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Liu S, Veranso-Libalah MC, Sukhorukov AP, Sun X, Nilova MV, Kushunina M, Mamut J, Wen Z. Phylogenetic placement of the monotypic Baolia (Amaranthaceae s.l.) based on morphological and molecular evidence. BMC PLANT BIOLOGY 2024; 24:456. [PMID: 38789931 PMCID: PMC11127444 DOI: 10.1186/s12870-024-05164-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/17/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Baolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences. RESULTS We sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade and sister to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat. CONCLUSIONS Comparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia).
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Affiliation(s)
- Shuai Liu
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Marie Claire Veranso-Libalah
- Biodiversität und Evolution der Pflanzen, Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 830052, München, Germany
| | - Alexander P Sukhorukov
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation.
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050,, Russian Federation.
| | - Xuegang Sun
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
| | - Maya V Nilova
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Maria Kushunina
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050,, Russian Federation
- Department of Plant Physiology, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Jannathan Mamut
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhibin Wen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Urumqi, 830011, China.
- Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, Urumqi, 830011, China.
- The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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Zhou F, Liu Y, Xiong S, Huang Y. The complete chloroplast genome of Illicium simonsii Maxim. (Illiciaceae), a species with important medicinal properties. Mitochondrial DNA B Resour 2024; 9:678-682. [PMID: 38800621 PMCID: PMC11123442 DOI: 10.1080/23802359.2024.2356753] [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: 10/26/2022] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Illicium simonsii Maxim (1888) is a medicinal species of the genus Illicium in the Illiciaceae family. It is commonly used to cure gastro-frigid vomiting, cystic hernia, gas pains in the chest, and scabies as folk medicine. To utilize its resources efficiently, the complete chloroplast genome of I. simonsii was sequenced, assembled, and annotated by using high-throughput sequencing data. The complete chloroplast genome was 143,038 bp in length, with a large single-copy region (LSC) of 101,094 bp, a short single-copy region (SSC) of 20,070 bp, and a pair of inverted repeats (IRs) of 21,874 bp. A total of 113 genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic tree exhibited that I. simonsii and Illicium burmanicum form a sister group, and were nested in the monophyletic clade of the Illicium genus.
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Affiliation(s)
- Fuqin Zhou
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
| | - Yunqi Liu
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
| | - Shuang Xiong
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
| | - Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, P. R. China
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Nyamgerel N, Baasanmunkh S, Oyuntsetseg B, Bayarmaa GA, Erst A, Park I, Choi HJ. Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe. Sci Rep 2023; 13:22014. [PMID: 38086985 PMCID: PMC10716127 DOI: 10.1038/s41598-023-49381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Adonis mongolica is a threatened species that is endemic to Mongolia. It is a medicinal plant from the Adonis genus and has been used to treat heart diseases. However, the genomics and evolution of this species have not been thoroughly studied. We sequenced the first complete plastome of A. mongolica and compared it with ten Adonideae species to describe the plastome structure and infer phylogenetic relationships. The complete plastome of A. mongolica was 157,521 bp long and had a typical quadripartite structure with numerous divergent regions. The plastomes of Adonideae had relatively constant genome structures and sizes, except for those of Adonis. The plastome structure was consistent across Adonis. We identified a 44.8 kb large-scale inversion within the large single-copy region and rpl32 gene loss in the Adonis plastomes compared to other members of the Adonideae tribe. Additionally, Adonis had a smaller plastome size (156,917-157,603 bp) than the other genera within the tribe (159,666-160,940 bp), which was attributed to deletions of intergenic regions and partial and complete gene losses. These results suggested that an intramolecular mutation occurred in the ancestor of the Adonis genus. Based on the phylogenetic results, Adonis separated earlier than the other genera within the Adonideae tribe. The genome structures and divergences of specific regions in the Adonis genus were unique to the Adonideae tribe. This study provides fundamental knowledge for further genomic research in Mongolia and a better understanding of the evolutionary history of endemic plants.
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Affiliation(s)
- Nudkhuu Nyamgerel
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - Shukherdorj Baasanmunkh
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Gun-Aajav Bayarmaa
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Andrey Erst
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Science, Novosibirsk, 630090, Russia
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea.
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea.
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Liu X, Du W, Wang C, Wu Y, Chen W, Zheng Y, Wang M, Liu H, Yang Q, Qian S, Chen L, Liu C. A multilocus DNA mini-barcode assay to identify twenty vertebrate wildlife species. iScience 2023; 26:108275. [PMID: 38026223 PMCID: PMC10651681 DOI: 10.1016/j.isci.2023.108275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The world faces significant challenges in preserving the diversity of vertebrate species due to wildlife crimes. DNA barcoding, an effective molecular marker for insufficient nuclear DNA, is an authentic and quick identification technique to trace the origin of seized samples in forensic investigations. Here, we present a multiplex assay capable of identifying twenty vertebrate wildlife species utilizing twenty species-specific primers that target short fragments of the mitochondrial Cyt b, COI, 16S rRNA, and 12S rRNA genes. The assay achieved strong species specificity and sensitivity with a detection limit as low as 5 pg of DNA input. Additionally, it effectively discriminated a minor contributor (≥1%) from binary mixtures and successfully identified of noninvasive samples, inhibited DNA samples, artificially degraded DNA samples, and case samples, demonstrating a sensitive, robust, practical and easily interpretable tool in screening, and investigating forensic wildlife crimes.
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Affiliation(s)
- Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Weian Du
- School of Stomatology and Medicine, Foshan University, Foshan, Guangdong 528000, China
- Guangdong Homy Genetics Ltd., Foshan, Guangdong 528000, China
| | - Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Yajiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Yangyang Zheng
- Guangdong Homy Genetics Ltd., Foshan, Guangdong 528000, China
| | - Mengge Wang
- Guangzhou Forensic Science Institute & Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou, Guangdong 510030, China
| | - Hong Liu
- Guangzhou Forensic Science Institute & Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou, Guangdong 510030, China
| | - Qianyong Yang
- College of Medicine of Jiujiang University, Jiujiang, Jiangxi 332000 China
| | - Shui Qian
- Foshan Public Security Bureau, Foshan, Guangdong 528000, China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, Guangdong 510230, China
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Zhang W, Zhang Z, Liu B, Chen J, Zhao Y, Huang Y. Comparative analysis of 17 complete chloroplast genomes reveals intraspecific variation and relationships among Pseudostellaria heterophylla (Miq.) Pax populations. FRONTIERS IN PLANT SCIENCE 2023; 14:1163325. [PMID: 37426955 PMCID: PMC10325831 DOI: 10.3389/fpls.2023.1163325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/17/2023] [Indexed: 07/11/2023]
Abstract
Pseudostellaria heterophylla (Miq.) Pax is a well-known medicinal and ecologically important plant. Effectively distinguishing its different genetic resources is essential for its breeding. Plant chloroplast genomes can provide much more information than traditional molecular markers and provide higher-resolution genetic analyses to distinguish closely related planting materials. Here, seventeen P. heterophylla samples from Anhui, Fujian, Guizhou, Hebei, Hunan, Jiangsu, and Shandong provinces were collected, and a genome skimming strategy was employed to obtain their chloroplast genomes. The P. heterophylla chloroplast genomes ranged from 149,356 bp to 149,592 bp in length, and a total of 111 unique genes were annotated, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. Codon usage analysis showed that leucine had the highest frequency, while UUU (encoding phenylalanine) and UGC (encoding cysteine) were identified as the most and least frequently used codons, respectively. A total of 75-84 SSRs, 16-21 short tandem repeats, and 27-32 long repeat structures were identified in these chloroplast genomes. Then, four primer pairs were revealed for identifying SSR polymorphisms. Palindromes are the dominant type, accounting for an average of 47.86% of all long repeat sequences. Gene orders were highly collinear, and IR regions were highly conserved. Genome alignment indicated that there were four intergenic regions (psaI-ycf4, ycf3-trnS, ndhC-trnV, and ndhI-ndhG) and three coding genes (ndhJ, ycf1, and rpl20) that were highly variable among different P. heterophylla samples. Moreover, 10 SNP/MNP sites with high polymorphism were selected for further study. Phylogenetic analysis showed that populations of Chinese were clustered into a monophyletic group, in which the non-flowering variety formed a separate subclade with high statistical support. In this study, the comparative analysis of complete chloroplast genomes revealed intraspecific variations in P. heterophylla and further supported the idea that chloroplast genomes could elucidate relatedness among closely related cultivation materials.
