1
|
Alzahrani DA, Abba A, Yaradua SS, Albokhari EJ. An insight on the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina, Asclepiadoideae (Apocynaceae). BRAZ J BIOL 2024; 84:e257145. [DOI: 10.1590/1519-6984.257145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 07/20/2022] [Indexed: 12/23/2022] Open
Abstract
Abstract We studied the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina from Asclepiadoideae subfamily; due to their medicinal importance and distribution worldwide their interest became high. In this study we analyzed the complete chloroplast genomes of G. siniacus and D. velutina using Illumina sequencing technology. The sequences were compared with the other species from Apocynaceae family. The complete genome of G. siniacus is 162,570 bp while D. velutina has154, 478 bp in length. Both genomes consist of 119 genes; encode 31 tRNA genes, and eight rRNA genes. Comparative studies of the two genomes showed variations in SSR markers in which G. siniacus possesses 223 while D. velutina has 186. This could be used for barcoding in order to aid in easy identification of the species. Phylogenetic analysis on the other hand reaffirms the tribal position of G. siniacus in Asclepiadeae and D. velutina in Ceropegieae. These findings could be used in subsequent research studies of angiosperms identification, genetic engineering, herb genomics and phylogenomic studies of Apocynaceae family.
Collapse
Affiliation(s)
| | - A. Abba
- King Abdulaziz University, Saudi Arabia; Federal University Lokoja, Nigeria
| | - S. S. Yaradua
- King Abdulaziz University, Saudi Arabia; Umaru Musa Yaradua University, Nigeria
| | - E. J. Albokhari
- King Abdulaziz University, Saudi Arabia; Umm Al-Qura University, Saudi Arabia
| |
Collapse
|
2
|
Chen Z, Liu Q, Xiao Y, Zhou G, Yu P, Bai J, Huang H, Gong Y. Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships. J Appl Genet 2023; 64:419-429. [PMID: 37380816 DOI: 10.1007/s13353-023-00767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar 'Zhuyeqi', followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of 'Zhuyeqi' was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of 'Zhuyeqi' were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of 'Zhuyeqi' were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to 'Zhuyeqi', indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.
Collapse
Affiliation(s)
- Zhiyin Chen
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Qing Liu
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Ying Xiao
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Guihua Zhou
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Penghui Yu
- Tea Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jing Bai
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Hua Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, People's Republic of China.
| | - Yihui Gong
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China.
| |
Collapse
|
3
|
Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
Collapse
Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| |
Collapse
|
4
|
Waswa EN, Mkala EM, Odago WO, Amenu SG, Mutinda ES, Muthui SW, Ding SX, Hu GW, Wang QF. Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume. Front Plant Sci 2023; 14:1179510. [PMID: 37396648 PMCID: PMC10313135 DOI: 10.3389/fpls.2023.1179510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.
Collapse
Affiliation(s)
- Emmanuel Nyongesa Waswa
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Elijah Mbandi Mkala
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Wyclif Ochieng Odago
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Sara Getachew Amenu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Elizabeth Syowai Mutinda
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Samuel Wamburu Muthui
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Xiong Ding
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
5
|
Waswa EN, Mkala EM, Odago WO, Amenu SG, Mutinda ES, Muthui SW, Ding SX, Hu GW, Wang QF. Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume. Front Plant Sci 2023; 14. [DOI: https:/doi.org/10.3389/fpls.2023.1179510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.
