Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> Species
<i>Malus baccata</i> (L.) Borkh. is an important wild species of <i>Malus</i>. Its rich variation types and population history are not well understood. Chloroplast genome mining plays an active role in germplasm identification and genetic evolution. In this study, by assembly...
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MDPI AG
2023-06-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/6/962 |
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| author | Xun Wang Ruifen Zhang Daru Wang Chen Yang Yawen Zhang Mengyi Sui Jian Quan Yi Sun Chunxiang You Xiang Shen |
| author_facet | Xun Wang Ruifen Zhang Daru Wang Chen Yang Yawen Zhang Mengyi Sui Jian Quan Yi Sun Chunxiang You Xiang Shen |
| author_sort | Xun Wang |
| collection | DOAJ |
| description | <i>Malus baccata</i> (L.) Borkh. is an important wild species of <i>Malus</i>. Its rich variation types and population history are not well understood. Chloroplast genome mining plays an active role in germplasm identification and genetic evolution. In this study, by assembly and annotation, six complete cp genome sequences, ranging in size from 160,083 to 160,295 bp, were obtained. The GC content of stable IR regions (42.7%) was significantly higher than that of full length (36.5%) and SC regions (LSC-34.2%, SSC-30.4%). Compared with other <i>Malus</i> species, it was found that there were more sites of polymorphisms and hotspots of variation in LSC and SSC regions, with high variation sites including <i>trnR/UCU</i>-<i>atpA</i>, <i>trnT/UGU</i>-<i>trnL/UAA</i>, <i>ndhF</i>-<i>rpl32</i> and <i>ccsA</i>-<i>ndhD</i>. The intraspecific and interspecific collinearity was good, and no structural rearrangement was observed. A large number of repeating elements and different boundary expansions may be involved in shaping the cp genome size. Up to 77 or 78 coding genes were annotated in the cp genomes of <i>M. baccata</i>, and high frequency codons such as UUA (Leu), GCU (Ala) and AGA (Arg) were identified by relative synonymous codon usage analysis. Phylogeographic analysis showed that 12 individuals of <i>M. baccata</i> clustered into three different groups with complex structure, whereas variant xiaojinensis (M.H. Cheng & N.G. Jiang) was not closely related to <i>M. baccata</i> evolutionarily. The phylogenetic analysis suggested that two main clades of different <i>M. baccata</i> in the genus <i>Malus</i> were formed and that I and II diverged about 9.7 MYA. In conclusion, through cp genome assembly and comparison, the interspecific relationships and molecular variations of <i>M. baccata</i> were further elucidated, and the results of this study provide valuable information for the phylogenetic evolution and germplasm conservation of <i>M. baccata</i> and <i>Malus</i>. |
| first_indexed | 2024-03-11T02:41:31Z |
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| last_indexed | 2024-03-11T02:41:31Z |
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| spelling | doaj.art-209a50111f954bc683e29ff7439c581d2023-11-18T09:31:15ZengMDPI AGBiomolecules2218-273X2023-06-0113696210.3390/biom13060962Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> SpeciesXun Wang0Ruifen Zhang1Daru Wang2Chen Yang3Yawen Zhang4Mengyi Sui5Jian Quan6Yi Sun7Chunxiang You8Xiang Shen9State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, ChinaQingdao Academy of Agricultural Sciences, Qingdao 266100, ChinaState Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, ChinaState Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, ChinaState Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, ChinaState Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, ChinaChina National Botanical Garden, Beijing 100093, ChinaChina National Botanical Garden, Beijing 100093, ChinaState Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, ChinaState Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China<i>Malus baccata</i> (L.) Borkh. is an important wild species of <i>Malus</i>. Its rich variation types and population history are not well understood. Chloroplast genome mining plays an active role in germplasm identification and genetic evolution. In this study, by assembly and annotation, six complete cp genome sequences, ranging in size from 160,083 to 160,295 bp, were obtained. The GC content of stable IR regions (42.7%) was significantly higher than that of full length (36.5%) and SC regions (LSC-34.2%, SSC-30.4%). Compared with other <i>Malus</i> species, it was found that there were more sites of polymorphisms and hotspots of variation in LSC and SSC regions, with high variation sites including <i>trnR/UCU</i>-<i>atpA</i>, <i>trnT/UGU</i>-<i>trnL/UAA</i>, <i>ndhF</i>-<i>rpl32</i> and <i>ccsA</i>-<i>ndhD</i>. The intraspecific and interspecific collinearity was good, and no structural rearrangement was observed. A large number of repeating elements and different boundary expansions may be involved in shaping the cp genome size. Up to 77 or 78 coding genes were annotated in the cp genomes of <i>M. baccata</i>, and high frequency codons such as UUA (Leu), GCU (Ala) and AGA (Arg) were identified by relative synonymous codon usage analysis. Phylogeographic analysis showed that 12 individuals of <i>M. baccata</i> clustered into three different groups with complex structure, whereas variant xiaojinensis (M.H. Cheng & N.G. Jiang) was not closely related to <i>M. baccata</i> evolutionarily. The phylogenetic analysis suggested that two main clades of different <i>M. baccata</i> in the genus <i>Malus</i> were formed and that I and II diverged about 9.7 MYA. In conclusion, through cp genome assembly and comparison, the interspecific relationships and molecular variations of <i>M. baccata</i> were further elucidated, and the results of this study provide valuable information for the phylogenetic evolution and germplasm conservation of <i>M. baccata</i> and <i>Malus</i>.https://www.mdpi.com/2218-273X/13/6/962<i>Malus baccata</i>chloroplast genomesequence similarityvariation and diversityphylogeographiccomparative genomic analysis |
| spellingShingle | Xun Wang Ruifen Zhang Daru Wang Chen Yang Yawen Zhang Mengyi Sui Jian Quan Yi Sun Chunxiang You Xiang Shen Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> Species Biomolecules <i>Malus baccata</i> chloroplast genome sequence similarity variation and diversity phylogeographic comparative genomic analysis |
| title | Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> Species |
| title_full | Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> Species |
| title_fullStr | Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> Species |
| title_full_unstemmed | Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> Species |
| title_short | Molecular Structure and Variation Characteristics of the Plastomes from Six <i>Malus baccata</i> (L.) Borkh. Individuals and Comparative Genomic Analysis with Other <i>Malus</i> Species |
| title_sort | molecular structure and variation characteristics of the plastomes from six i malus baccata i l borkh individuals and comparative genomic analysis with other i malus i species |
| topic | <i>Malus baccata</i> chloroplast genome sequence similarity variation and diversity phylogeographic comparative genomic analysis |
| url | https://www.mdpi.com/2218-273X/13/6/962 |
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