
doi: 10.1186/s12864-024-10296-0.

The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers

Xiaolin Gu  1 , Lingling Li  1 , Xiaona Zhong  1 , Yingjuan Su  2   3 , Ting Wang  4
Affiliations

The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers

Xiaolin Gu et al. BMC Genomics. .

Abstract

Background: While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts.

Results: Poor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family.

Conclusions: This study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research.

Keywords: Chloroplast; Divergence time; Evolutionary genomics; Pteridaceae; Structural comparison.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Comparison of repetitive sequences among the 41 Pteridaceae cpDNAs. (A) The number of SSRs among each species. (B) The percentage of SSRs located in different cpDNA regions and gene sequence regions. (C) The size distribution of dispersed repeats and tandem repeats among the 41 Pteridaceae cpDNAs. (D) The percentage of dispersed repeats and tandem repeats located in different cpDNA regions and gene sequence regions
Fig. 2
Fig. 2
Comparison of IR/SC boundaries among the 41 Pteridaceae cpDNAs. The numbers above, below, or adjacent to genes represent gene length or the distances from the front or end of genes to the boundary sites. Figure features are not to scale
Fig. 3
Fig. 3
Comparison of chloroplast genome features in the 41 Pteridaceae species. (A) Comparison of the cpDNA sizes with the overlong IGSs; even if the overlong IGS is in the IR regions, the figure only shows the length of one copy of the IGS. (B) Comparison of the lengths of the LSC, SSC, and IR regions; with * indicating regions containing overlong IGS. (C) The correlation between IGS length and cpDNA sizes
Fig. 4
Fig. 4
Comparison of (A) GC content and (B) number of repeats between overlong and non-overlong IGSs. (C) Correlation among SSRs, tandem repeats, dispersed repeats, and the length of overlong IGSs. *p < 0.05; **p < 0.01; ***p < 0.001
Fig. 5
Fig. 5
Phylogenetic relationship (right) and divergent time estimate (left) of the 41 Pteridaceae species. The mean divergence time of the nodes is shown next to the nodes while the blue bars correspond to the 95% highest posterior density (HPD). The red dots represent species within the branch that contain overlong IGS. Bootstrap value/posterior probabilities < 100%/1 are displayed on the branches
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