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Affiliation(s)
- Wujun Zhang
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Baocai Liu
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jingying Chen
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yunqing Zhao
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yingzhen Huang
- Institute of Agricultural Bioresources, Fujian Academy of Agricultural Sciences, Fuzhou, China
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6
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Chen S, Yin X, Han J, Sun W, Yao H, Song J, Li X. DNA barcoding in herbal medicine: Retrospective and prospective. J Pharm Anal 2023; 13:431-441. [PMID: 37305789 PMCID: PMC10257146 DOI: 10.1016/j.jpha.2023.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 06/13/2023] Open
Abstract
DNA barcoding has been widely used for herb identification in recent decades, enabling safety and innovation in the field of herbal medicine. In this article, we summarize recent progress in DNA barcoding for herbal medicine to provide ideas for the further development and application of this technology. Most importantly, the standard DNA barcode has been extended in two ways. First, while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples, super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic levels. Second, mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials. In addition, some molecular techniques, such as high-throughput sequencing and isothermal amplification, are combined with DNA barcodes for species identification, which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding era. Furthermore, standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference sequences for species identification, which increases the accuracy and credibility of species discrimination based on DNA barcodes. In summary, DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.
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Affiliation(s)
- Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- 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
| | - Xianmei Yin
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, 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
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiwen Li
- 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
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Zhou J, He W, Wang J, Liao X, Xiang K, Ma M, Liu Z, Li Y, Tembrock LR, Wu Z, Liu L. The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence. BMC PLANT BIOLOGY 2023; 23:212. [PMID: 37088810 PMCID: PMC10123988 DOI: 10.1186/s12870-023-04218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated. RESULTS In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya. CONCLUSIONS The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.
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Affiliation(s)
- Jiawei Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- College of Science, Health, Engineering and Education, Murdoch University, Western Australia, Perth, 6150, Australia
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Kunli Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingchuan Ma
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Yongyao Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhiqiang Wu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
- College of Horticulture, Shanxi Agricultural University, Shanxi, 030801, China.
| | - Longlong Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China.
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China.
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Zong D, Qiao Z, Zhou J, Li P, Gan P, Ren M, He C. Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes. BMC Genomics 2023; 24:56. [PMID: 36721120 PMCID: PMC9887819 DOI: 10.1186/s12864-023-09154-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important commercial arbor species, which can provide us with the raw lacquer, an excellent adhesive and painting material used to make lacquer ware. Compared with diploid, triploid lacquer tree has a higher yield of raw lacquer and stronger resistance to stress. Triploid T. vernicifluum was a newly discovered natural triploid lacquer tree. However, the taxonomy of triploid T. vernicifluum has remained uncertain. Here, we sequenced and analyzed the complete chloroplast (cp) genome of triploid T. vernicifluum and compared it with related species of Toxicodendron genus based on chloroplast genome and SSR markers. RESULTS The plastome of triploid T. vernicifluum is 158,221 bp in length, including a pair of inverted repeats (IRs) of 26,462 bp, separated by a large single-copy region of 86,951 bp and a small single-copy region of 18,346 bp. In total, 132 genes including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified in the triploid T. vernicifluum. Among these, 16 genes were duplicated in the IR regions, 14 genes contain one intron, while three genes contain two introns. After nucleotide substitutions, seven small inversions were analyzed in the chloroplast genomes, eight hotspot regions were found, which could be useful molecular genetic markers for future population genetics. Phylogenetic analyses showed that triploid T. vernicifluum was a sister to T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi. Moreover, phylogenetic clustering based on the SSR markers showed that all the samples of triploid T. vernicifluum, T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi in one group, while the samples of T. vernicifluum and T. succedaneum in another group, which is consistent with the cp genome and morphological analysis. CONCLUSIONS The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, variety identification, breeding and resource exploitation, and future genetic diversity-related studies of T. vernicifluum.
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Affiliation(s)
- Dan Zong
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Zhensheng Qiao
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jintao Zhou
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Peiling Li
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Peihua Gan
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Meirong Ren
- grid.412720.20000 0004 1761 2943Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Chengzhong He
- grid.412720.20000 0004 1761 2943Key Laboratory for Forestry Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory for Forest Genetics and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China ,grid.412720.20000 0004 1761 2943Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
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Wanichthanarak K, Nookaew I, Pasookhush P, Wongsurawat T, Jenjaroenpun P, Leeratsuwan N, Wattanachaisaereekul S, Visessanguan W, Sirivatanauksorn Y, Nuntasaen N, Kuhakarn C, Reutrakul V, Ajawatanawong P, Khoomrung S. Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae. BMC PLANT BIOLOGY 2023; 23:59. [PMID: 36707785 PMCID: PMC9883906 DOI: 10.1186/s12870-023-04074-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed. RESULTS The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis. CONCLUSIONS In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.
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Affiliation(s)
- Kwanjeera Wanichthanarak
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Phongthana Pasookhush
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Namkhang Leeratsuwan
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Wonnop Visessanguan
- Functional Ingredients and Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Phathumthani, 12120, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Narong Nuntasaen
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, 10900, Thailand
| | - Chutima Kuhakarn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Vichai Reutrakul
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Pravech Ajawatanawong
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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10
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Wang Y, Xu J, Hu B, Dong C, Sun J, Li Z, Ye K, Deng F, Wang L, Aslam M, Lv W, Qin Y, Cheng Y. Assembly, annotation, and comparative analysis of Ipomoea chloroplast genomes provide insights into the parasitic characteristics of Cuscuta species. FRONTIERS IN PLANT SCIENCE 2023; 13:1074697. [PMID: 36733590 PMCID: PMC9887335 DOI: 10.3389/fpls.2022.1074697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
In the Convolvulaceae family, around 1650 species belonging to 60 genera are widely distributed globally, mainly in the tropical and subtropical regions of America and Asia. Although a series of chloroplast genomes in Convolvulaceae were reported and investigated, the evolutionary and genetic relationships among the chloroplast genomes of the Convolvulaceae family have not been extensively elucidated till now. In this study, we first reported the complete chloroplast genome sequence of Ipomoea pes-caprae, a widely distributed coastal plant with medical values. The chloroplast genome of I. pes-caprae is 161667 bp in length, and the GC content is 37.56%. The chloroplastic DNA molecule of I. pes-caprae is a circular structure composed of LSC (large-single-copy), SSC (small-single-copy), and IR (inverted repeat) regions, with the size of the three regions being 88210 bp, 12117 bp, and 30670 bp, respectively. The chloroplast genome of I. pes-caprae contains 141 genes, and 35 SSRs are identified in the chloroplast genome. Our research results provide important genomic information for the molecular phylogeny of I. pes-caprae. The Phylogenetic analysis of 28 Convolvulaceae chloroplast genomes showed that the relationship of I. pes-caprae with I. involucrata or I. obscura was much closer than that with other Convolvulaccae species. Further comparative analyses between the Ipomoea species and Cuscuta species revealed the mechanism underlying the formation of parasitic characteristics of Cuscuta species from the perspective of the chloroplast genome.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Xu
- Clinical College of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Bin Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chunxing Dong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixian Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kangzhuo Ye
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fang Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lulu Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Mohammad Aslam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Wenliang Lv
- Clinical College of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
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11
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Pham MH, Tran TH, Le TD, Le TL, Hoang H, Chu HH. The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships. Genes (Basel) 2023; 14:genes14010227. [PMID: 36672968 PMCID: PMC9859165 DOI: 10.3390/genes14010227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/19/2022] [Accepted: 01/07/2023] [Indexed: 01/18/2023] Open
Abstract
Ophiorrhiza baviensis Drake, a flowering medical plant in the Rubiaceae, exists uncertainly within the Ophiorrhiza genus' evolutionary relationships. For the first time, the whole chloroplast (cp) genome of an O. baviensis Drake species was sequenced and annotated. Our findings demonstrate that the complete cp genome of O. baviensis is 154,770 bp in size, encoding a total of 128 genes, including 87 protein-coding genes, 8 rRNAs, and 33 tRNAs. A total of 59 SSRs were screened in the studied cp genome, along with six highly variable loci, which can be applied to generate significant molecular markers for the Ophiorrhiza genus. The comparative analysis of the O. baviensis cp genome with two published others of the Ophiorrhiza genus revealed a high similarity; however, there were some notable gene rearrangements in the O. densa plastome. The maximum likelihood phylogenetic trees were constructed based on the concatenation of the rps16 gene and the trnL-trnF intergenic spacer sequence, indicating a close relationship between the studied O. baviensis and other Ophiorrhiza. This study will provide a theoretical molecular basis for identifying O. baviensis Drake, as well as species of the Ophiorrhiza genus, and contribute to shedding light on the chloroplast genome evolution of Rubiaceae.
