Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes
Abstract 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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-01-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.8499 |
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| author | Jingyao Ping Jing Hao Jinye Li Yiqing Yang Yingjuan Su Ting Wang |
| author_facet | Jingyao Ping Jing Hao Jinye Li Yiqing Yang Yingjuan Su Ting Wang |
| author_sort | Jingyao Ping |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-10T15:02:56Z |
| format | Article |
| id | doaj.art-4723e7bee3bc459391cf5b0a1f9f9cf8 |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-04-10T15:02:56Z |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-4723e7bee3bc459391cf5b0a1f9f9cf82023-02-15T09:06:07ZengWileyEcology and Evolution2045-77582022-01-01121n/an/a10.1002/ece3.8499Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genesJingyao Ping0Jing Hao1Jinye Li2Yiqing Yang3Yingjuan Su4Ting Wang5College of Life Sciences South China Agricultural University Guangzhou ChinaCollege of Life Sciences South China Agricultural University Guangzhou ChinaCollege of Life Sciences South China Agricultural University Guangzhou ChinaCollege of Life Science and Technology Central South University of Forestry and Technology Changsha ChinaSchool of Life Sciences Sun Yat‐sen University Guangzhou ChinaCollege of Life Sciences South China Agricultural University Guangzhou ChinaAbstract 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.https://doi.org/10.1002/ece3.8499conifergymnosperminverted repeat regionrate heterogeneityselection pressure |
| spellingShingle | Jingyao Ping Jing Hao Jinye Li Yiqing Yang Yingjuan Su Ting Wang Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes Ecology and Evolution conifer gymnosperm inverted repeat region rate heterogeneity selection pressure |
| title | Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes |
| title_full | Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes |
| title_fullStr | Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes |
| title_full_unstemmed | Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes |
| title_short | Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes |
| title_sort | loss of the ir region in conifer plastomes changes in the selection pressure and substitution rate of protein coding genes |
| topic | conifer gymnosperm inverted repeat region rate heterogeneity selection pressure |
| url | https://doi.org/10.1002/ece3.8499 |
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