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Dong L, Wang R, Liu H, Xia G, Quan J, Guo L, Chen M. The complete chloroplast genome sequence of Malus × adstringens Zabel 'Hopa' (Rosaceae). Mitochondrial DNA B Resour 2024; 9:173-177. [PMID: 38282982 PMCID: PMC10812852 DOI: 10.1080/23802359.2023.2292158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 12/03/2023] [Indexed: 01/30/2024] Open
Abstract
Malus × adstringens Zabel 'Hopa' is an important crabapple cultivar with significant ornamental value. Here, we assembled its complete chloroplast (cp) genome using the next-generation sequencing technology to clarify the phylogenetic relationships in Malus. The total length of the complete chloroplast genome was 160,230 base pairs (bp) with a GC content of 36.50%, consisting of a large single-copy (LSC) region with a sequence length of 88,310 bp, a small single-copy (SSC) region with a sequence length of 19,196 bp, and a pair of inverted repeat (IR) regions of 26,362 bp. The complete chloroplast genome contained 128 genes, namely 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. In addition, 73 SSRs were found in the M. 'Hopa' cp genome. The phylogenetic relationship of M. 'Hopa' in Malus is closely related to M. spectabilis (Aiton) Borkh. and then to M. sieversii (Lebed.) M. Roem. Our results demonstrate that it is feasible to resolve the phylogenetic relationships of crabapple cultivars and identify their putative maternal lineages using cp genomic data.
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Affiliation(s)
- Leiming Dong
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, China
| | - Ruizhen Wang
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, China
| | - Hengxing Liu
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, China
| | - Guowei Xia
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, China
| | - Jian Quan
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, China
| | - Ling Guo
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, China
| | - Minghui Chen
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, China
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Qin X, Hao Q, Wang X, Liu Y, Yang C, Sui M, Zhang Y, Hu Y, Chen X, Mao Z, Mao Y, Shen X. Complete chloroplast genome of the Malus baccata var. gracilis provides insights into the evolution and phylogeny of Malus species. Funct Integr Genomics 2024; 24:13. [PMID: 38236432 DOI: 10.1007/s10142-024-01291-5] [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: 12/24/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Malus baccata (L.) var. gracilis (Rehd.) has high ornamental value and breeding significance, and comparative chloroplast genome analysis was applied to facilitate genetic breeding for desired traits and resistance and provide insight into the phylogeny of this genus. Using data from whole-genome sequencing, a tetrameric chloroplast genome with a length of 159,992 bp and a total GC content of 36.56% was constructed. The M. baccata var. gracilis chloroplast genome consists of a large single-copy sequence (88,100 bp), a short single-copy region (19,186 bp), and two inverted repeat regions, IRa (26,353 bp) and IRb (26,353 bp). This chloroplast genome contains 112 annotated genes, including 79 protein-coding genes (nine multicopy), 29 tRNA genes (eight multicopy), and four rRNA genes (all multicopy). Calculating the relative synonymous codon usage revealed a total of 32 high-frequency codons, and the codons exhibited a biased usage pattern towards A/U as the ending nucleotide. Interspecific sequence comparison and boundary analysis revealed significant sequence variation in the vast single-copy region, as well as generally similar expansion and contraction of the SSC and IR regions for 10 analyzed Malus species. M. baccata var. gracilis and Malus hupehensis were grouped together into one branch based on phylogenetic analysis of chloroplast genome sequences. The chloroplast genome of Malus species provides an important foundation for species identification, genetic diversity analysis, and Malus chloroplast genetic engineering. Additionally, the results can facilitate the use of pendant traits to improve apple tree shape.
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Affiliation(s)
- Xin Qin
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Qiang Hao
- China National Botanical Garden (North Garden), Beijing, China
| | - Xun Wang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yangbo Liu
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Chen Yang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Mengyi Sui
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yawen Zhang
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yanli Hu
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Xuesen Chen
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yunfei Mao
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
| | - Xiang Shen
- College of Horticulture Science and Engineering, National Apple Engineering and Technology Research Center, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
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Chen X, Cornille A, An N, Xing L, Ma J, Zhao C, Wang Y, Han M, Zhang D. The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties. Mol Ecol 2023; 32:5125-5139. [PMID: 35510734 DOI: 10.1111/mec.16485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/09/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.