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Affiliation(s)
- Mai Huong Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Thu Hoai Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Thi Dung Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Tung Lam Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Ha Hoang
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science & Technology (VAST), Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, VAST, Hanoi 100000, Vietnam
- Correspondence:
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12
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Gao Y, Liu K, Li E, Wang Y, Xu C, Zhao L, Dong W. Dynamic evolution of the plastome in the Elm family (Ulmaceae). PLANTA 2022; 257:14. [PMID: 36526857 DOI: 10.1007/s00425-022-04045-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
This study compared the plastomes of Ulmaceae allowing analyses of the dynamic evolution, including genome structure, codon usage bias, repeat sequences, molecular mutation rates, and phylogenetic inferences. Ulmaceae is a small family in the order Rosales. This family consists of seven genera, including Ulmus, Zelkova, Planera, Hemiptelea, Phyllostylon, Ampelocera, and Holoptelea. Ulmaceae is an interesting lineage from plant biogeographic, systematic, evolutionary, and paleobotanic perspectives. It is also a good model to investigate the evolution of the plastomes in woody plants. In this study, we sequenced and assembled the complete plastomes of the six Ulmaceae genera to compare genomic structures and reveal the molecular evolutionary patterns. The size of the quadripartite plastomes ranged from 158,290 bp to 161,886 bp. The genomes contained 131 genes, including 87 coding genes, 36 tRNA, and 8 rRNA. The gene number, gene content, and genomic structure were highly consistent among the Ulmaceae genera. Nine variable regions including ndhA intron, ndhF-rpl32, ycf1, psbK-trnS, rps16-trnQ, trnT-trnL, trnT-psbD, trnS-trnG, and rpl32-trnL, were identified in Ulmaceae plastomes according to the nucleotide diversity values. Condon usage was biased among the genes and showed consistent trends in the seven genera. Molecular evolution analyses revealed that most of the genes and all gene groups were under widespread purifying selection. Twelve genes (ccsA, matK, psbH, psbK, rbcL, rpl22, rpl32, rpoA, rps12, rps15, rps16, and ycf2) were under positive selection. Phylogenetic analyses supported that Ulmaceae should be divided into two main clades, such as the temperate clade, including Ulmus, Zelkova, Planera, and Hemiptelea and the tropical clade, including Phyllostylon, Ampelocera and Holoptelea. This study reports the structure and evolutionary characteristics of the Elm family. These new genomic data will benefit assessments of genomic evolution and provide information to elucidate the phylogenetic relationships among Ulmaceae species.
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Affiliation(s)
- Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Kangjia Liu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Enzhe Li
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yushuang Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liangcheng Zhao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
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13
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Yaradua SS, Yessoufou K. The Complete Chloroplast Genome of Hypoestes forskaolii (Vahl) R.Br: Insights into Comparative and Phylogenetic Analyses within the Tribe Justiceae. Genes (Basel) 2022; 13:genes13122259. [PMID: 36553525 PMCID: PMC9778027 DOI: 10.3390/genes13122259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Hypoestes forskaolii is one of the most important species of the family Acanthaceae, known for its high economic and medicinal importance. It is well distributed in the Arab region as well as on the African continent. Previous studies on ethnomedicine have reported that H. forskaolii has an anti-parasitic effect as well as antimalarial and anthelmintic activities. Previous studies mainly focused on the ethnomedicinal properties, hence, there is no information on the genomic architecture and phylogenetic positions of the species within the tribe Justiceae. The tribe Justicieae is the most taxonomically difficult taxon in Acanthoideae due to its unresolved infratribal classification. Therefore, by sequencing the complete chloroplast genome (cp genome) of H. forskaolii, we explored the evolutionary patterns of the cp genome and reconstructed the phylogeny of Justiceae. The cp genome is quadripartite and circular in structure and has a length of 151,142 bp. There are 130 genes (86 coding for protein, 36 coding for tRNA and 8 coding for rRNA) present in the plastome. Analyses of long repeats showed only three types of repeats: forward, palindromic and reverse were present in the genome. Microsatellites analysis revealed 134 microsatellites in the cp genome with mononucleotides having the highest frequency. Comparative analyses within Justiceae showed that genomes structure and gene contents were highly conserved but there is a slight distinction in the location of the genes in the inverted repeat and single copy junctions. Additionally, it was discovered that the cp genome includes variable hotspots that can be utilized as DNA barcodes and tools for determining evolutionary relationships in the Justiceae. These regions include: atpH-atpI, trnK-rps16, atpB-rbcL, trnT-trnL, psbI-trnS, matK, trnH-psbA, and ndhD. The Bayesian inference phylogenetic tree showed that H. forskaolii is a sister to the Dicliptra clade and belongs to Diclipterinae. The result also confirms the polyphyly of Justicia and inclusion of Diclipterinae within justicioid. This research has revealed the phylogenetic position of H. forskaolii and also reported the resources that can be used for evolutionary and phylogenetic studies of the species and the Justicieae.
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Affiliation(s)
- Samaila Samaila Yaradua
- Department of Geography, Environmental Management and Energy Studies, APK Campus, University of Johannesburg, Johannesburg 2006, South Africa
- Department of Biology, Umaru Musa Yaradua University, Katsina 820102, Nigeria
- Correspondence:
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, APK Campus, University of Johannesburg, Johannesburg 2006, South Africa
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14
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Wang Y, Sun J, Qiao P, Wang J, Wang M, Du Y, Xiong F, Luo J, Yuan Q, Dong W, Huang L, Guo L. Evolutionary history of genus Coptis and its dynamic changes in the potential suitable distribution area. FRONTIERS IN PLANT SCIENCE 2022; 13:1003368. [PMID: 36507390 PMCID: PMC9727247 DOI: 10.3389/fpls.2022.1003368] [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: 08/22/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
The genus Coptis belongs to the Ranunculaceae family, containing 15 recognized species highly diverse in morphology. It is a conspicuous taxon with special evolutionary position, distribution pattern and medicinal value, which makes it to be of great research and conservation significance. In order to better understand the evolutionary dynamics of Coptis and promote more practical conservation measures, we performed plastome sequencing and used the sequencing data in combination with worldwide occurrence data of Coptis to estimate genetic diversity and divergence times, rebuild biogeographic history and predict its potential suitable distribution area. The average nucleotide diversity of Coptis was 0.0067 and the hotspot regions with the highest hypermutation levels were located in the ycf1 gene. Coptis is most likely to have originated in North America and Japanese archipelago and has a typical Eastern Asian and North American disjunct distribution pattern, while the species diversity center is located in Mid-West China and Japan. The crown age of the genus is estimated at around 8.49 Mya. The most suitable climatic conditions for Coptis were as follows: precipitation of driest quarter > 25.5 mm, annual precipitation > 844.9 mm and annual mean temperature -3.1 to 19 °C. The global and China suitable area shows an upward trend in the future when emission of greenhouse gases is well controlled, but the area, especially in China, decreases significantly without greenhouse gas policy interventions. The results of this study provide a comprehensive insight into the Coptis evolutionary dynamics and will facilitate future conservation efforts.
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Affiliation(s)
- Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ping Qiao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyi Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengli Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongxi Du
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Feng Xiong
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jun Luo
- Kunming Xishan Forestry and Grassland Comprehensive Service Center, Kunming, China
| | - Qingjun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
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15
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Zhang X, Yang H, Wu B, Chen H. The chloroplast genome of the Iris japonica Thunberg (Butterfly flower) reveals the genomic and evolutionary characteristics of Iris species. Mitochondrial DNA B Resour 2022; 7:1776-1782. [PMID: 36245810 PMCID: PMC9559474 DOI: 10.1080/23802359.2022.2118000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Iris japonica Thunberg is one of the horticultural species belonging to the Iris genus and Iridaceae family. Previous studies have revealed its hepatoprotective activity and ornamental values. However, little genetic and genomic information about this species is available. Here, to decipher the chloroplast genome and reveal its evolutionary characteristics, we sequenced, de novo assembled, and comprehensively analyzed the chloroplast genome of I. japonica. The genome was 152,453 bp in length and displayed a circular structure with a large single-copy region, a small single-copy region, and two inverted repeat regions. It contained 131 genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. We also identified 23 microsatellite repeat sequences, 34 tandem repeat sequences, and 60 dispersed repeat sequences in the chloroplast genome of I. japonica. Sequence divergence analyses of the chloroplast genomes of 20 Iris species revealed that the top four most highly variable regions were ndhC-trnV-UAC, rpl22-rps19, rps16-trnQ-UUG, and trnG-UCC-trnR-UCU. Phylogenetic analysis showed that I. japonica was most closely related to I. tectorum. This study reported a new chloroplast genome of I. japonica and performed comparative analyses of 20 Iris chloroplast genomes. The results would facilitate the evolutionary research and development of molecular markers for Iris species.
