Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae
Abstract Background The structure of chloroplast genomes (cpDNAs) in Fabaceae (Fab.) has undergone significant evolutionary modifications. Within the Papilionoideae (Pap.), the emergence of the Inverted Repeat-Lacking Clade (IRLC) represents a major genomic alteration. However, the molecular evoluti...
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2025-02-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06138-0 |
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| author | Qian Qin Yanjing Dong Jialong Chen Bo Wang Yuxin Peng XinPeng Zhang Xiaoyun Wang Jinxiang Zeng Guoyue Zhong Shouwen Zhang Xiaolang Du |
| author_facet | Qian Qin Yanjing Dong Jialong Chen Bo Wang Yuxin Peng XinPeng Zhang Xiaoyun Wang Jinxiang Zeng Guoyue Zhong Shouwen Zhang Xiaolang Du |
| author_sort | Qian Qin |
| collection | DOAJ |
| description | Abstract Background The structure of chloroplast genomes (cpDNAs) in Fabaceae (Fab.) has undergone significant evolutionary modifications. Within the Papilionoideae (Pap.), the emergence of the Inverted Repeat-Lacking Clade (IRLC) represents a major genomic alteration. However, the molecular evolution and phylogenetic relationships within Pap. remain poorly resolved due to limited molecular data and incomplete research, highlighting the need for systematic investigation. Purpose This study presents an in-depth analysis of the cpDNAs within the Pap., with the aim of unraveling the molecular evolution and phylogenetic interconnections among its species. Methods Complete cpDNAs of 18 Pap. species were sequenced using the Illumina Novaseq 6000 platform, followed by assembly and annotation. Comparative genomic analyses were conducted to elucidate structural variations and phylogenetic relationships. Results The research has uncovered significant differences in the structure and characteristics of the cpDNAs within the Pap.. The lengths of the cpDNAs of 18 species range from 121,190 bp to 158,539 bp, and they contain between 107 and 112 unique genes. Five species, namely Desmodium elegans and Indigofera bracteata, exhibit a typical quadripartite structure, while thirteen species from genera such as Astragalus (Ast.), Hedysarum (Hed.), and Caragana (Car.) are grouped within the Inverted Repeat-Lacking Clade (IRLC). Genetic characteristic analysis revealed a plentiful presence of SSR loci, with single-nucleotide repeats and dinucleotide (A/T) repeats being the most predominant. Notably, the cpDNAs of five species including D. elegans have experienced significant rearrangements. For example, an inversion of approximately 23 kilobase (kb) pairs was observed in Pueraria peduncularis and Sophora moorcroftiana. These species exhibit pronounced differences in their non-coding regions. Comparative genomic variations at cpDNA sites were identified. Moreover, by using D. elegans as a reference, six genes (ycf4, clpP, ycf1, trnI-GAU, accD, rpl32) displayed high nucleotide polymorphism (Pi > 0.1), and the Ka/Ks ratio for all protein-coding genes was determined to be less than 1. The topological structure of the constructed phylogenetic tree of 85 species was basically consistent with that of Pap.. Seven main clades were formed and relatively high bootstrap values were exhibited, further clarifying the evolutionary relationships among them. Conclusion This study provides novel insights into the molecular evolution and phylogeny of Pap., offering a foundational resource for future taxonomic and evolutionary research. |
| format | Article |
| id | doaj-art-3f09936a40464a5c92a266105942fa7f |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
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| spelling | doaj-art-3f09936a40464a5c92a266105942fa7f2025-02-09T12:28:02ZengBMCBMC Plant Biology1471-22292025-02-0125112010.1186/s12870-025-06138-0Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of FabaceaeQian Qin0Yanjing Dong1Jialong Chen2Bo Wang3Yuxin Peng4XinPeng Zhang5Xiaoyun Wang6Jinxiang Zeng7Guoyue Zhong8Shouwen Zhang9Xiaolang Du10Chinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineChinese Medicine Resources and Ethnic Medicine Research Center, Jiangxi University of Chinese MedicineAbstract Background The structure of chloroplast genomes (cpDNAs) in Fabaceae (Fab.) has undergone significant evolutionary modifications. Within the Papilionoideae (Pap.), the emergence of the Inverted Repeat-Lacking Clade (IRLC) represents a major genomic alteration. However, the molecular evolution and phylogenetic relationships within Pap. remain poorly resolved due to limited molecular data and incomplete research, highlighting the need for systematic investigation. Purpose This study presents an in-depth analysis of the cpDNAs within the Pap., with the aim of unraveling the molecular evolution and phylogenetic interconnections among its species. Methods Complete cpDNAs of 18 Pap. species were sequenced using the Illumina Novaseq 6000 platform, followed by assembly and annotation. Comparative genomic analyses were conducted to elucidate structural variations and phylogenetic relationships. Results The research has uncovered significant differences in the structure and characteristics of the cpDNAs within the Pap.. The lengths of the cpDNAs of 18 species range from 121,190 bp to 158,539 bp, and they contain between 107 and 112 unique genes. Five species, namely Desmodium elegans and Indigofera bracteata, exhibit a typical quadripartite structure, while thirteen species from genera such as Astragalus (Ast.), Hedysarum (Hed.), and Caragana (Car.) are grouped within the Inverted Repeat-Lacking Clade (IRLC). Genetic characteristic analysis revealed a plentiful presence of SSR loci, with single-nucleotide repeats and dinucleotide (A/T) repeats being the most predominant. Notably, the cpDNAs of five species including D. elegans have experienced significant rearrangements. For example, an inversion of approximately 23 kilobase (kb) pairs was observed in Pueraria peduncularis and Sophora moorcroftiana. These species exhibit pronounced differences in their non-coding regions. Comparative genomic variations at cpDNA sites were identified. Moreover, by using D. elegans as a reference, six genes (ycf4, clpP, ycf1, trnI-GAU, accD, rpl32) displayed high nucleotide polymorphism (Pi > 0.1), and the Ka/Ks ratio for all protein-coding genes was determined to be less than 1. The topological structure of the constructed phylogenetic tree of 85 species was basically consistent with that of Pap.. Seven main clades were formed and relatively high bootstrap values were exhibited, further clarifying the evolutionary relationships among them. Conclusion This study provides novel insights into the molecular evolution and phylogeny of Pap., offering a foundational resource for future taxonomic and evolutionary research.https://doi.org/10.1186/s12870-025-06138-0FabaceaePapilionoideaeChloroplast GenomeMolecular EvolutionPhylogenetic Analysis |
| spellingShingle | Qian Qin Yanjing Dong Jialong Chen Bo Wang Yuxin Peng XinPeng Zhang Xiaoyun Wang Jinxiang Zeng Guoyue Zhong Shouwen Zhang Xiaolang Du Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae BMC Plant Biology Fabaceae Papilionoideae Chloroplast Genome Molecular Evolution Phylogenetic Analysis |
| title | Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae |
| title_full | Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae |
| title_fullStr | Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae |
| title_full_unstemmed | Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae |
| title_short | Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae |
| title_sort | comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the papilionoideae of fabaceae |
| topic | Fabaceae Papilionoideae Chloroplast Genome Molecular Evolution Phylogenetic Analysis |
| url | https://doi.org/10.1186/s12870-025-06138-0 |
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