Collapse
|
6
|
Zhang X, Gu C, Zhang T, Tong B, Zhang H, Wu Y, Yang C. Chloroplast (Cp) Transcriptome of P. davidiana Dode×P. bolleana Lauch provides insight into the Cp drought response and Populus Cp phylogeny. BMC Evol Biol 2020; 20:51. [PMID: 32375634 PMCID: PMC7201580 DOI: 10.1186/s12862-020-01622-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023] Open
Abstract
Background Raw second-generation (2G) lignocellulosic biomass materials have the potential for development into a sustainable and renewable source of energy. Poplar is regarded as a promising 2G material (P. davidiana Dode×P. bolleana Lauch, P. bolleana, P. davidiana, P. euphratica, et al). However, their large-scale commercialization still faces many obstacles. For example, drought prevents sufficient irrigation or rainfall, which can reduce soil moisture and eventually destroy the chloroplast, the plant photosynthetic organelle. Heterosis is widely used in the production of drought-tolerant materials, such as the superior clone “Shanxinyang” selected from the offspring of Populus davidiana Dode×Populus bolleana Lauch. Because it produces good wood and is easily genetically transformed, “Shanxinyang” has become a promising material for use in tree genetics. It is also one of the most abundant biofuel plants in northern China. Understanding the genetic features of chloroplasts, the cp transcriptome and physiology is crucial to elucidating the chloroplast drought-response model. Results In this study, the whole genome of “Shanxinyang” was sequenced. The chloroplast genome was assembled, and chloroplast structure was analysed and compared with that of other popular plants. Chloroplast transcriptome analysis was performed under drought conditions. The total length of the “Shanxinyang” chloroplast genome was 156,190 bp, the GC content was 36.75%, and the genome was composed of four typical areas (LSC, IRa, IRb, and SSC). A total of 114 simple repeats were detected in the chloroplast genome of “Shanxinyang”. In cp transcriptome analysis, we found 161 up-regulated and 157 down-regulated genes under drought, and 9 cpDEGs was randomly selected to conduct reverse transcription (RT)–qPCR., in which the Log2 (fold change) was significantly consistent with the qPCR results. The analysis of chloroplast transcription under drought provided clues for understanding chloroplast function under drought. The phylogenetic position of “Shanxinyang” within Populus was analysed by using the chloroplast genome sequences of 23 Populus plants, showing that “Shanxinyang” belongs to Sect. Populus and is sister to Populus davidiana. Further, mVISTA analysis showed that the variation in non-coding (regulatory) regions was greater than that in coding regions, which suggests that further attention should be paid to the chloroplast in order to obtain new evolutionary or functional insights related to aspects of plant biology. Conclusions Our findings indicate that complex prokaryotic genome regulation occurs when processing transcripts under drought stress. The results not only offer clues for understanding the chloroplast genome and transcription features in woody plants but also serve as a basis for future molecular studies on poplar species.
Collapse
Affiliation(s)
- Xin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.,School of Forestry, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 10866, China
| | - Chenrui Gu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Tianxu Zhang
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Heng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yueliang Wu
- School of Forestry, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 10866, China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| |
Collapse
|
7
|
Magdy M, Ouyang B. The complete mitochondrial genome of the chiltepin pepper ( Capsicum annuum var. glabriusculum), the wild progenitor of Capsicum annuum L. Mitochondrial DNA B Resour 2020; 5:683-684. [PMID: 33366702 PMCID: PMC7748824 DOI: 10.1080/23802359.2020.1714496] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The complete mitochondrial genome of chiltepin pepper (Capsicum annuum var glabriusculum) was sequenced. The mitogenome of the American bird pepper was 505,190 bp, with 44.4% of GC content. A total of 218 genes were fully annotated, including 190 CDS (31 known genes and 158 open reading frames), three rRNA, and 25 tRNA genes. The gene synteny and number were equal to those of C. annuum var annuum, except for the partial annotation of ATP subunit 6 and the absence of ORF172 and ORF104b. The complete mt genome sequence was deposited to the GenBank (NCBI, Accession number: MN196478).
Collapse
Affiliation(s)
- Mahmoud Magdy
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.,Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
8
|
Cui Y, Zhou J, Chen X, Xu Z, Wang Y, Sun W, Song J, Yao H. Complete chloroplast genome and comparative analysis of three Lycium (Solanaceae) species with medicinal and edible properties. Gene Reports 2019. [DOI: 10.1016/j.genrep.2019.100464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
9
|
Magdy M, Ou L, Yu H, Chen R, Zhou Y, Hassan H, Feng B, Taitano N, van der Knaap E, Zou X, Li F, Ouyang B. Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species. Hortic Res 2019; 6:108. [PMID: 31645963 PMCID: PMC6804749 DOI: 10.1038/s41438-019-0191-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/19/2019] [Accepted: 08/03/2019] [Indexed: 05/19/2023]
Abstract
Pepper species (Capsicum spp.) are widely used as food, spice, decoration, and medicine. Despite the recent old-world culinary impact, more than 50 commercially recognized pod types have been recorded worldwide from three taxonomic complexes (A, B, and P). The current study aimed to apply a pan-plastome approach to resolve the plastomic boundaries among those complexes and identify effective loci for the taxonomical resolution and molecular identification of the studied species/varieties. High-resolution pan-plastomes of five species and two varieties were assembled and compared from 321 accessions. Phyloplastomic and network analyses clarified the taxonomic position of the studied species/varieties and revealed a pronounced number of accessions to be the rare and endemic species, C. galapagoense, that were mistakenly labeled as C. annuum var. glabriusculum among others. Similarly, some NCBI-deposited plastomes were clustered differently from their labels. The rpl23-trnI intergenic spacer contained a 44 bp tandem repeat that, in addition to other InDels, was capable of discriminating the investigated Capsicum species/varieties. The rps16-trnQ/rbcL-accD/ycf3-trnS gene set was determined to be sufficiently polymorphic to retrieve the complete phyloplastomic signal among the studied Capsicum spp. The pan-plastome approach was shown to be useful in resolving the taxonomical complexes, settling the incomplete lineage sorting conflict and developing a molecular marker set for Capsicum spp. identification.