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Affiliation(s)
- Xilong Chen
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Na An
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Libo Xing
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Juanjuan Ma
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Caiping Zhao
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Yibin Wang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
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Wang X, Zhang R, Wang D, Yang C, Zhang Y, Sui M, Quan J, Sun Y, You C, Shen X. Molecular Structure and Variation Characteristics of the Plastomes from Six Malus baccata (L.) Borkh. Individuals and Comparative Genomic Analysis with Other Malus Species. Biomolecules 2023; 13:962. [PMID: 37371542 DOI: 10.3390/biom13060962] [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: 05/07/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Malus baccata (L.) Borkh. is an important wild species of Malus. 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 Malus 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 trnR/UCU-atpA, trnT/UGU-trnL/UAA, ndhF-rpl32 and ccsA-ndhD. 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 M. baccata, 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 M. baccata clustered into three different groups with complex structure, whereas variant xiaojinensis (M.H. Cheng & N.G. Jiang) was not closely related to M. baccata evolutionarily. The phylogenetic analysis suggested that two main clades of different M. baccata in the genus Malus 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 M. baccata were further elucidated, and the results of this study provide valuable information for the phylogenetic evolution and germplasm conservation of M. baccata and Malus.
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Affiliation(s)
- Xun Wang
- State 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
| | - Ruifen Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao 266100, China
| | - Daru Wang
- State 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
| | - Chen Yang
- State 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
| | - Yawen Zhang
- State 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
| | - Mengyi Sui
- State 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
| | - Jian Quan
- China National Botanical Garden, Beijing 100093, China
| | - Yi Sun
- China National Botanical Garden, Beijing 100093, China
| | - Chunxiang You
- State 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
| | - Xiang Shen
- State 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
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The Complete Chloroplast Genome Sequence of Laportea bulbifera (Sieb. et Zucc.) Wedd. and Comparative Analysis with Its Congeneric Species. Genes (Basel) 2022; 13:genes13122230. [PMID: 36553498 PMCID: PMC9778553 DOI: 10.3390/genes13122230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Laportea bulbifera (L. bulbifera) is an important medicinal plant of Chinese ethnic minorities, with high economic and medicinal value. However, the medicinal materials of the genus Laportea are prone to be misidentified due to the similar morphological characteristics of the original plants. Thus, it is crucial to discover their molecular marker points and to precisely identify these species for their exploitation and conservation. Here, this study reports detailed information on the complete chloroplast (cp) of L. bulbifera. The result indicates that the cp genome of L. bulbifera of 150,005 bp contains 126 genes, among them, 37 tRNA genes and 81 protein-coding genes. The analysis of repetition demonstrated that palindromic repeats are more frequent. In the meantime, 39 SSRs were also identified, the majority of which were mononucleotides Adenine-Thymine (A-T). Furthermore, we compared L. bulbifera with eight published Laportea plastomes, to explore highly polymorphic molecular markers. The analysis identified four hypervariable regions, including rps16, ycf1, trnC-GCA and trnG-GCC. According to the phylogenetic analysis, L. bulbifera was most closely related to Laportea canadensis (L. canadensis), and the molecular clock analysis speculated that the species originated from 1.8216 Mya. Overall, this study provides a more comprehensive analysis of the evolution of L. bulbifera from the perspective of phylogenetic and intrageneric molecular variation in the genus Laportea, which is useful for providing a scientific basis for further identification, taxonomic, and evolutionary studies of the genus.
