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Xie P, Wu J, Lu M, Tian T, Wang D, Luo Z, Yang D, Li L, Yang X, Liu D, Cheng H, Tan J, Yang H, Zhu D. Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant. BMC Genomics 2024; 25:773. [PMID: 39118028 PMCID: PMC11312713 DOI: 10.1186/s12864-024-10680-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported. RESULTS The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense. CONCLUSIONS In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.
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Affiliation(s)
- Ping Xie
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Jingru Wu
- Affiliated Stomatological Hospital, Jiamusi University, Jiamusi, 154002, Heilongjiang, China
| | - Mengyue Lu
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Tongxin Tian
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Dongmei Wang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Zhiwen Luo
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Donghong Yang
- Affiliated Stomatological Hospital, Jiamusi University, Jiamusi, 154002, Heilongjiang, China
| | - Lili Li
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Xuewen Yang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Decai Liu
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Haitao Cheng
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Jiaxin Tan
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China
| | - Hongsheng Yang
- College of Biology and Agriculture, Jiamusi University, Jiamusi, 154007, Heilongjiang, China.
| | - Dequan Zhu
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang, 550025, Guizhou, China.
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Xu L, Wang J, Zhang T, Xiao H, Wang H. Characterizing complete mitochondrial genome of Aquilegia amurensis and its evolutionary implications. BMC PLANT BIOLOGY 2024; 24:142. [PMID: 38413922 PMCID: PMC10900605 DOI: 10.1186/s12870-024-04844-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution. RESULTS The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736 bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes. CONCLUSIONS In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia.
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Affiliation(s)
- Luyuan Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jinghan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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Yang J, Zhang X, Hua Z, Jia H, Li K, Ling C. High-Quality Assembly and Analysis of the Complete Mitogenomes of German Chamomile ( Matricaria recutita) and Roman Chamomile ( Chamaemelum nobile). Genes (Basel) 2024; 15:301. [PMID: 38540360 PMCID: PMC10970603 DOI: 10.3390/genes15030301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 06/14/2024] Open
Abstract
German chamomile (Matricaria chamomilla L.) and Roman chamomile (Chamaemelum nobile) are the two well-known chamomile species from the Asteraceae family. Owing to their essential oils and higher medicinal value, these have been cultivated widely across Europe, Northwest Asia, North America, and Africa. Regarding medicinal applications, German chamomile is the most commonly utilized variety and is frequently recognized as the "star among medicinal species". The insufficient availability of genomic resources may negatively impact the progression of chamomile industrialization. Chamomile's mitochondrial genome is lacking in extensive empirical research. In this study, we achieved the successful sequencing and assembly of the complete mitochondrial genome of M. chamomilla and C. nobile for the first time. An analysis was conducted on codon usage, sequence repeats within the mitochondrial genome of M. chamomilla and C. nobile. The phylogenetic analysis revealed a consistent positioning of M. chamomilla and C. nobile branches within both mitochondrial and plastid-sequence-based phylogenetic trees. Furthermore, the phylogenetic analysis also showed a close relationship between M. chamomilla and C. nobile within the clade comprising species from the Asteraceae family. The results of our analyses provide valuable resources for evolutionary research and molecular barcoding in chamomile.
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Affiliation(s)
- Jun Yang
- College of Food and Bioengineering, Bengbu University, Bengbu 233030, China; (X.Z.); (Z.H.); (H.J.); (K.L.); (C.L.)
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Yu X, Feng Y, Zhang J. Characterization of the Complete Mitochondrial Genome of Wintersweet ( Chimonanthus praecox) and Comparative Analysis within Magnoliids. Life (Basel) 2024; 14:182. [PMID: 38398691 PMCID: PMC10890521 DOI: 10.3390/life14020182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as "La Mei" in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (-0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T's and G's in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution.