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Affiliation(s)
- Xinyi Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Heyu Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China,Bin Wu Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing100093, P.R. China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China,CONTACT Haimei Chen
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16
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Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China. Int J Mol Sci 2022; 23:ijms231911617. [PMID: 36232915 PMCID: PMC9569570 DOI: 10.3390/ijms231911617] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022] Open
Abstract
Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China.
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Zhu S, Liu Q, Qiu S, Dai J, Gao X. DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances. Chin Med 2022; 17:112. [PMID: 36171596 PMCID: PMC9514984 DOI: 10.1186/s13020-022-00655-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.
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Affiliation(s)
- Shuang Zhu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Qiaozhen Liu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Simin Qiu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jiangpeng Dai
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment. Genes (Basel) 2022; 13:genes13091673. [PMID: 36140840 PMCID: PMC9498722 DOI: 10.3390/genes13091673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Saxifraga species are widely distributed in alpine and arctic regions in the Northern hemisphere. Highly morphological diversity within this genus brings great difficulties for species identification, and their typical highland living properties make it interesting how they adapt to the extreme environment. Here, we newly generated the chloroplast (cp) genomes of two Saxifraga species and compared them with another five Saxifraga cp genomes to understand the characteristics of cp genomes and their potential roles in highland adaptation. The genome size, structure, gene content, GC content, and codon usage pattern were found to be highly similar. Cp genomes ranged from 146,549 bp to 151,066 bp in length, most of which comprised 130 predicted genes. Yet, due to the expansion of IR regions, the second copy of rps19 in Saxifraga stolonifera was uniquely kept. Through sequence divergence analysis, we identified seven hypervariable regions and detected some signatures of regularity associated with genetic distance. We also identified 52 to 89 SSRs and some long repeats among seven Saxifraga species. Both ML and BI phylogenetic analyses confirmed that seven Saxifraga species formed a monophyletic clade in the Saxifragaceae family, and their intragenus relationship was also well supported. Additionally, the ndhI and ycf1 genes were considered under positive selection in species inhabiting relatively high altitudes. Given the conditions of intense light and low CO2 concentration in the highland, the products of these two genes might participate in the adaptation to the extreme environment.
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Yang L, Abduraimov O, Tojibaev K, Shomurodov K, Zhang YM, Li WJ. Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L. BMC Genomics 2022; 23:643. [PMID: 36076164 PMCID: PMC9461113 DOI: 10.1186/s12864-022-08868-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/30/2022] [Indexed: 11/11/2022] Open
Abstract
Background Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species. Results The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. Conclusion Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08868-z.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China.,Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, No.818 South Beijing Road, Urumqi, 830011, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China
| | - Ozodbek Abduraimov
- Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125
| | - Komiljon Tojibaev
- Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125
| | - Khabibullo Shomurodov
- Institute of Botany, Uzbekistan Academy of Sciences, No.32 Durmon Yuli Street, Tashkent, Uzbekistan, 100125
| | - Yuan-Ming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China.,Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, No.818 South Beijing Road, Urumqi, 830011, China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, No.818 South Beijing Road, Urumqi, 830011, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Shijingshan District, No.19(A) Yuquan Road, Beijing, 100049, China. .,Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, No.818 South Beijing Road, Urumqi, 830011, China. .,The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [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] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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Wang Y, Sun J, Zhao Z, Xu C, Qiao P, Wang S, Wang M, Xu Z, Yuan Q, Guo L, Huang L. Multiplexed Massively Parallel Sequencing of Plastomes Provides Insights Into the Genetic Diversity, Population Structure, and Phylogeography of Wild and Cultivated Coptis chinensis. FRONTIERS IN PLANT SCIENCE 2022; 13:923600. [PMID: 35873994 PMCID: PMC9302112 DOI: 10.3389/fpls.2022.923600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/07/2022] [Indexed: 05/31/2023]
Abstract
Root rot has been a major problem for cultivated populations of Coptis chinensis var. chinensis in recent years. C. chinensis var. brevisepala, the closest wild relative of C. chinensis var. chinensis, has a scattered distribution across southwestern China and is an important wild resource. Genetic diversity is associated with greater evolutionary potential and resilience of species or populations and is important for the breeding and conservation of species. Here, we conducted multiplexed massively parallel sequencing of the plastomes of 227 accessions of wild and cultivated C. chinensis using 111 marker pairs to study patterns of genetic diversity, population structure, and phylogeography among wild and cultivated C. chinensis populations. Wild and cultivated resources diverged approximately 2.83 Mya. The cultivated resources experienced a severe genetic bottleneck and possess highly mixed germplasm. However, high genetic diversity has been retained in the wild resources, and subpopulations in different locations differed in genotype composition. The significant divergence in the genetic diversity of wild and cultivated resources indicates that they require different conservation strategies. Wild resources require in situ conservation strategies aiming to expand population sizes while maintaining levels of genetic diversity; by contrast, germplasm resource nurseries with genotypes of cultivated resources and planned distribution measures are needed for the conservation of cultivated resources to prevent cultivated populations from undergoing severe genetic bottlenecks. The results of this study provide comprehensive insights into the genetic diversity, population structure, and phylogeography of C. chinensis and will facilitate future breeding and conservation efforts.
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Affiliation(s)
- Yiheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiahui Sun
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhenyu Zhao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ping Qiao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Academician Workstation, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengli Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zegang Xu
- Lichuan Jianzhuxi Huanglian Cooperative, Lichuan, China
| | - Qingjun Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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22
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Dong Z, Zhang R, Shi M, Song Y, Xin Y, Li F, Ma J, Xin P. The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis. PLoS One 2022; 17:e0269819. [PMID: 35771795 PMCID: PMC9246242 DOI: 10.1371/journal.pone.0269819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022] Open
Abstract
Brassaiopsis angustifolia K.M. Feng belongs to the family Araliaceae, and is an endangered shrub species in southwest China. Despite the importance of this species, the plastid genome has not been sequenced and analyzed. In this study, the complete plastid genome of B. angustifolia was sequenced, analyzed, and compared to the eight species in the Araliaceae family. Our study reveals that the complete plastid genome of B. angustifolia is 156,534 bp long, with an overall GC content of 37.9%. The chloroplast genome (cp) encodes 133 genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. Five highly divergent regions were successfully identified that could be used as potential genetic markers of Brassaiopsis and Asian Palmate group. Phylogenetic analysis of 47 plastomes, representing 19 genera of Araliaceae and two related families, was performed to reconstruct highly supported relationships for the Araliaceae, which highlight four well-supported clades of the Hydrocotyle group, Greater Raukaua group, Aralia-Panax group, and Asian Palmate group. The genus Brassaiopsis can be divided into four groups using internal transcribed spacer (ITS) data. The results indicate that plastome and ITS data can contribute to investigations of the taxonomy, and phylogeny of B. angustifolia. This study provides a theoretical basis for species identification and future biological research on resources of the genus Brassaiopsis.
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Affiliation(s)
- Zhanghong Dong
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Ruli Zhang
- Sympodial Bamboos Technological and Engineering Research Center, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Ming Shi
- Sympodial Bamboos Technological and Engineering Research Center, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Normal University, Guilin, China
| | - Yaxuan Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Feng Li
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Jianzhong Ma
- Yunnan Academy of Forestry and Grassland, Kunming, China
- * E-mail: (JM); (PX)
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- * E-mail: (JM); (PX)
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Xia X, Peng J, Yang L, Zhao X, Duan A, Wang D. Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus. Life (Basel) 2022; 12:life12060848. [PMID: 35743879 PMCID: PMC9224849 DOI: 10.3390/life12060848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/30/2022] Open
Abstract
The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89−104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.
