Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata
Abstract Background The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additional...
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2025-01-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06070-3 |
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| author | Ting Wang Huan Feng Huan Zhu Bojian Zhong |
| author_facet | Ting Wang Huan Feng Huan Zhu Bojian Zhong |
| author_sort | Ting Wang |
| collection | DOAJ |
| description | Abstract Background The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additionally, there are currently no reports on the chloroplast genome of Crucigenia. Results In this study, we utilize molecular phylogenetics and comparative genomics to show that C. quadrata belongs to Chlorophyceae rather than Trebouxiophyceae. The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. Our study presents the first complete chloroplast genome of C. quadrata, which is 197,184 bp in length and has a GC content of 31%. It has a typical quadripartite structure, and the chloroplast genome codons exhibit usage bias. Nucleotide diversity analysis highlights six genes (ccsA, psbF, chlN, cemA, rps3, rps18) as hotspots for genetic variation. Coding gene sequence divergence analyses indicate that four genes (cemA, clpP, psaA, rps3) are subject to positive selection. Conclusions The determination of the phylogenetic status and the comparative chloroplast genomic analyses of C. quadrata will not only be useful in enhancing our understanding of the intricacy of Crucigenia taxonomy but also provide the important basis for studying the evolution of the incertae sedis taxa within Trebouxiophyceae. |
| format | Article |
| id | doaj-art-294ce210677d47ffbd6fc9a1b1ce6cbe |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-294ce210677d47ffbd6fc9a1b1ce6cbe2025-01-19T12:16:55ZengBMCBMC Plant Biology1471-22292025-01-0125111310.1186/s12870-025-06070-3Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrataTing Wang0Huan Feng1Huan Zhu2Bojian Zhong3College of Life Sciences, Nanjing Normal UniversityCollege of Life Sciences, Nanjing Normal UniversityInstitute of Hydrobiology, Chinese Academy of SciencesCollege of Life Sciences, Nanjing Normal UniversityAbstract Background The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additionally, there are currently no reports on the chloroplast genome of Crucigenia. Results In this study, we utilize molecular phylogenetics and comparative genomics to show that C. quadrata belongs to Chlorophyceae rather than Trebouxiophyceae. The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. Our study presents the first complete chloroplast genome of C. quadrata, which is 197,184 bp in length and has a GC content of 31%. It has a typical quadripartite structure, and the chloroplast genome codons exhibit usage bias. Nucleotide diversity analysis highlights six genes (ccsA, psbF, chlN, cemA, rps3, rps18) as hotspots for genetic variation. Coding gene sequence divergence analyses indicate that four genes (cemA, clpP, psaA, rps3) are subject to positive selection. Conclusions The determination of the phylogenetic status and the comparative chloroplast genomic analyses of C. quadrata will not only be useful in enhancing our understanding of the intricacy of Crucigenia taxonomy but also provide the important basis for studying the evolution of the incertae sedis taxa within Trebouxiophyceae.https://doi.org/10.1186/s12870-025-06070-3Crucigenia quadrataPhylogenetic analysesPlastid genomeComparative genomics |
| spellingShingle | Ting Wang Huan Feng Huan Zhu Bojian Zhong Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata BMC Plant Biology Crucigenia quadrata Phylogenetic analyses Plastid genome Comparative genomics |
| title | Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata |
| title_full | Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata |
| title_fullStr | Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata |
| title_full_unstemmed | Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata |
| title_short | Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata |
| title_sort | molecular phylogeny and comparative chloroplast genome analysis of the type species crucigenia quadrata |
| topic | Crucigenia quadrata Phylogenetic analyses Plastid genome Comparative genomics |
| url | https://doi.org/10.1186/s12870-025-06070-3 |
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