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Comparative Analysis on the Codon Usage Pattern of the Chloroplast Genomes in Malus Species. Biochem Genet 2022; 61:1050-1064. [DOI: 10.1007/s10528-022-10302-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
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Zhou D, Mehmood F, Lin P, Cheng T, Wang H, Shi S, Zhang J, Meng J, Zheng K, Poczai P. Characterization of the Evolutionary Pressure on Anisodus tanguticus Maxim. with Complete Chloroplast Genome Sequence. Genes (Basel) 2022; 13:2125. [PMID: 36421800 PMCID: PMC9690199 DOI: 10.3390/genes13112125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 10/15/2023] Open
Abstract
Anisodus tanguticus Maxim. (Solanaceae), a traditional endangered Tibetan herb, is endemic to the Qinghai-Tibet Plateau. Here, we report the de novo assembled chloroplast (cp) genome sequences of A. tanguticus (155,765 bp). The cp contains a pair of inverted repeated (IRa and IRb) regions of 25,881 bp that are separated by a large single copy (LSC) region (86,516 bp) and a small single copy SSC (17,487 bp) region. A total of 132 functional genes were annotated in the cp genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Moreover, 199 simple sequence repeats (SSR) and 65 repeat structures were detected. Comparative plastome analyses revealed a conserved gene order and high similarity of protein-coding sequences. The A. tanguticus cp genome exhibits contraction and expansion, which differs from Przewalskia tangutica and other related Solanaceae species. We identified 30 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which may be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Anisodus and family Solanaceae. Analysis of the Ka/Ks ratios of the Hyoscyameae tribe revealed significant positive selection exerted on the cemA, rpoC2, and clpP genes, which suggests that protein metabolism may be an important strategy for A. tanguticus and other species in Hyoscyameae in adapting to the adverse environment on the Qinghai-Tibetan Plateau. Phylogenetic analysis revealed that A. tanguticus clustered closer with Hyoscyamus niger than P. tangutica. Our results provide reliable genetic information for future exploration of the taxonomy and phylogenetic evolution of the Hyoscyameae tribe and related species.
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Affiliation(s)
- Dangwei Zhou
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Department of Biochemistry, Faculty of Sciences, University of Sialkot, Daska Road, Punjab 51040, Pakistan
| | - Pengcheng Lin
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Tingfeng Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Huan Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Shenbo Shi
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Jinkui Zhang
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Jing Meng
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Kun Zheng
- The College of Pharmacy, Qinghai Nationalities University, Xining 810007, China
| | - Péter Poczai
- Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
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Li Y, Jian Y, Mao Y, Meng F, Shao Z, Wang T, Zheng J, Wang Q, Liu L. "Omics" insights into plastid behavior toward improved carotenoid accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:1001756. [PMID: 36275568 PMCID: PMC9583013 DOI: 10.3389/fpls.2022.1001756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Plastids are a group of diverse organelles with conserved carotenoids synthesizing and sequestering functions in plants. They optimize the carotenoid composition and content in response to developmental transitions and environmental stimuli. In this review, we describe the turbulence and reforming of transcripts, proteins, and metabolic pathways for carotenoid metabolism and storage in various plastid types upon organogenesis and external influences, which have been studied using approaches including genomics, transcriptomics, proteomics, and metabonomics. Meanwhile, the coordination of plastid signaling and carotenoid metabolism including the effects of disturbed carotenoid biosynthesis on plastid morphology and function are also discussed. The "omics" insight extends our understanding of the interaction between plastids and carotenoids and provides significant implications for designing strategies for carotenoid-biofortified crops.