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Affiliation(s)
- Xi Xia
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Jingyu Peng
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100089, China;
| | - Lin Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Xueli Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Anan Duan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Dawei Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
- Correspondence: ; Tel.: +86-138-8891-5161
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Ye H, Liu H, Hu G, Zhao P. The complete chloroplast genome sequence of Paphiopedilum henryanum (Orchidaceae). Mitochondrial DNA B Resour 2022; 7:1174-1176. [PMID: 35935683 PMCID: PMC9354640 DOI: 10.1080/23802359.2022.2088310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Guojia Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
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Yu J, Xia M, Wang Y, Chi X, Xu H, Chen S, Zhang F. Short and long reads chloroplast genome assemblies and phylogenomics of Artemisia tangutica (Asteraceae). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Wang G, Bai X, Chen X, Ren Y, Pang X, Han J. Detection of Adulteration and Pesticide Residues in Chinese Patent Medicine Qipi Pill Using KASP Technology and GC-MS/MS. Front Nutr 2022; 9:837268. [PMID: 35369100 PMCID: PMC8965643 DOI: 10.3389/fnut.2022.837268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Chinese patent medicines (CPMs) are of great value for the prevention and treatment of diseases. However, adulterants and pesticide residues in CPMs have become the “bottleneck” impeding the globalization of traditional Chinese medicine. In this study, 12 batches of commercially available Qipi pill (a famous CPM recorded in Chinese Pharmacopeia) from different manufacturers were investigated to evaluate their authenticity and quality safety. Considering the severely degraded DNA in CPMs, kompetitive allele specific PCR (KASP) technology combined with DNA mini-barcodes was proposed for the quality regulation of a large number of products in CPM market. The residues of four kinds of pesticides including pentachloronitrobenzene (PCNB), hexachlorocyclohexane (HCH), aldrin, and dichlorodiphenyltrichloroethane (DDT) were quantified using gas chromatography and tandem mass spectrometry (GC-MS/MS). The results indicated that in two of the 12 batches of Qipi pill, the main herbal ingredient Panax ginseng was completely substituted by P. quinquefolius, and one sample was partially adulterated with P. quinquefolius. The PCNB residue was detected in 11 batches of Qipi pill, ranging from 0.11 to 0.46 mg/kg, and the prohibited pesticide HCH was present in four samples. Both adulteration and banned pesticides were found in two CPMs. This study suggests that KASP technology combined with DNA mini-barcodes can be used for the quality supervision of large sample size CPMs with higher efficiency but lower cost. Our findings also provide the insight that pesticide residues in CPMs should be paid more attention in the future.
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Guan YH, Liu WW, Duan BZ, Zhang HZ, Chen XB, Wang Y, Xia CL. The first complete chloroplast genome of Vicatia thibetica de Boiss.: genome features, comparative analysis, and phylogenetic relationships. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:439-454. [PMID: 35400891 PMCID: PMC8943076 DOI: 10.1007/s12298-022-01154-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/13/2021] [Accepted: 02/18/2022] [Indexed: 06/03/2023]
Abstract
UNLABELLED Vicatia thibetica de Boiss.: a herb in the family Apiaceae, has been used for over a hundred years as an essential medicinal and edible plant in the Bai ethnic group of Dali City. However, due to the lack of study on plastid genomes of V. thibetica, studies of comparison and phylogeny with other related species remain scarce. In the current study, we assembled, annotated, and characterized the entire chloroplast (cp) genome of V. thibetica through high-throughput sequencing for the first time, compared with published whole chloroplast genomes from the same family. A phylogenetic analysis of the chloroplast genome has also been performed. The whole chloroplast genome of V. thibetica was 145,796 in size and consisted of a large single-copy region (LSC; 92,186 bp), a small single-copy region (SSC; 17,452 bp), and a pair of inverted repeat regions (IRs; 18,079 bp) forming a circular quadripartite structure. Annotation resulted in 128 genes, including 84 protein-coding genes (PCGs), 35 transfer RNA genes (tRNAs), eight ribosomal genes (rRNAs), and one pseudogene. Repeat sequence analysis displayed V. thibetica plastid genome contains 75 simple repeats, 37 long repeats, and 29 tandem repeats. Compared with the cp genome of other Apiaceae species, a common feature was that the IR regions of the genome were more conservative compared to the LSC and SSC regions. Highly variable hotspots included rps16, ndhC-trnV-UAC, clpP, ycf1, and ndhB in the genomes, which supply valuable molecular markers for phylogeny, identification, and classification in the Apiaceae family. The results of phylogenetic analysis strongly supported the genus Vicatia as an independent genus in the family Apiaceae, in which the closest affinities to the related species of Angelica, Peucedanum, and Ligusticum were observed. In conclusion, the first chloroplast genome of Vicatia reported in this study may improve our understanding of phylogenetic relationship of different genera of Apiaceae. In addition, the current data will be valuable as chloroplast genomic resource for species identification and population genetics. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01154-y.
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Affiliation(s)
- Yun-hui Guan
- College of Pharmacy, Dali University, Dali, 671000 China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000 China
| | - Wen-wen Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai, 200237 China
| | - Bao-zhong Duan
- College of Pharmacy, Dali University, Dali, 671000 China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000 China
| | - Hai-zhu Zhang
- College of Pharmacy, Dali University, Dali, 671000 China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000 China
| | - Xu-bing Chen
- College of Pharmacy, Dali University, Dali, 671000 China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000 China
| | - Ying Wang
- College of Pharmacy, Dali University, Dali, 671000 China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000 China
| | - Cong-long Xia
- College of Pharmacy, Dali University, Dali, 671000 China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000 China
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Saldaña CL, Rodriguez-Grados P, Chávez-Galarza JC, Feijoo S, Guerrero-Abad JC, Vásquez HV, Maicelo JL, Jhoncon JH, Arbizu CI. Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona ( Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species. Genes (Basel) 2022; 13:genes13010113. [PMID: 35052453 PMCID: PMC8774758 DOI: 10.3390/genes13010113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022] Open
Abstract
Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.
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Affiliation(s)
- Carla L. Saldaña
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Pedro Rodriguez-Grados
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
- Facultad de Ciencias, Universidad Nacional José Faustino Sánchez Carrión, Av. Mercedes Indacochea Nro. 609, Huacho 15136, Peru
| | - Julio C. Chávez-Galarza
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Shefferson Feijoo
- Estación Experimental Agraria San Bernardo, Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Carretera Cusco, Puerto Maldonado, Tambopata, Madre de Dios 17000, Peru;
| | - Juan Carlos Guerrero-Abad
- Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru;
| | - Héctor V. Vásquez
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Jorge L. Maicelo
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
| | - Jorge H. Jhoncon
- Centro de Investigación de Plantas Andinas y Nativas, Facultad de Ciencias, Universidad Nacional de Educación Enrique Guzmán y Valle, Av. Enrique Guzmán y Valle s/n, Lima 15472, Peru;
- Unidad de Investigación, Perú Maca SAC, Panamericana Sur KM. 37.2 Mz. D1. Lote 03A, Lima 15823, Peru
| | - Carlos I. Arbizu
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru; (C.L.S.); (P.R.-G.); (J.C.C.-G.); (H.V.V.); (J.L.M.)
- Correspondence:
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Chen L, Ren W, Zhang B, Chen W, Fang Z, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Zhang Y. Organelle Comparative Genome Analysis Reveals Novel Alloplasmic Male Sterility with orf112 in Brassica oleracea L. Int J Mol Sci 2021; 22:ijms222413230. [PMID: 34948024 PMCID: PMC8703919 DOI: 10.3390/ijms222413230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
B. oleracea Ogura CMS is an alloplasmic male-sterile line introduced from radish by interspecific hybridization and protoplast fusion. The introduction of alien cytoplasm resulted in many undesirable traits, which affected the yield of hybrids. Therefore, it is necessary to identify the composition and reduce the content of alien cytoplasm in B. oleracea Ogura CMS. In the present study, we sequenced, assembled, and compared the organelle genomes of Ogura CMS cabbage and its maintainer line. The chloroplast genome of Ogura-type cabbage was completely derived from normal-type cabbage, whereas the mitochondrial genome was recombined from normal-type cabbage and Ogura-type radish. Nine unique regions derived from radish were identified in the mitochondrial genome of Ogura-type cabbage, and the total length of these nine regions was 35,618 bp, accounting for 13.84% of the mitochondrial genome. Using 32 alloplasmic markers designed according to the sequences of these nine regions, one novel sterile source with less alien cytoplasm was discovered among 305 materials and named Bel CMS. The size of the alien cytoplasm in Bel CMS was 21,587 bp, accounting for 8.93% of its mtDNA, which was much less than that in Ogura CMS. Most importantly, the sterility gene orf138 was replaced by orf112, which had a 78-bp deletion, in Bel CMS. Interestingly, Bel CMS cabbage also maintained 100% sterility, although orf112 had 26 fewer amino acids than orf138. Field phenotypic observation showed that Bel CMS was an excellent sterile source with stable 100% sterility and no withered buds at the early flowering stage, which could replace Ogura CMS in cabbage heterosis utilization.