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Affiliation(s)
- Xianxian Yu
- College of Urban and Environmental Sciences, Xuchang University, Xuchang 461000, China;
| | - Yanlei Feng
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China;
| | - Jie Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
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Zhou P, Zhang Q, Li F, Huang J, Zhang M. Assembly and comparative analysis of the complete mitochondrial genome of Ilex metabaptista (Aquifoliaceae), a Chinese endemic species with a narrow distribution. BMC PLANT BIOLOGY 2023; 23:393. [PMID: 37580695 PMCID: PMC10424370 DOI: 10.1186/s12870-023-04377-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/12/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Ilex metabaptista is a woody tree species with strong waterlogging tolerance and is also admired as a landscape plant with high development prospects and scientific research value. Unfortunately, populations of this species have declined due to habitat loss. Thus, it is a great challenge for us to efficiently protect I. metabaptista resources from extinction. Molecular biology research can provide the scientific basis for the conservation of species. However, the study of I. metabaptista genetics is still in its infancy. To date, no mitochondrial genome (mitogenome) in the genus Ilex has been analysed in detail. RESULTS The mitogenome of I. metabaptista was assembled based on the reads from Illumina and Nanopore sequencing platforms; it was a typical circular DNA molecule of 529,560 bp with a GC content of 45.61% and contained 67 genes, including 42 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 286 dispersed repeats, 140 simple repeats, 18 tandem repeats, and 543 RNA editing sites. Analysis of codon usage showed that codons ending in A/T were preferred. Gene migration was observed to occur between the mitogenome and chloroplast genome via the detection of homologous fragments. In addition, Ka/Ks analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB gene had undergone potential positive selection in most asterids. Nucleotide polymorphism analysis revealed the variation in each gene, with atp9 being the most notable. Furthermore, comparative analysis showed that the GC contents were conserved, but the sizes and structure of mitogenomes varied greatly among asterids. Phylogenetic analysis based on the mitogenomes reflected the exact evolutionary and taxonomic status of I. metabaptista. CONCLUSION In this study, we sequenced and annotated the mitogenome of I. metabaptista and compared it with the mitogenomes of other asterids, which provided essential background information for further understanding of the genetics of this plant and helped lay the foundation for future studies on molecular breeding of I. metabaptista.
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Affiliation(s)
- Peng Zhou
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Qiang Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 210037, Nanjing, China.
| | - Fei Li
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Jing Huang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Min Zhang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China.
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Gao C, Li T, Zhao X, Wu C, Zhang Q, Zhao X, Wu M, Lian Y, Li Z. Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis. BMC PLANT BIOLOGY 2023; 23:318. [PMID: 37316771 DOI: 10.1186/s12870-023-04338-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND The genus Rosa (Rosaceae) contains approximately 200 species, most of which have high ecological and economic values. Chloroplast genome sequences are important for studying species differentiation, phylogeny, and RNA editing. RESULTS In this study, the chloroplast genomes of three Rosa species, Rosa hybrida, Rosa acicularis, and Rosa rubiginosa, were assembled and compared with other reported Rosa chloroplast genomes. To investigate the RNA editing sites in R. hybrida (commercial rose cultivar), we mapped RNA-sequencing data to the chloroplast genome and analyzed their post-transcriptional features. Rosa chloroplast genomes presented a quadripartite structure and had highly conserved gene order and gene content. We identified four mutation hotspots (ycf3-trnS, trnT-trnL, psbE-petL, and ycf1) as candidate molecular markers for differentiation in the Rosa species. Additionally, 22 chloroplast genomic fragments with a total length of 6,192 bp and > 90% sequence similarity with their counterparts were identified in the mitochondrial genome, representing 3.96% of the chloroplast genome. Phylogenetic analysis including all sections and all subgenera revealed that the earliest divergence in the chloroplast phylogeny roughly distinguished species of sections Pimpinellifoliae and Rosa and subgenera Hulthemia. Moreover, DNA- and RNA-sequencing data revealed 19 RNA editing sites, including three synonymous and 16 nonsynonymous, in the chloroplast genome of R. hybrida that were distributed among 13 genes. CONCLUSIONS The genome structure and gene content of Rosa chloroplast genomes are similar across various species. Phylogenetic analysis based on the Rosa chloroplast genomes has high resolution. Additionally, a total of 19 RNA editing sites were validated by RNA-Seq mapping in R. hybrida. The results provide valuable information for RNA editing and evolutionary studies of Rosa and a basis for further studies on genomic breeding of Rosa species.
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Affiliation(s)
- Chengwen Gao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China.
| | - Teng Li
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
- School of Public Health, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Xia Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Chuanhong Wu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Qian Zhang
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Xiangzhong Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Mingxuan Wu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Yihong Lian
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China
| | - Zhiqiang Li
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shangdong, China.