Collapse
Affiliation(s)
- Mahmoud Magdy
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241 Egypt
| | - Lijun Ou
- College of Horticulture and Landscape, Hunan Agricultural University, 410128 Changsha, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Rong Chen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Heba Hassan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Bihong Feng
- College of Agriculture, Guangxi University, 530004 Nanning, China
| | - Nathan Taitano
- Department of Horticulture, College of Agriculture & Environmental Sciences, University of Georgia, Athens, GA 30602 USA
| | - Esther van der Knaap
- Department of Horticulture, College of Agriculture & Environmental Sciences, University of Georgia, Athens, GA 30602 USA
| | - Xuexiao Zou
- College of Horticulture and Landscape, Hunan Agricultural University, 410128 Changsha, China
| | - Feng Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| |
Collapse
|
10
|
Zhong Q, Yang S, Sun X, Wang L, Li Y. The complete chloroplast genome of the Jerusalem artichoke ( Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene. PeerJ 2019; 7:e7596. [PMID: 31531272 PMCID: PMC6718157 DOI: 10.7717/peerj.7596] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/31/2019] [Indexed: 12/20/2022] Open
Abstract
Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China, and it has become an emerging economic crop that is rapidly developing. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (83,981 bp), and a small single-copy region (18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. A total of 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased toward A/T bases. A total of 32 SSRs were distributed in the non-coding regions. A comparative analysis of the chloroplast genome sequence of the Jerusalem artichoke and other species of the composite family revealed that the chloroplast genome sequences of plants of the composite family were highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. A phylogenetic analysis showed that H. petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.
Collapse
Affiliation(s)
- Qiwen Zhong
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Xining, Qinghai, China.,Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Shipeng Yang
- Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Xuemei Sun
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Xining, Qinghai, China.,Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Lihui Wang
- Agriculture and Forestry Sciences of Qinghai University, Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, Qinghai, China.,Qinghai University, The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Xining, Qinghai, China
| | - Yi Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Xining, Qinghai, China
| |
Collapse
|
11
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
12
|
D'Agostino N, Tamburino R, Cantarella C, De Carluccio V, Sannino L, Cozzolino S, Cardi T, Scotti N. The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution. Genes (Basel) 2018; 9:E503. [PMID: 30336638 PMCID: PMC6210379 DOI: 10.3390/genes9100503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 11/16/2022] Open
Abstract
Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes.
Collapse
Affiliation(s)
- Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Valentina De Carluccio
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy.
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy.
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy.
| |
Collapse
|
13
|
Meng XX, Xian YF, Xiang L, Zhang D, Shi YH, Wu ML, Dong GQ, Ip SP, Lin ZX, Wu L, Sun W. Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species. Molecules 2018; 23:E2137. [PMID: 30149578 PMCID: PMC6225366 DOI: 10.3390/molecules23092137] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/20/2018] [Accepted: 08/23/2018] [Indexed: 11/25/2022] Open
Abstract
The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405⁻85,557 bp), small single-copy regions (SSC; 18,550⁻18,768 bp), and a pair of inverted repeats (IRs; 25,576⁻25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39⁻53 long repeats and 79⁻91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.
Collapse
Affiliation(s)
- Xiang-Xiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yan-Fang Xian
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin 999077, N.T., Hong Kong, China.
| | - Li Xiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Dong Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yu-Hua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Ming-Li Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Gang-Qiang Dong
- Amway (China) Botanical Research and Development Center, Wuxi 214145, China.
| | - Siu-Po Ip
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin 999077, N.T., Hong Kong, China.
| | - Zhi-Xiu Lin
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin 999077, N.T., Hong Kong, China.
| | - Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin 999077, N.T., Hong Kong, China.
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| |
Collapse
|
14
|
Zhou J, Cui Y, Chen X, Li Y, Xu Z, Duan B, Li Y, Song J, Yao H. Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis. Molecules 2018; 23:E437. [PMID: 29462921 PMCID: PMC6017017 DOI: 10.3390/molecules23020437] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 11/17/2022] Open
Abstract
Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three Papaver species. These differences include the ycf1 gene and intergenic regions, such as rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, and ccsA-ndhD. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of Papaver species and will benefit further investigations of these species.
Collapse
Affiliation(s)
- Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Xinlian Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Yonghua Li
- Department of Pharmacy, Guangxi Traditional Chinese Medicine University, Nanning 530200, China.
