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Corvalán LCJ, Sobreiro MB, Carvalho LR, Dias RO, Braga-Ferreira RS, Targueta CP, Silva-Neto CME, Berton BW, Pereira AMS, Diniz-filho JAF, Telles MPC, Nunes R. Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1258794. [PMID: 37822334 PMCID: PMC10562606 DOI: 10.3389/fpls.2023.1258794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
Abstract
Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.
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Affiliation(s)
| | - Mariane B. Sobreiro
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Larissa R. Carvalho
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Renata O. Dias
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Ramilla S. Braga-Ferreira
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, Rondonópolis, Brazil
| | - Cintia P. Targueta
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | | | | | | | - José A. F. Diniz-filho
- Laboratório de Ecologia Teórica e Síntese, Universidade Federal de Goiás, Goiânia, Brazil
| | - Mariana P. C. Telles
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto Federal de Goiás, Goiás, Brazil
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Huang X, Tan W, Li F, Liao R, Guo Z, Shi T, Gao Z. The chloroplast genome of Prunus zhengheensis: Genome comparative and phylogenetic relationships analysis. Gene 2021; 793:145751. [PMID: 34062257 DOI: 10.1016/j.gene.2021.145751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
Prunus zhengheensis is a novel species originated in Fujian province, China. However, there is no further information available on its classification and molecular biology study. In this study, we first report the complete chloroplast (cp) genome sequence of P. zhengheensis. The cp genome of P. zhengheensis is 158,106 bp and GC content is 36.73%, is a circular structure composed of LSC (large single copy), SSC (small single copy), and IR (inverted repeat) regions, with the size of the three regions being 86,321 bp, 18,999 bp and 26,393 bp, respectively. The cp genome of P. zhengheensis contains 130 genes, and 242 SSRs are identified in the cp genome. The comparative analysis of cp genomes in eight Prunus plants demonstrates the subtle divergences occur in the protein-coding gene rps18, rps12, psbF, rpl33, matK, and rbcL, and that the KA/KS nucleotide substitution ratio of the ndhF of P. zhengheensis and P. armeniaca is 1.79636. The phylogenetic results indicate that the P. zhengheensis is closely related to P. mume, compared to other species of Prunus. Our research results provide the important genomic information for molecular phylogeny of P. zhengheensis.
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Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Li
- Jilin Academy of Agricultural Sciences, Jilin 136100, China.
| | - Ruyu Liao
- Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
| | - Zhongren Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Krüger M, Abeyawardana OAJ, Krüger C, Juříček M, Štorchová H. Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion. Cells 2020; 9:cells9122700. [PMID: 33339225 PMCID: PMC7766179 DOI: 10.3390/cells9122700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphrodite flower buds, making it possible to compare the transcriptomes derived from three genomes in the same RNA specimen. We assembled de novo transcriptomes for two haplotypes of S. vulgaris and identified differentially expressed genes between the females and hermaphrodites, associated with stress response or pollen development. The gene for alternative oxidase was downregulated in females. The genetic pathways controlling CMS in S. vulgaris are similar to those in crops. The high number of the differentially expressed nuclear genes contrasts with the uniformity of organellar transcriptomes across genders, which suggests these pathways are evolutionarily conserved and that selective mechanisms may shield organellar transcription against changes in the cytoplasmic transcriptome.
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Affiliation(s)
- Manuela Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Oushadee A. J. Abeyawardana
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
- Department of Horticulture, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague 6-Suchdol, Czech Republic
| | - Claudia Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Miloslav Juříček
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
| | - Helena Štorchová
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic; (M.K.); (O.A.J.A.); (C.K.); (M.J.)
- Correspondence: ; Tel.: +420-225-106-828
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Ren T, Li ZX, Xie DF, Gui LJ, Peng C, Wen J, He XJ. Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships. BMC PLANT BIOLOGY 2020; 20:519. [PMID: 33187470 PMCID: PMC7663912 DOI: 10.1186/s12870-020-02696-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/12/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. RESULTS Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. CONCLUSION The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.
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Affiliation(s)
- Ting Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zi-Xuan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ling-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang Peng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jun Wen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Barrett CF. Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L. PeerJ 2020; 8:e9315. [PMID: 32587799 PMCID: PMC7304433 DOI: 10.7717/peerj.9315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/17/2020] [Indexed: 12/12/2022] Open
Abstract
Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
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Wang W, Chen S, Guo W, Li Y, Zhang X. Tropical plants evolve faster than their temperate relatives: a case from the bamboos (Poaceae: Bambusoideae) based on chloroplast genome data. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1773312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Wencai Wang
- Molecular Genetics Group, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China
- Molecular Genetics Group, Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China
| | - Siyun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan Province, PR China
| | - Wei Guo
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, PR China
| | - Yongquan Li
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, PR China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, PR China
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