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Affiliation(s)
- Li Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Ren
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wendi Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China; (L.C.); (W.R.); (B.Z.); (W.C.); (Z.F.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
- Correspondence:
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Philippe F, Dubrulle N, Marteaux B, Bonnet B, Choisy P, Berthon JY, Garnier L, Leconte N, Milesi S, Morvan PY, Saunois A, Sun JS, Weber S, Giraud N. Combining DNA Barcoding and Chemical fingerprints to authenticate Lavender raw material. Int J Cosmet Sci 2021; 44:91-102. [PMID: 34860432 PMCID: PMC9305429 DOI: 10.1111/ics.12757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 12/01/2021] [Indexed: 11/30/2022]
Abstract
Objective This study was initiated and conducted by several laboratories, 3 of the main cosmetic ingredient suppliers and 4 brands of cosmetics in France. Its objective is to show the interest and robustness of coupling chemical and genetic analyses in the identification of plant species. In this study, the Lavandula genus was used. Methods In this study, we used two analytical methods. Chemical analysis from UHPLC (ultra‐high‐performance liquid chromatography) and genetic analysis from barcoding with genetic markers. Results Eleven lavender species were selected (botanically authenticated) and analysed. The results show that three chemical compounds (coumaric acid hexoside, ferulic acid hexoside and rosmarinic acid) and three genetic markers (RbcL, trnH‐psbA and ITS) are of interest for the differentiation of species of the genus lavandula. Conclusion The results show that the combination of complementary analytical methods is a relevant system to prove the botanical identification of lavender species. This first study, carried out on a plant of interest for cosmetics, demonstrates the need for authentication using a tool combining genetic and chemical analysis as an advance over traditional investigation methods used alone, in terms of identification and authentication reliability.
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Affiliation(s)
- Florian Philippe
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
| | - Nelly Dubrulle
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
| | - Benjamin Marteaux
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
| | | | | | | | | | | | | | | | | | - Jian-Sheng Sun
- Structure et Instabilite des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, Paris, 75005, France
| | | | - Nicole Giraud
- DNA Gensee, 17 rue du lac saint andré, Le Bourget du Lac, 73370, France
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A Review on Application of DNA Barcoding Technology for Rapid Molecular Diagnostics of Adulterants in Herbal Medicine. Drug Saf 2021; 45:193-213. [PMID: 34846701 DOI: 10.1007/s40264-021-01133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
The rapid molecular diagnostics of adulterants in herbal medicine using DNA barcoding forms the core of this meticulously detailed review, based on two decades of data. With 80% of the world's population using some form of herbal medicine, authentication, quality control, and detection of adulterants warrant DNA barcoding. A combined group of keywords were used for literature review using the PubMed, the ISI Web of Knowledge, Web of Science (WoS), and Google Scholar databases. All the papers (N = 210) returned by the search engines were downloaded and systematically analyzed. Detailed analysis of conventional DNA barcodes were based on retrieved sequences for internal transcribed spacer (ITS) (412,189), rbcL (251,598), matK (210,835), and trnH-psbA (141,846). The utility of databases such as The Barcode of Life Data System (BOLD), NCBI, GenBank, and Medicinal Materials DNA Barcode Database (MMDBD) has been critically examined for the identification of unknown species from known databases. The current review gives an overview of the ratio of adulterated to authentic drugs for some countries along with the state of the art technology currently being used in the identification of adulterated medicines. In this review, efforts were made to systematically analyze and arrange the research and reviews on the basis of technical progress. The review concludes with the future of DNA-based herbal medicine adulteration detection, forecasting the reliance on the metabarcoding technology. DNA barcoding technology for differentiating adulterated herbal medicine.
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Wu S, Jiang C, Feng X, Yang C, Yu Z. The complete chloroplast genome of Lonicera similis Hemsl. and its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:3151-3153. [PMID: 34746389 PMCID: PMC8567915 DOI: 10.1080/23802359.2021.1987167] [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: 11/11/2022] Open
Abstract
Lonicera similis Hemsl. belongs to the Caprifoliaceae family and used as a substitute for ‘jin yin hua’. Recent years, it demonstrates great economic value because of its rich chemical composition. However, the phylogenetic relationship between L. similis and other family members remains unclear. In this paper, we assembled the cp genome of L. similis using the high-throughput Illumina pair-end sequencing data. The circular cp genome was 155,207 bp in size, including a large single-copy (LSC) region of 88994 bp and a small single-copy (SSC) region of 18,633 bp, which were separated by two inverted repeat (IR) regions (23,790 bp each). A total of 121 genes were predicted, including eight ribosomal RNAs (rRNAs), 36 transfer RNAs (tRNAs), and 77 protein-coding genes (PCGs). In addition, the result of phylogenetic analysis indicated that L. similis formed a close relationship from another congeneric species (Lonicera confusa). This study provides helpful information for future genetic study of L. similis.
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Affiliation(s)
- ShaoXiong Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - ChunYan Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - XiaYu Feng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - ChenJu Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - ZhengWen Yu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
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Phylogenetic inference of Ericales based on plastid genomes and implication of cp-SSRs. BIOTECHNOLOGIA 2021; 102:277-283. [PMID: 36606144 PMCID: PMC9642927 DOI: 10.5114/bta.2021.108723] [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: 01/30/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 01/09/2023] Open
Abstract
Ericales is an ancient eudicot order encompassing numerous species of economic and ornamental values. Despite several phylogenomic studies, the evolutionary relationship among certain families of this group remains uncertain. The present study assessed a multilocus species tree of Ericales based on 107 chloroplast genomes. The plastome derived microsatellite motifs were also simultaneously explored to check their dynamicity in corroboration of species phylogeny and systematics. In addition to resolving the usual hierarchy, the present phylogenetic analysis enabled to resolve the persisting lineage disparity with valid statistical support. Accordingly, divergence incongruences of Primulaceae, Ebenaceae, and Sapotaceae from earlier reports were reinstated in presently inferred phylogeny, which further supported the latest transcriptome-based relationship of the corresponding group. Various SSR motif characteristics emerged following the recognition of the evolutionary pathway. Numerical variation in tetranucleotide repeats showed even intraspecific or varietal differences in Camellia sinensis. Validation of plastome microsatellite-based polymorphism among the related taxa might pave the way for future phylogenetic and population studies of this economically important group.
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Geographic source estimation using airborne plant environmental DNA in dust. Sci Rep 2021; 11:16238. [PMID: 34376726 PMCID: PMC8355115 DOI: 10.1038/s41598-021-95702-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Information obtained from the analysis of dust, particularly biological particles such as pollen, plant parts, and fungal spores, has great utility in forensic geolocation. As an alternative to manual microscopic analysis of dust components, we developed a pipeline that utilizes the airborne plant environmental DNA (eDNA) in settled dust to estimate geographic origin. Metabarcoding of settled airborne eDNA was used to identify plant species whose geographic distributions were then derived from occurrence records in the USGS Biodiversity in Service of Our Nation (BISON) database. The distributions for all plant species identified in a sample were used to generate a probabilistic estimate of the sample source. With settled dust collected at four U.S. sites over a 15-month period, we demonstrated positive regional geolocation (within 600 km2 of the collection point) with 47.6% (20 of 42) of the samples analyzed. Attribution accuracy and resolution was dependent on the number of plant species identified in a dust sample, which was greatly affected by the season of collection. In dust samples that yielded a minimum of 20 identified plant species, positive regional attribution was achieved with 66.7% (16 of 24 samples). For broader demonstration, citizen-collected dust samples collected from 31 diverse U.S. sites were analyzed, and trace plant eDNA provided relevant regional attribution information on provenance in 32.2% of samples. This showed that analysis of airborne plant eDNA in settled dust can provide an accurate estimate regional provenance within the U.S., and relevant forensic information, for a substantial fraction of samples analyzed.
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35
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Lugon MD, dos Santos PHD, Oliveira PV, de Almeida FAN, Luber J, Forzza RC, Jardim MAG, Paneto GG. Is Your Açaí Really from Amazon? Using DNA Barcoding to Authenticate Commercial Products. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-01998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Fu CN, Mo ZQ, Yang JB, Cai J, Ye LJ, Zou JY, Qin HT, Zheng W, Hollingsworth PM, Li DZ, Gao LM. Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron. Mol Ecol Resour 2021; 22:404-414. [PMID: 34310851 DOI: 10.1111/1755-0998.13479] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/22/2021] [Accepted: 07/05/2021] [Indexed: 12/01/2022]
Abstract
Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.
