The highly conserved rps12 gene in ferns provides strong evidence for decreased substitution rates in the inverted repeat region

Ping, Jingyao; Li, Aimin; Feng, Peipei; Zhu, Min; Su, Yingjuan; Wang, Ting

doi:10.1007/s00606-021-01750-7

Cited by 5 publications

(10 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genes in the IR region tend to have a low substitution rate (Li, Kuo, et al, 2016; Li, Gao, et al, 2016; Ping, Feng, et al, 2021; Ping, Li, et al, 2021). In this study, ycf2 in the IR region showed a reduced substitution rate (Figure 4) but weak selection pressure ( ω IR‐21 = 0.76124, ω SC‐57 = 0.67832), indicating the lack of correlation between these factors.…”

Section: Discussionmentioning

confidence: 99%

“…Genes in the IR region experience strong negative selection (Ping, Feng, et al, 2021; Ping, Li, et al, 2021). The IR region is important for genome structural stability, and genomes lacking an IR region may experience different natural selection effects.…”

Section: Discussionmentioning

confidence: 99%

“…However, the IR region, as a hot spot of structural rearrangement, often contracts, expands, or is lost. In related species, the boundary of the IR region changes little, resulting in the gain or loss of a small number of genes (Downie & Jansen, 2015 ; Li et al, 2016 ; Ping, Li, et al, 2021 ; Wicke et al, 2014 ). The IR region of Pelargonium , Psilotum , and Trochodendraceae has undergone large‐scale expansion, gaining a large number of genes from the SC region (Chumley et al, 2006 ; Grewe et al, 2013 ; Sun et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

“…In ferns, psbA , rps7 , 3'‐ rps12 , and ycf2 showed a reduced substitution rate and increased GC content after entering the IR region (Li, Kuo, et al, 2016). Recently, Ping, Feng, et al (2021), Ping, Li, et al (2021) reported that the substitution rate of 3'‐ rps12 in the IR region is lower than that of 5'‐ rps12 in the SC region in ferns and gymnosperms.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes

Ping

Hao

et al. 2022

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein‐coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non‐conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non‐conifers. It is more obvious that in non‐conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6‐ to 3.1‐fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2‐ to 3.6‐fold of non‐conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein‐coding genes due to gene function, plant habitat, or newly acquired IRs.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes

Ping

Hao

et al. 2022

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

show abstract

“…It has been observed that cp genes exhibit varying nucleotide substitution rates across different lineages, locations, and functional genomes [17][18][19][20]. Several factors contribute to this rate variation and influence the evolution of cp genes.…”

Section: Introductionmentioning

confidence: 99%

The Broken Chloroplast Gene Clusters in Gymnosperms Exhibit Elevated Substitution Rates

Ping,

Zhong,

Wang

et al. 2023

Forests

Self Cite

View full text Add to dashboard Cite

Plant chloroplast (cp) gene clusters consist of genes arranged closely together on the cp genome. These genes are organized in operon structures and participate in cotranscription, typically exhibiting conservation. Broken gene clusters have been observed in gymnosperms. In order to investigate whether the substitution rates and selection pressure of associated genes are affected following the disruption of gene clusters, the cp genomes of 80 species (78 gymnosperms and 2 outgroups) were analyzed. A phylogenetic analysis was conducted using 58 shared genes to examine the evolutionary rates and selection pressure of genes associated with gene clusters and protein-coding genes in Sciadopitys verticillata. The results demonstrate that S. verticillata exhibited the highest number of rearrangements compared to the Cycas revoluta genome. Four gene clusters (rps2, psbB, rpoB, and petL clusters) in S. verticillata were disrupted, while rps2 in Callitris rhomboidea experienced disruption. Significantly increased evolutionary rates were observed in 12 out of 18 gene cluster-related genes in S. verticillata. Following disruption, S. verticillata and C. rhomboidea exhibited an increase in gene cluster-related genes, particularly rps2, and higher selection pressure on both rps2 and atpA genes compared to other species. Furthermore, among the 58 genes shared by S. verticillata, the evolutionary rates of 36 genes increased, and the selection pressure on 13 genes exceeded that of other species. These results indicate an increased substitution rate of gene clusters in S. verticillata and C. rhomboidea. The large-scale rearrangement and elevated substitution rates of the cp genome in S. verticillata were revealed. This study sheds light on the heterogeneity of cp genome evolution in gymnosperms.

show abstract

Comparative chloroplast genomes of Annonaceae species: Enlargement of plastomes in size, IR region, and gene content

Gan

Liu

Ping

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

In recent years, the evolution and phylogeny of plastid genomes have attracted much attention from scholars all over the world. Annonaceae is the largest family in Magnoliales with the greatest diversity among and within genera. Thus comparative analyses of its plastomes will be informative. In this study, the complete chloroplast genome of Miliusa glochidioides was sequenced by next-generation sequencing technology. Using two Magnoliaceae species as out-group, a comparative analysis of the existing 13 Annonaceae plastomes was conducted, and a phylogenetic relationship was constructed based on four methods. Our results show that the Annonaceae plastomes have great variation in the evolution process. The genome size is between 159kb and 202kb while the gene content ranges from 127 to 165. The number of genes in the IR region is between 5 and 39. Plastomes underwent significant structural rearrangements, including one inversion and multiple large-scale expansion (6-20kb) in the lR region, and shrinkage and inversions in the SSC region. Compared with Magnoliaceae, two fragments (pafII-atpE and 5'-rps12-psbJ) were inversed in Annonaceae. The phylogenetic relationship based on 78 common protein genes showed that Cananga odorata was located at the base of Annonaceae. Annonoideae was a monophyletic group, and Chieniodendron hainanense was located inside the Malmeoideae. A total of 737 simple sequence repeats (SSRs) were detected in the study, and the distribution of SSRs varied from species. It is mainly dominated by A/T bases (mononucleotide) and is located in the intergenic region. In conclusion, the plastomes of Annonaceae have undergone great variation during evolution, especially the large-scale expansion of the IR region. Our study provides more information for studying the plastome evolution of Annonaceae.

show abstract

The highly conserved rps12 gene in ferns provides strong evidence for decreased substitution rates in the inverted repeat region

Cited by 5 publications

References 20 publications

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes

The Broken Chloroplast Gene Clusters in Gymnosperms Exhibit Elevated Substitution Rates

Comparative chloroplast genomes of Annonaceae species: Enlargement of plastomes in size, IR region, and gene content

Contact Info

Product

Resources

About