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Affiliation(s)
- Yuanyuan Li
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yue Jian
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yuanyu Mao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Fanliang Meng
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhiyong Shao
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Tonglin Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jirong Zheng
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Lihong Liu
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou, China
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Mao Y, Cui X, Wang H, Qin X, Liu Y, Hu Y, Chen X, Mao Z, Shen X. Study of the grafting compatibility of the apple rootstock 12-2, resistant to apple replant diseases (ARD). BMC PLANT BIOLOGY 2022; 22:468. [PMID: 36180863 PMCID: PMC9524102 DOI: 10.1186/s12870-022-03847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Cultivation of resistant rootstocks can effectively prevent apple replant disease (ARD), and grafting tests are an important means of evaluating the compatibility of rootstocks with scions. METHODS The apple rootstocks 12-2 (self-named) and Malus hupehensis Rehd. (PYTC) were planted in a replanted 20-year-old apple orchard. The two rootstocks were grafted with scions of 13 apple varieties. Multiple aboveground physiological parameters of the grafted combinations were measured and evaluated to verify the grafting affinity of 12-2 with the scions as compared to Malus hupehensis Rehd. (PYTC). RESULTS The graft survival rate and graft interface healing of 12-2 did not differ significantly from those of PYTC. Mechanical strength tests of the grafted interfaces showed that some mechanical strength indices of Redchief, Jonagold, Starking, Goldspur and Yinv apple varieties were significantly higher when they were grafted onto 12-2 compared to the PYTC control. The height and diameter of shoots and the relative chlorophyll content, photosynthetic and fluorescence parameters, antioxidant enzyme activities and malondialdehyde content of leaves showed that Fuji 2001, Tengmu No.1, RedChief, Gala, USA8, and Shoufu1 grew similarly on the two rootstocks, but Tianhong 2, Lvguang, Jonagold, Starking, Goldspur, Yinv and Luli grew better when grafted onto 12-2 than onto the PYTC control. The rootstock 12-2, therefore, showed good grafting affinity. CONCLUSION These results provide experimental materials and theoretical guidance for the cultivation of a new grafting compatible rootstock to the 13 studied apple cultivars.
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Affiliation(s)
- Yunfei Mao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Xueli Cui
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Haiyan Wang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Xin Qin
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yangbo Liu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Yanli Hu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Xuesen Chen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Zhiquan Mao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China
| | - Xiang Shen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, People's Republic of China.
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Identification of the Complete Chloroplast Genome of Malus zhaojiaoensis Jiang and Its Comparison and Evolutionary Analysis with Other Malus Species. Genes (Basel) 2022; 13:genes13040560. [PMID: 35456366 PMCID: PMC9028542 DOI: 10.3390/genes13040560] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/19/2022] [Accepted: 03/19/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Malus is rich in species and many of its plastid genomes have been released. However, limited resources and few markers are not conducive to the comparison of differences among species and resource identification and evaluation. In this study, the complete chloroplast genome of Malus zhaojiaoensis was studied by NGS sequencing, with a total length of 159998 bp. It consists of four regions, LSC (88,070 bp), IRB (26,359 bp), SSC (19,210 bp) and IRA (26,359 bp). M. zhaojiaoensis cp genome contained a total of 111 genes made up of three classes: 78 coding sequences, 29 tRNA genes, and four rRNA genes. In addition, a total of 91 SSRs and 43 INEs were found in the M. zhaojiaoensis cp genome, which was slightly different from M. baccata and M. hupehensis in number. The analysis of codon usage and RNA editing showed that high-frequency codons tended to end at A/U bases and RNA editing mainly occurred at the second codon. Comparative genome analysis suggested that the cp genomes of eight Malus species had higher overall similarity, but there were more variation hotspots (rps16_trnK-UUU, trnG-UCC_atpA, atpH_atpF, trnT-GGU_psbD, etc.) in the LSC region. By building evolutionary trees, it can be clearly observed that M. zhaojiaoensis formed a large group with eight species of Malus, but was relatively independent in differentiation. In conclusion, this study provides high-quality chloroplast genome resources of M. zhaojiaoensis and discusses the genetic variation characteristics of Malus genus. The findings of this study will provide a good reference for plastid genome assembly and interspecific comparison in the future.