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Affiliation(s)
- Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | | | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.,Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
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Huang CH, Chen CC, Lin YC, Chen CH, Lee AY, Liou JS, Gu CT, Huang L. The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa. Microorganisms 2021; 9:microorganisms9081570. [PMID: 34442649 PMCID: PMC8399863 DOI: 10.3390/microorganisms9081570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022] Open
Abstract
The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
- Correspondence:
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Chun-Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China;
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
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Li J, Price M, Su DM, Zhang Z, Yu Y, Xie DF, Zhou SD, He XJ, Gao XF. Phylogeny and Comparative Analysis for the Plastid Genomes of Five Tulipa (Liliaceae). BIOMED RESEARCH INTERNATIONAL 2021; 2021:6648429. [PMID: 34239930 PMCID: PMC8235973 DOI: 10.1155/2021/6648429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/09/2021] [Indexed: 11/17/2022]
Abstract
Species of Tulipa (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary diversity centres of Tulipa, but the molecular studies of Tulipa species from this location are lacking. In our study, we assembled four Tulipa plastid genomes from the Tien Shan Mountains, T. altaica, T. iliensis, T. patens, and T. thianschanica, combined with the plastid genome of T. sylvestris to compare against other Liliaceae plastid genomes. We focussed on the species diversity and evolution of their plastid genomes. The five Tulipa plastid genomes proved highly similar in overall size (151,691-152,088 bp), structure, gene order, and content. With comparative analysis, we chose 7 mononucleotide SSRs from the Tulipa species that could be used in further population studies. Phylogenetic analyses based on 24 plastid genomes robustly supported the monophyly of Tulipa and the sister relationship between Tulipa and Amana, Erythronium. T. iliensis, T. thianschanica, and T. altaica were clustered together, and T. patens was clustered with T. sylvestris, with our results clearly demonstrating the relationships between these five Tulipa species. Our results provide a more comprehensive understanding of the phylogenomics and comparative genomics of Tulipa.
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Affiliation(s)
- Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Zhen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan, China
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Zhang XF, Landis JB, Wang HX, Zhu ZX, Wang HF. Comparative analysis of chloroplast genome structure and molecular dating in Myrtales. BMC PLANT BIOLOGY 2021; 21:219. [PMID: 33992095 PMCID: PMC8122561 DOI: 10.1186/s12870-021-02985-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. RESULTS A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214-171,315 bp and exhibit a typical four part structure. The IR region is between 23,901-36,747 bp, with the large single copy region spanning 83,691-91,249 bp and the small single copy region spanning 11,150-19,703 bp. In total, 123-133 genes are present in the chloroplasts including 77-81 protein coding genes, four rRNA genes and 30-31 tRNA genes. The GC content was 36.9-38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7-37.3%, 30.6-36.8% and 39.7-43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88-114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50-118.62 Ma). CONCLUSIONS The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.
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Affiliation(s)
- Xiao-Feng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Hong-Xin Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China.
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Xu G, Xu W. Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis. PROTOPLASMA 2021; 258:559-571. [PMID: 33230625 DOI: 10.1007/s00709-020-01585-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
As a basalmost family of Vitaceae, Chinese wild Vitis species offer key insights into the demographic history of grapes. In this study, we obtained 10 complete chloroplast (cp) genomes from Chinese wild-growing Vitis species based on our whole genome re-sequencing data. These chloroplast genomes ranged from 160,838 to 232,020 bp in size and exhibited typical quadripartite structures. Comparative analyses revealed that inverted repeat (IR) regions are especially abundant and contribute to cp genome arrangements. Phylogenetic analysis of the whole Vitis cp genomes supported three clearly partitioned main origins, in keeping with their geographic distributions, among which East Asian species from China were found to be sister species with Eurasian Vitis species but exhibited significant divergence from the North American group. Two well-supported subgroups were observed within the Chinese wild-growing Vitis species. Among these species, Vitis piasezkii and Vitis betulifolia were closely related species, exhibiting a support rate of 100%. The molecular clock-based divergence time suggested that the earliest split subspecies was Vitis pseudoreticulata, which further indicated that the origin and initial gene pool are located in southern China (the habitat of V. pseudoreticulata is located in the region). Coincidentally, the divergence time was during the Pleistocene period (2.6-0.1 Ma). Due to glacial/interglacial temperature fluctuations, cold-adapted subspecies, e.g., Vitis amurensis, could re-colonize new habitats. Our results may help to elucidate the adaptive radiation of Chinese wild Vitis species in different environments.
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Affiliation(s)
- Guangya Xu
- School of Agronomy, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China
| | - Weirong Xu
- School of Food & Wine, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, People's Republic of China.
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China.
- Chinese Wine Industry Technology Institute, Yinchuan, 750021, China.
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Dong W, Liu Y, Xu C, Gao Y, Yuan Q, Suo Z, Zhang Z, Sun J. Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae). BMC Genomics 2021; 22:293. [PMID: 33888057 PMCID: PMC8060999 DOI: 10.1186/s12864-021-07590-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 04/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes. RESULTS The Distylium chloroplast genome size was 159,041-159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. CONCLUSIONS The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately.
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Affiliation(s)
- Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yongwei Gao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Qingjun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhili Suo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Tang D, Wei F, Zhou R. Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line. Sci Rep 2021; 11:5301. [PMID: 33674697 PMCID: PMC7935921 DOI: 10.1038/s41598-021-84567-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
Kenaf is a great source of bast fiber and possesses significantly industrial interests. Cytoplasmic male sterility (CMS) is the basis of heterosis utilization in kenaf. Chloroplast, an important organelle for photosynthesis, could be associated with CMS. To understand the phylogenetic position and molecular basis of kenaf CMS from the perspective of chloroplast, the chloroplast (cp) genomes of the CMS line P3A and its maintainer line P3B were characterized and their comparative analysis was also performed. In this study, the chloroplast genomes of P3B and P3A were sequenced with 163,597 bp and 163,360 bp in length, respectively. A total of 131 genes including 85 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes, and 8 ribosome RNA (rRNA) genes were annotated in P3B, while 132 genes containing 83 PCGs, 41 tRNA genes, and 8 rRNA genes were found in P3A. The phylogenetic tree revealed that kenaf was closely related to Hibiscus syriacus and Abelmoschus esculentus. Further analysis of single nucleotide polymorphism (SNP) and insertion and deletion (InDel) showed that compared with P3B, a total of 22 SNPs and 53 InDels were detected in gene coding region, gene intron, and intergenic regions of P3A. Remarkably, a total of 9 SNPs including 6 synonymous SNPs and 3 nonsynonymous SNPs were found in psbK, atpA, rpoC2, atpB, rpl20, clpP, rpoA, and ycf1. The present study provided basic information for further study of kenaf CMS mechsnism.
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Affiliation(s)
- Danfeng Tang
- grid.256609.e0000 0001 2254 5798College of Agriculture, Guangxi University, Nanning, 530004 China ,Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023 China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023 China
| | - Ruiyang Zhou
- grid.256609.e0000 0001 2254 5798College of Agriculture, Guangxi University, Nanning, 530004 China
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Zheng XH, Duan HC, Li SM, Dong Q. The complete chloroplast genome of Crateva unilocularis (Capparaceae). Mitochondrial DNA B Resour 2021; 6:658-659. [PMID: 33763540 PMCID: PMC7927983 DOI: 10.1080/23802359.2021.1878949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/27/2020] [Indexed: 11/28/2022] Open
Abstract
Crateva unilocularis is naturally distributed in Southern China, which is an elite natural tree with high edible and medicinal value. In this study, whole chloroplast (cp) genome of Crateva unilocularis was assembled and characterized on the basis of Illumina pair-end sequencing data. The complete cp genome was 156,417 bp in length, containing a large single-copy region (LSC) of 85,607 bp and a small single-copy region (SSC) of 18,164 bp, which were separated by a pair of 26,323 bp inverted repeat regions (IRs). The genome contained 128 genes, including 85 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The overall GC content is 36.32%, while the corresponding values of the LSC, SSC, and IR regions were 33.98, 29.45, and 42.48%, respectively. The maximum-likelihood phylogenetic analysis showed a strong sister relationship with Crateva tapia. These findings provide a foundation for further investigation of cp genome evolution in Crateva unilocularis and other higher plants.
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Affiliation(s)
- Xin-hua Zheng
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Kunming, China
- Forestry College, Southwest Forestry University, Kunming, China
| | - Hua-chao Duan
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Kunming, China
- Forestry College, Southwest Forestry University, Kunming, China
| | - Shi-min Li
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Kunming, China
- Forestry College, Southwest Forestry University, Kunming, China
| | - Qiong Dong
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Kunming, China
- Forestry College, Southwest Forestry University, Kunming, China
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Alzahrani DA. Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis. PLANTS 2021; 10:plants10020270. [PMID: 33573201 PMCID: PMC7911161 DOI: 10.3390/plants10020270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 12/30/2022]
Abstract
Abutilon fruticosum is one of the endemic plants with high medicinal and economic value in Saudi Arabia and belongs to the family Malvaceae. However, the plastome sequence and phylogenetic position have not been reported until this study. In this research, the complete chloroplast genome of A. fruticosum was sequenced and assembled, and comparative and phylogenetic analyses within the Malvaceae family were conducted. The chloroplast genome (cp genome) has a circular and quadripartite structure with a total length of 160,357 bp and contains 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). The repeat analyses indicate that all the types of repeats (palindromic, complement, forward and reverse) were present in the genome, with palindromic occurring more frequently. A total number of 212 microsatellites were identified in the plastome, of which the majority are mononucleotides. Comparative analyses with other species of Malvaceae indicate a high level of resemblance in gene content and structural organization and a significant level of variation in the position of genes in single copy and inverted repeat borders. The analyses also reveal variable hotspots in the genomes that can serve as barcodes and tools for inferring phylogenetic relationships in the family: the regions include trnH-psbA, trnK-rps16, psbI-trnS, atpH-atpI, trnT-trnL, matK, ycf1 and ndhH. Phylogenetic analysis indicates that A. fruticosum is closely related to Althaea officinalis, which disagrees with the previous systematic position of the species. This study provides insights into the systematic position of A. fruticosum and valuable resources for further phylogenetic and evolutionary studies of the species and the Malvaceae family to resolve ambiguous issues within the taxa.