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| |
Collapse
|
15
|
Song Y, Wang S, Ding Y, Xu J, Li MF, Zhu S, Chen N. Chloroplast Genomic Resource of Paris for Species Discrimination. Sci Rep 2017; 7:3427. [PMID: 28611359 DOI: 10.1038/s41598-017-02083-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/06/2017] [Indexed: 01/23/2023] Open
Abstract
Paris is famous in China for its medicinal value and has been included in the Chinese Pharmacopoeia. Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Due to the plasticity of the morphological characteristics, correct identification among Paris species remains problematic. In this regard, we report the complete chloroplast genome of P. thibetica and P. rugosa to develop highly variable molecular markers. Comparing three chloroplast genomes, we sought out the most variable regions to develop the best cpDNA barcodes for Paris. The size of Paris chloroplast genome ranged from 162,708 to 163,200 bp. A total of 134 genes comprising 81 protein coding genes, 45 tRNA genes and 8 rRNA genes were observed in all three chloroplast genomes. Eight rapidly evolving regions were detected, as well as the difference of simple sequence repeats (SSR) and repeat sequence. Two regions of the coding gene ycf1, ycf1a and ycf1b, evolved the quickest and were proposed as core barcodes for Paris. The complete chloroplast genome sequences provide more integrated and adequate information for better understanding the phylogenetic pattern and improving efficient discrimination during species identification.
Collapse
|
16
|
Abstract
Eggplant Solanum melongena L. is one of the most economically important vegetable crops. Here, we report the complete chloroplast (cp) genome of eggplant. The cp genome size was 154,289 bp that contained a pair of IR regions of 25,566 bp, one large single-copy (LSC) of 84,749 bp and a small single-copy (SSC) of 18,408bp, respectively. It encoded 125 predicted unique functional genes, including 84 tRNA genes, 85 protein-coding genes and 8 rRNA genes. The GC content was 37.86%. Phylogenetic analysis clearly showed a close evolutionary relationship between S. melongena and other species in the genus Solanum. The complete chloroplast genome of S. melongena provides valuable data for genetic improvement and allele mining of eggplant germplasm.
Collapse
Affiliation(s)
- Qing-Xia Ding
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jia Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li-Zhi Gao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Plant Germplasm and Genomics Center, Kunming, China
| |
Collapse
|
17
|
Xiang B, Li X, Qian J, Wang L, Ma L, Tian X, Wang Y. The Complete Chloroplast Genome Sequence of the Medicinal Plant Swertia mussotii Using the PacBio RS II Platform. Molecules 2016; 21:molecules21081029. [PMID: 27517885 PMCID: PMC6274542 DOI: 10.3390/molecules21081029] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/21/2016] [Accepted: 08/04/2016] [Indexed: 11/16/2022] Open
Abstract
Swertia mussotii is an important medicinal plant that has great economic and medicinal value and is found on the Qinghai Tibetan Plateau. The complete chloroplast (cp) genome of S. mussotii is 153,431 bp in size, with a pair of inverted repeat (IR) regions of 25,761 bp each that separate an large single-copy (LSC) region of 83,567 bp and an a small single-copy (SSC) region of 18,342 bp. The S. mussotii cp genome encodes 84 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The identity, number, and GC content of S. mussotii cp genes were similar to those in the genomes of other Gentianales species. Via analysis of the repeat structure, 11 forward repeats, eight palindromic repeats, and one reverse repeat were detected in the S. mussotii cp genome. There are 45 SSRs in the S. mussotii cp genome, the majority of which are mononucleotides found in all other Gentianales species. An entire cp genome comparison study of S. mussotii and two other species in Gentianaceae was conducted. The complete cp genome sequence provides intragenic information for the cp genetic engineering of this medicinal plant.
Collapse
Affiliation(s)
- Beibei Xiang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Anshan Road 312, Tianjin 300193, China.
| | - Xiaoxue Li
- College of Life Science, Nankai University, Weijin Road 94, Tianjin 300071, China.
| | - Jun Qian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Malianwa North Road 151, Beijing 100193, China.
| | - Lizhi Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Anshan Road 312, Tianjin 300193, China.
| | - Lin Ma
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Anshan Road 312, Tianjin 300193, China.
| | - Xiaoxuan Tian
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Anshan Road 312, Tianjin 300193, China.
| | - Yong Wang
- College of Life Science, Nankai University, Weijin Road 94, Tianjin 300071, China.
| |
Collapse
|
18
|
Shim D, Raveendar S, Lee JR, Lee GA, Ro NY, Jeon YA, Cho GT, Lee HS, Ma KH, Chung JW. The complete chloroplast genome of Capsicum frutescens (Solanaceae). Appl Plant Sci 2016; 4:apps1600002. [PMID: 27213127 PMCID: PMC4873274 DOI: 10.3732/apps.1600002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/05/2016] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. METHODS AND RESULTS Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. CONCLUSIONS The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.
Collapse
Affiliation(s)
- Donghwan Shim
- Department of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441-350, Republic of Korea
| | - Sebastin Raveendar
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jung-Ro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Na-Young Ro
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Young-Ah Jeon
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Ho-Sun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Kyung-Ho Ma
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jong-Wook Chung
- National Agrobiodiversity Center, National Institute of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| |
Collapse
|