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Characterization of the complete chloroplast genome of Zephyranthes phycelloides ( Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile. Saudi J Biol Sci 2022; 29:650-659. [PMID: 35002462 PMCID: PMC8716934 DOI: 10.1016/j.sjbs.2021.10.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Sporadic rains in the Atacama Desert reveal a high biodiversity of plant species that only occur there. One of these rare species is the “Red añañuca” (Zephyranthes phycelloides), formerly known as Rhodophiala phycelloides. Many species of Zephyranthes in the Atacama Desert are dangerously threatened, due to massive extraction of bulbs and cutting of flowers. Therefore, studies of the biodiversity of these endemic species, which are essential for their conservation, should be conducted sooner rather than later. There are some chloroplast genomes available for Amaryllidaceae species, however there is no complete chloroplast genome available for any of the species of Zephyranthes subgenus Myostemma. The aim of the present work was to characterize and analyze the chloroplast of Z. phycelloides by NGS sequencing. The chloroplast genome of the Z. phycelloides consists of 158,107 bp, with typical quadripartite structures: a large single copy (LSC, 86,129 bp), a small single copy (SSC, 18,352 bp), and two inverted repeats (IR, 26,813 bp). One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. The number of SSRs was 64 in Z. phycelloides and a total of 43 repeats were detected. The phylogenetic analysis of Z. phycelloides shows a distinct subclade with respect to Z. mesochloa. The average nucleotide variability (Pi) between Z. phycelloides and Z. mesochloa was of 0.02000, and seven loci with high variability were identified: psbA, trnSGCU-trnGUCC, trnDGUC-trnYGUA, trnLUAA-trnFGAA, rbcL, psbE-petL and ndhG-ndhI. The differences between the species are furthermore confirmed by the high amount of SNPs between these two species. Here, we report for the first time the complete cp genome of one species of the Zephyranthes subgenus Myostemma, which can be used for phylogenetic and population genomic studies.
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Ulaszewski B, Jankowska-Wróblewska S, Świło K, Burczyk J. Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112534. [PMID: 34834899 PMCID: PMC8618278 DOI: 10.3390/plants10112534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Several genera formerly contained within the genus Sorbus L. sensu lato have been proposed as separate taxa, including Aria, Chamaemespilus and Torminalis. However, molecular evidence for such distinctions are rather scarce. We assembled the complete chloroplast genome of Sorbus aucuparia, another representative of Sorbus s.s., and performed detailed comparisons with the available genomes of Aria edulis, Chamaemespilus alpina and Torminalis glaberrima. Additionally, using 110 complete chloroplast genomes of the Maleae representatives, we constructed the phylogenetic tree of the tribe using Maximum Likelihood methods. The chloroplast genome of S. aucuparia was found to be similar to other species within Maleae. The phylogenetic tree of the Maleae tribe indicated that A. edulis, C. alpina and T. glaberrima formed a concise group belonging to a different clade (related to Malus) than the one including Sorbus s.s. (related to Pyrus). However, Aria and Chamaemespilus appeared to be more closely related to each other than to Torminalis. Our results provide additional support for considering Aria, Chamaemespilus and Torminalis as separate genera different from Sorbus s.s.
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Ren Q, Wang YC, Lin Y, Zhen Z, Cui Y, Qin S. The extremely large chloroplast genome of the green alga Haematococcus pluvialis: Genome structure, and comparative analysis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Li XD, Pan H, Lu XJ, Wei XY, Shi M, Lu P. Complete chloroplast genome sequencing of Job's tears ( Coix L.): genome structure, comparative analysis, and phylogenetic relationships. Mitochondrial DNA B Resour 2021; 6:1399-1405. [PMID: 33948493 PMCID: PMC8057079 DOI: 10.1080/23802359.2021.1911704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/25/2021] [Indexed: 12/30/2022] Open
Abstract
Job's tears, also known as adlay, is a valuable plant that has commonly been used in traditional Chinese medicine, as well as an edible food. Due to the lack of knowledge of its genetics and gaps in its evolutionary analysis, breeding of adlay has been hindered. Here, we report five complete chloroplast genomes of various species and varieties in the genus by Illumina sequencing, while their genome structure, comparative analysis, and phylogenetic relationships were conducted. Genome sizes ranged from 140,860 to 140,864 bp in length, GC contents were 38.43%, and genome architecture was of a typical quadripartite structure. We annotated 82~83 protein-coding genes and 46~47 non-coding RNA genes in each genome and they functionally associated with self-replication, photosynthesis, cytochrome synthesis and other unknown functions. Three codons that encoded tryptophan, arginine and leucine were used frequently at rates of 41.42, 37.98, and 32.28% respectively. The preferred codons consistently ended with A or T. A total of 146 simple sequence repeats (SSR), 9 insertions and deletions (InDels) and 143 single nucleotide polymorphisms (SNPs) were observed among genomes. The InDel and SNP variations were mostly distributed in intergenic regions. It confirmed that Coix, Sorghum, Saccharum, Zea, Tripsacum and Saccharum were closely genera and the genetic distance of Sorghum to Coix was closer than Zea to Coix. These results give us more insight into the evolution of Coix in a wide range of evolutionary studies.