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Affiliation(s)
- Dhafer A Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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Ichim MC, de Boer HJ. A Review of Authenticity and Authentication of Commercial Ginseng Herbal Medicines and Food Supplements. Front Pharmacol 2021; 11:612071. [PMID: 33505315 PMCID: PMC7832030 DOI: 10.3389/fphar.2020.612071] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022] Open
Abstract
Ginseng traditional medicines and food supplements are the globally top selling herbal products. Panax ginseng, Panax quinquefolius and Panax notoginseng are the main commercial ginseng species in herbal medicine. Prices of ginseng products vary widely based on the species, quality, and purity of the used ginseng, and this provides a strong driver for intentional adulteration. Our systematic literature search has reviewed the authenticity results of 507 ginseng-containing commercial herbal products sold in 12 countries scattered across six continents. The analysis of the botanical and chemical identity of all these products shows that 76% are authentic while 24% were reported as adulterated. The number of commercial products as well as the percentage of adulteration varies significantly between continents, being highest in South America (100%) and Australia (75%), and lower in Europe (35%), North America (23%), Asia (21%) and Africa (0%). At a national level, from the five countries for which more than 10 products have been successfully authenticated, the highest percentage of adulterated ginseng products were purchased from Taiwan (49%), followed by Italy (37%), China (21%), and USA (12%), while all products bought in South Korea were reported to be authentic. In most cases, labeled Panax species were substituted with other Panax species, but substitution of ginseng root, the medicinally recommended plant part, with leaves, stems or flowers was also reported. Efficient and practical authentication using biomarkers to distinguish the main ginseng varieties and secondary metabolite spectra for age determination are essential to combat adulteration in the global marketplace.
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Affiliation(s)
- Mihael Cristin Ichim
- “Stejarul” Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamt, Romania
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Yu X, Tan W, Gao H, Miao L, Tian X. Development of a Specific Mini-Barcode From Plastome and its Application for Qualitative and Quantitative Identification of Processed Herbal Products Using DNA Metabarcoding Technique: A Case Study on Senna. Front Pharmacol 2021; 11:585687. [PMID: 33390955 PMCID: PMC7773718 DOI: 10.3389/fphar.2020.585687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/26/2020] [Indexed: 01/04/2023] Open
Abstract
Herbal products play an important role globally in the pharmaceutical and healthcare industries. However, some specific groups of herbal products are easily adulterated by confused materials on the market, which seriously reduces the products’ quality. Universal conventional DNA barcodes would function poorly since the processed herbal products generally suffer from varying degrees of DNA degradation and DNA mixing during processing or manufacturing. For quality control purposes, an accurate and effective method should be provided for species identification of these herbal products. Here, we provided a strategy of developing the specific mini-barcode using Senna as an example, and by coupling with the metabarcoding technique, it realized the qualitative and quantitative identification of processed herbal products. The plastomes of Senna obtusifolia (L.) H.S.Irwin & Barneby and Senna occidentalis (L.) Link were newly assembled, and the hypervariable coding-regions were identified by comparing their genomes. Then, the specific mini-barcodes were developed based on the identified hypervariable regions. Finally, we applied the DNA metabarcoding technique to the developed mini-barcodes. Results showed that the lengths of plastomes of S. obtusifolia and S. occidentalis were 162,426 and 159,993 bp, respectively. Four hypervariable coding-regions ycf1, rpl23, petL, and matK were identified. Two specific mini-barcodes were successfully developed from matK, and the mini-barcode of primer 647F-847R was proved to be able to qualitatively and quantitatively identify these two processed Senna seeds. Overall, our study established a valuable way to develop the specific mini-barcode, which may provide a new idea for the quality control of processed herbal products.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Tan W, Gao H, Jiang W, Zhang H, Yu X, Liu E, Tian X. The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes. Sci Rep 2020; 10:16309. [PMID: 33005000 PMCID: PMC7529812 DOI: 10.1038/s41598-020-73392-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
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Affiliation(s)
- Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Weiling Jiang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Huanyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Erwei Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
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Dong W, Xu C, Wen J, Zhou S. Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae. BMC Evol Biol 2020; 20:96. [PMID: 32736519 PMCID: PMC7393888 DOI: 10.1186/s12862-020-01661-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Chloroplast genome sequence data is very useful in studying/addressing the phylogeny of plants at various taxonomic ranks. However, there are no empirical observations on the patterns, directions, and mutation rates, which are the key topics in chloroplast genome evolution. In this study, we used Calycanthaceae as a model to investigate the evolutionary patterns, directions and rates of both nucleotide substitutions and structural mutations at different taxonomic ranks. RESULTS There were 2861 polymorphic nucleotide sites on the five chloroplast genomes, and 98% of polymorphic sites were biallelic. There was a single-nucleotide substitution bias in chloroplast genomes. A → T or T → A (2.84%) and G → C or C → G (3.65%) were found to occur significantly less frequently than the other four transversion mutation types. Synonymous mutations kept balanced pace with nonsynonymous mutations, whereas biased directions appeared between transition and transversion mutations and among transversion mutations. Of the structural mutations, indels and repeats had obvious directions, but microsatellites and inversions were non-directional. Structural mutations increased the single nucleotide mutations rates. The mutation rates per site per year were estimated to be 0.14-0.34 × 10- 9 for nucleotide substitution at different taxonomic ranks, 0.64 × 10- 11 for indels and 1.0 × 10- 11 for repeats. CONCLUSIONS Our direct counts of chloroplast genome evolution events provide raw data for correctly modeling the evolution of sequence data for phylogenetic inferences.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jun Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Wei F, Tang D, Wei K, Qin F, Li L, Lin Y, Zhu Y, Khan A, Kashif MH, Miao J. The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis. Sci Rep 2020; 10:12473. [PMID: 32719421 PMCID: PMC7385175 DOI: 10.1038/s41598-020-69549-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/14/2020] [Indexed: 12/20/2022] Open
Abstract
Sophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.
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Affiliation(s)
- Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China
| | - Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China
| | - Fang Qin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China
| | - Linxuan Li
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China
| | - Yang Lin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China
| | - Yanxia Zhu
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China
| | - Aziz Khan
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, Guangxi, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, 530005, Guangxi, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, Guangxi, China.
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Sun J, Wang Y, Liu Y, Xu C, Yuan Q, Guo L, Huang L. Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species. Sci Rep 2020; 10:11466. [PMID: 32651417 PMCID: PMC7351712 DOI: 10.1038/s41598-020-67943-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/10/2020] [Indexed: 01/23/2023] Open
Abstract
Chaenomeles (family Rosaceae) is a genus of five diploid species of deciduous spiny shrubs that are native to Central Asia and Japan. It is an important horticultural crop (commonly known as flowering quinces) in Europe and Asia for its high yield in fruits that are rich in juice, aroma, and dietary fiber. Therefore, the development of effective genetic markers of Chaenomeles species is advantageous for crop improvement through breeding and selection. In this study, we successfully assembled and analyzed the chloroplast genome of five Chaenomeles species. The chloroplast genomes of the five Chaenomeles species were very similar with no structural or content rearrangements among them. The chloroplast genomes ranged from 159,436 to 160,040 bp in length and contained a total of 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Three highly variable regions, including trnR-atpA, trnL-F, and rpl32-ccsA, were identified. Phylogenetic analysis based on the complete chloroplast genome showed that Chaenomeles forms a monophyletic clade and had a close relationship with the genera Docynia and Malus. Analyses for phylogenetic relationships and the development of available genetic markers in future could provide valuable information regarding genetics and breeding mechanisms of the Chaenomeles species.
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Affiliation(s)
- Jiahui Sun
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yiheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qingjun Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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