Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species
Abstract Background The genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four ch...
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2024-11-01
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| author | Li-Fang Li Min Yang Ying Qi Peng-Hua Gao Shao-Wu Yang Yong-Teng Zhao Jian-Wei Guo Huan-Yu Wei Jia-Ni Liu Jian-Rong Zhao Fei-Yan Huang Lei Yu |
| author_facet | Li-Fang Li Min Yang Ying Qi Peng-Hua Gao Shao-Wu Yang Yong-Teng Zhao Jian-Wei Guo Huan-Yu Wei Jia-Ni Liu Jian-Rong Zhao Fei-Yan Huang Lei Yu |
| author_sort | Li-Fang Li |
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| description | Abstract Background The genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four chloroplast genomes of Amorphophallus were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13 Amorphophallus species in conjunction with nine published sequences. Results The Amorphophallus chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 − 98,561 bp), a small single copy (SSC, 14,172 − 21,575 bp), and a pair of inverted repeats (IRs, 26,225 − 35,204 bp). The genomes contain 108 − 113 unique genes, including 76 − 79 protein-coding genes, 28 − 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within Amorphophallus were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including trnM-atpE, atpB, atpB-rbcL and ycf1 were identified. They could identify and phylogeny future species in the genus Amorphophallus. Positive selection was found for rpl36, ccsA, rpl16, rps4, rps8, rps11, rps12, rps14, clpP, rps3, ycf1, rpl20, rps2, rps18, rps19, atpA, atpF, rpl14, rpoA, rpoC1, rpoC2 and rps15 based on the analyses of Ka/Ks ratios. Phylogenetic inferences based on the complete chloroplast genomes revealed a sister relationship between Amorphophallus and Caladieae. All Amorphophallus species formed a monophyletic evolutionary clade and were divided into three groups, including CA-II, SEA, and CA-I. Amorphophallus albus, A. krausei , A. kachinensis and A. konjac were clustered into the CA-II clade, A. paeoniifolius and A. titanum were clustered into the SEA clade, A. muelleri ‘zhuyajin1’, Amorphophallus sp, A. coaetaneus, A. tonkinensis and A. yunnanensis were clustered into CA- I clade. Conclusions The genome structure and gene content of Amorphophallus chloroplast genomes are consistent across various species. In this study, the structural variation and comparative genome of chloroplast genomes of Amorphophallus were comprehensively analyzed for the first time. The results provide important genetic information for species classification, identification, molecular breeding, and evolutionary exploration of the genus Amorphophallus. |
| format | Article |
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| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-e3b65c0960084eeea5554b9c9098ff292025-08-20T02:22:33ZengBMCBMC Genomics1471-21642024-11-0125112010.1186/s12864-024-11053-zChloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus speciesLi-Fang Li0Min Yang1Ying Qi2Peng-Hua Gao3Shao-Wu Yang4Yong-Teng Zhao5Jian-Wei Guo6Huan-Yu Wei7Jia-Ni Liu8Jian-Rong Zhao9Fei-Yan Huang10Lei Yu11Yunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityYunnan Key Laboratory of Konjac Biology, College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming UniversityAbstract Background The genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four chloroplast genomes of Amorphophallus were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13 Amorphophallus species in conjunction with nine published sequences. Results The Amorphophallus chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 − 98,561 bp), a small single copy (SSC, 14,172 − 21,575 bp), and a pair of inverted repeats (IRs, 26,225 − 35,204 bp). The genomes contain 108 − 113 unique genes, including 76 − 79 protein-coding genes, 28 − 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within Amorphophallus were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including trnM-atpE, atpB, atpB-rbcL and ycf1 were identified. They could identify and phylogeny future species in the genus Amorphophallus. Positive selection was found for rpl36, ccsA, rpl16, rps4, rps8, rps11, rps12, rps14, clpP, rps3, ycf1, rpl20, rps2, rps18, rps19, atpA, atpF, rpl14, rpoA, rpoC1, rpoC2 and rps15 based on the analyses of Ka/Ks ratios. Phylogenetic inferences based on the complete chloroplast genomes revealed a sister relationship between Amorphophallus and Caladieae. All Amorphophallus species formed a monophyletic evolutionary clade and were divided into three groups, including CA-II, SEA, and CA-I. Amorphophallus albus, A. krausei , A. kachinensis and A. konjac were clustered into the CA-II clade, A. paeoniifolius and A. titanum were clustered into the SEA clade, A. muelleri ‘zhuyajin1’, Amorphophallus sp, A. coaetaneus, A. tonkinensis and A. yunnanensis were clustered into CA- I clade. Conclusions The genome structure and gene content of Amorphophallus chloroplast genomes are consistent across various species. In this study, the structural variation and comparative genome of chloroplast genomes of Amorphophallus were comprehensively analyzed for the first time. The results provide important genetic information for species classification, identification, molecular breeding, and evolutionary exploration of the genus Amorphophallus.https://doi.org/10.1186/s12864-024-11053-zAmorphophallusChloroplast genomeGenome comparisonPhylogenetic analysis |
| spellingShingle | Li-Fang Li Min Yang Ying Qi Peng-Hua Gao Shao-Wu Yang Yong-Teng Zhao Jian-Wei Guo Huan-Yu Wei Jia-Ni Liu Jian-Rong Zhao Fei-Yan Huang Lei Yu Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species BMC Genomics Amorphophallus Chloroplast genome Genome comparison Phylogenetic analysis |
| title | Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species |
| title_full | Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species |
| title_fullStr | Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species |
| title_full_unstemmed | Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species |
| title_short | Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species |
| title_sort | chloroplast genome of four amorphophallus species genomic features comparative analysis and phylogenetic relationships among amorphophallus species |
| topic | Amorphophallus Chloroplast genome Genome comparison Phylogenetic analysis |
| url | https://doi.org/10.1186/s12864-024-11053-z |
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