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Affiliation(s)
- Xiang-Dong Li
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Hong Pan
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Xiu-Juan Lu
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Xin-Yuan Wei
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Ming Shi
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Zhu B, Qian F, Hou Y, Yang W, Cai M, Wu X. Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PLoS One 2021; 16:e0248556. [PMID: 33711072 PMCID: PMC7954331 DOI: 10.1371/journal.pone.0248556] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/01/2021] [Indexed: 12/05/2022] Open
Abstract
Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.
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Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunfeng Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Weicheng Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xiaoming Wu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Yang J, Chiang YC, Hsu TW, Kim SH, Pak JH, Kim SC. Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan. Sci Rep 2021; 11:1152. [PMID: 33441744 PMCID: PMC7806662 DOI: 10.1038/s41598-020-80143-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Genus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Tsai-Wen Hsu
- Taiwan Endemic Species Research Institute, 1 Mingshen East Road, Chichi Township, Nantou, 55244, Taiwan
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Jae-Hong Pak
- Department of Biology, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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Wu S, Wang Y, Zhang J, Wang Y, Yang Y, Chen X, Wang Y. How does Malus crabapple resist ozone? Transcriptomics and metabolomics analyses. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110832. [PMID: 32563158 DOI: 10.1016/j.ecoenv.2020.110832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Ozone (O3), an oxidizing toxic air pollutant, is ubiquitous in industrialized and developing countries. To understand the effects of O3 exposure on apple (Malus) and to explore its defense mechanisms, we exposed 'Hongjiu' crabapple to O3 and monitored its responses using physiological, transcriptomics, and metabolomics analyses. Exposure to 300 nL L-1 O3 for 3 h caused obvious damage to the leaves of Malus crabapple, affected chlorophyll and anthocyanin contents, and activated antioxidant enzymes. The gene encoding phospholipase A was highly responsive to O3 in Malus crabapple. McWRKY75 is a key transcription factor in the response to O3 stress, and its transcript levels were positively correlated with those of flavonoid-related structural genes (McC4H, McDFR, and McANR). The ethylene response factors McERF019 and McERF109-like were also up-regulated by O3. Exogenous methyl jasmonate (MeJA) decreased the damaging effects of O3 on crabapple and was most effective at 200 μmol L -1. Treatments with MeJA altered the metabolic pathways of crabapple under O3 stress. In particular, MeJA activated the flavonoid metabolic pathway in Malus, which improved its resistance to O3 stress.
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Affiliation(s)
- Shuqing Wu
- College of Forestry, Shandong Agricultural University, Tai-An, 271000, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai-An, 271000, China
| | - Yao Wang
- College of Forestry, Shandong Agricultural University, Tai-An, 271000, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai-An, 271000, China
| | - Junkang Zhang
- College of Forestry, Shandong Agricultural University, Tai-An, 271000, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai-An, 271000, China
| | - Yicheng Wang
- Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271000, China
| | - Yuwei Yang
- College of Forestry, Shandong Agricultural University, Tai-An, 271000, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai-An, 271000, China
| | - Xuesen Chen
- Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271000, China.
| | - Yanling Wang
- College of Forestry, Shandong Agricultural University, Tai-An, 271000, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai-An, 271000, China.
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Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots. PLANTS 2019; 8:plants8110476. [PMID: 31698805 PMCID: PMC6918244 DOI: 10.3390/plants8110476] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/14/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.