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Characterization and Phylogenetic Analyses of the Complete Mitochondrial Genome of Sugarcane (Saccharum spp. Hybrids) Line A1. DIVERSITY 2022. [DOI: 10.3390/d14050333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Modern sugarcane cultivars are highly polyploid with complex nuclear genomic genetic background, while their mitochondrion (mt) genomes are much simpler, smaller and more manageable and could provide useful phylogenetic information. In this study, the mt genome of a modern commercial cultivar A1 was sequenced via Illumina Hiseq XTen and PacBio Sequel platform. The assembled and annotated mitochondrial genomes of A1 were composed of two circular DNA molecules, one large and one small, which were named Chromosome 1 and Chromosome 2. The two distinct circular chromosomes of mitogenome construct is consisted with other sugarcane cultivars i.e., Saccharum officinarum Khon Kaen 3 and Saccharum spp. hybrids ROC22 and FN15. The Chromosome 1 of A1 mitogenome is 300,822 bp in length with the GC content of 43.94%, and 7.14% of Chromosome 1 sequences (21,468 nucleotides) are protein coding genes (PCGs) while 92.86% (279,354 nucleotides) are intergenic region. The length of Chromosome 2 is 144,744 bp with the GC content of 43.57%, and 8.20% of Chromosome 2 sequences (11,865 nucleotides) are PCGs while 91.80% (132,879 nucleotides) are intergenic region. A total of 43 genes are located on Chromosome 1, which contains 22 PCGs (six nad genes, four rps genes, four atp genes, three ccm genes, three cox genes, one mat gene and one mtt gene) and 21 non-coding genes including 15 tRNAs and 6 rRNAs. Chromosome 2 includes 18 genes in total, which contains 13 PCGs (four nad genes, three rps genes, two atp genes, one ccm gene, one cob gene, one cox gene and one rpl gene) and five non-coding genes (tRNA genes). Analysis of codon usage of 35 PCGs showed that codon ending in A/U was preferred. Investigation of gene composition indicated that the types and copy numbers of CDS genes, tRNAs and rRNAs of A1 and FN15 were identical. The cox1 gene has two copies and the trnP gene has one copy in A1, FN15 and ROC22 three lines, while there is only one copy of cox1 and two copies of trnP in S. officinarum Khon Kaen 3. In addition, S. officinarum Khon Kaen 3 have no nad1 gene and rps7 gene. 100 sequence repeats, 38 SSRs and 444 RNA editing sites in A1 mt genome were detected. Moreover, the maximum likelihood phylogenetic analysis found that A1 were more closely related to S. spp. hybrid (ROC22 and FN15) and S. officinarum (Khon Kaen 3). Herein, the complete mt genome of A1 will provide essential DNA molecular information for further phylogenetic and evolutionary analysis for Saccharum and Poaceae.
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Niu Y, Gao C, Liu J. Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes. BMC Genomics 2022; 23:147. [PMID: 35183120 PMCID: PMC8857841 DOI: 10.1186/s12864-022-08383-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/11/2022] [Indexed: 01/30/2023] Open
Abstract
Abstract
Background
Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species.
Results
Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63–69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24–27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7–10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407 to 6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value.
Conclusions
We sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.
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Lin Y, Li P, Zhang Y, Akhter D, Pan R, Fu Z, Huang M, Li X, Feng Y. Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes. BMC Biol 2022; 20:49. [PMID: 35172831 PMCID: PMC8851834 DOI: 10.1186/s12915-022-01250-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 02/08/2022] [Indexed: 01/01/2023] Open
Abstract
Background The morning glories (Convolvulaceae) are distributed worldwide and produce economically important crops, medicinal herbs, and ornamentals. Members of this family are diverse in morphological characteristics and trophic modes, including the leafless parasitic Cuscuta (dodders). Organelle genomes were generally used for studying plant phylogeny and genomic variations. Notably, plastomes in parasitic plants always show non-canonical features, such as reduced size and accelerated rates. However, few organelle genomes of this group have been sequenced, hindering our understanding of their evolution, and dodder mitogenome in particular. Results We assembled 22 new mitogenomes and 12 new plastomes in Convolvulaceae. Alongside previously known ones, we totally analyzed organelle genomes of 23 species in the family. Our sampling includes 16 leafy autotrophic species and 7 leafless parasitic dodders, covering 8 of the 12 tribes. Both the plastid and mitochondrial genomes of these plants have encountered variations that were rarely observed in other angiosperms. All of the plastomes possessed atypical IR boundaries. Besides the gene and IR losses in dodders, some leafy species also showed gene and intron losses, duplications, structural variations, and insertions of foreign DNAs. The phylogeny reconstructed by plastid protein coding sequences confirmed the previous relationship of the tribes. However, the monophyly of ‘Merremieae’ and the sister group of Cuscuta remained uncertain. The mitogenome was significantly inflated in Cuscuta japonica, which has exceeded over 800 kb and integrated massive DNAs from other species. In other dodders, mitogenomes were maintained in small size, revealing divergent evolutionary strategies. Mutations unique to plants were detected in the mitochondrial gene ccmFc, which has broken into three fragments through gene fission and splicing shift. The unusual changes likely initially happened to the common ancestor of the family and were caused by a foreign insertion from rosids followed by double-strand breaks and imprecise DNA repairs. The coding regions of ccmFc expanded at both sides after the fission, which may have altered the protein structure. Conclusions Our family-scale analyses uncovered unusual scenarios for both organelle genomes in Convolvulaceae, especially in parasitic plants. The data provided valuable genetic resources for studying the evolution of Convolvulaceae and plant parasitism. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01250-1.
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Affiliation(s)
- Yanxiang Lin
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
| | - Pan Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yuchan Zhang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Delara Akhter
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet Division 3100, Sylhet, Bangladesh
| | - Ronghui Pan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Zhixi Fu
- College of Life Science, Sichuan Normal University, Chengdu, 610101, Sichuan, China
| | - Mingqing Huang
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian, China
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang, China
| | - Yanlei Feng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China. .,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang, China.
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