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Yang J, Takayama K, Pak JH, Kim SC. Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula. Genes (Basel) 2019; 10:E774. [PMID: 31581648 PMCID: PMC6826710 DOI: 10.3390/genes10100774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 12/03/2022] Open
Abstract
Rubus boninensis is a rare endemic species found on the Bonin Islands with a very restricted distribution. It is morphologically most closely related to Rubus trifidus, occurring widely in the southern Korean peninsula and Japan. This species pair provides a good example of anagenetic speciation on an oceanic island in the northwestern Pacific Ocean-R. trifidus as a continental progenitor and R. boninensis as an insular derivative species. In this study, we firstly characterized the complete plastome of R. boninensis and R. trifidus and compared this species pair to another anagenetically derived species pair (R. takesimensis-R. crataegifolius). The complete plastome of R. trifidus was 155,823 base pairs (bp) long, slightly longer (16 bp) than that of R. boninensis (155,807 bp). No structural or content rearrangements were found between the species pair. Eleven hotspot regions, including trnH/psbA, were identified between R. trifidus and R. boninensis. Phylogenetic analysis of 19 representative plastomes within the family Rosaceae suggested sister relationships between R. trifidus and R. boninensis, and between R. crataegifolius and R. takesimensis. The plastome resources generated by the present study will help elucidate plastome evolution and resolve phylogenetic relationships within highly complex and reticulated lineages of the genus Rubus.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea.
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Jae-Hong Pak
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, Korea.
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20
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Zhao X, Yan M, Ding Y, Chen X, Yuan Z. The complete chloroplast genome of apple rootstock ‘M9’. Mitochondrial DNA B Resour 2019; 4:2187-2188. [PMID: 33365467 PMCID: PMC7687421 DOI: 10.1080/23802359.2019.1624642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The dwarf M9 (Malus domestica ‘M9’) rootstock is the most widely available Malus rootstock, here we report the complete chloroplast (cp) genome of ‘M9’ rootstock. The size of the complete cp genome was 159,926 bp, with the large-copy (LSC, 88,065 bp) regions, small single-copy (SSC, 19,157 bp) regions, and two inverted repeat regions (IRs, 26,352 bp each). It contained 110 genes, including 78 protein-coding genes, 28 transfer RNA genes (tRNA), and 4 ribosomal RNA genes (rRNA). A phylogenetic tree demonstrated that ‘M9’ rootstock was closely related to M. hupehensis, M. baccata, M. prunifolia, M. micromalus, and M. tschonoskii.
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Affiliation(s)
- Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ming Yan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yu Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
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Sathishkumar R, Kumar SR, Hema J, Baskar V. Green Biotechnology: A Brief Update on Plastid Genome Engineering. ADVANCES IN PLANT TRANSGENICS: METHODS AND APPLICATIONS 2019. [PMCID: PMC7120283 DOI: 10.1007/978-981-13-9624-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plant genetic engineering has become an inevitable tool in the molecular breeding of crops. Significant progress has been made in the generation of novel plastid transformation vectors and optimized transformation protocols. There are several advantages of plastid genome engineering over conventional nuclear transformation. Some of the advantages include multigene engineering by expression of biosynthetic pathway genes as operons, extremely high-level expression of protein accumulation, lack of transgene silencing, etc. Transgene containment owing to maternal inheritance is another important advantage of plastid genome engineering. Chloroplast genome modification usually results in alteration of several thousand plastid genome copies in a cell. Several therapeutic proteins, edible vaccines, antimicrobial peptides, and industrially important enzymes have been successfully expressed in chloroplasts so far. Here, we critically recapitulate the latest developments in plastid genome engineering. Latest advancements in plastid genome sequencing are briefed. In addition, advancement of extending the toolbox for plastid engineering for selected applications in the area of molecular farming and production of industrially important enzyme is briefed.
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Affiliation(s)
- Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
| | | | - Jagadeesan Hema
- Department of Biotechnology, PSG College of Technology, Coimbatore, Tamil Nadu India
| | - Venkidasamy Baskar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu India
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