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Taylor BA, Tembrock LR, Sankovitz M, Wilson TM, Looney C, Takahashi J, Gilligan TM, Smith-Pardo AH, Harpur BA. Population genomics of the invasive Northern Giant Hornet Vespa mandarinia in North America and across its native range. Sci Rep 2024; 14:10803. [PMID: 38734771 PMCID: PMC11088652 DOI: 10.1038/s41598-024-61534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
The northern giant hornet Vespa mandarinia (NGH) is a voracious predator of other insect species, including honey bees. NGH's native range spans subtropical and temperate regions across much of east and southeast Asia and, in 2019, exotic populations of the species were discovered in North America. Despite this broad range and invasive potential, investigation of the population genomic structure of NGH across its native and introduced ranges has thus far been limited to a small number of mitochondrial samples. Here, we present analyses of genomic data from NGH individuals collected across the species' native range and from exotic individuals collected in North America. We provide the first survey of whole-genome population variation for any hornet species, covering this species' native and invasive ranges, and in doing so confirm likely origins in Japan and South Korea for the two introductions. We additionally show that, while this introduced population exhibited strongly elevated levels of inbreeding, these signatures of inbreeding are also present in some long-standing native populations, which may indicate that inbreeding depression alone is insufficient to prevent the persistence of NGH populations. As well as highlighting the importance of ongoing monitoring and eradication efforts to limit the spread of this species outside of its natural range, our data will serve as a foundational database for future genomic studies into introduced hornet populations.
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Affiliation(s)
- Benjamin A Taylor
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Madison Sankovitz
- Department of Ecology and Evolutionary Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Telissa M Wilson
- Washington State Department of Agriculture, Olympia, WA, 98501, USA
| | - Chris Looney
- Washington State Department of Agriculture, Olympia, WA, 98501, USA
| | - Junichi Takahashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8047, Japan
| | - Todd M Gilligan
- USDA Animal and Plant Health Inspection Service (APHIS), Fort Collins, CO, 80526-1825, USA
| | - Allan H Smith-Pardo
- USDA Animal and Plant Health Inspection Service (APHIS), Fort Collins, CO, 80526-1825, USA
| | - Brock A Harpur
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
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Kang ES, Son DC, Kim SC. The complete chloroplast genome assembly of Solidago altissima (Lineaus, 1753) (Astereae; Asteraceae). Mitochondrial DNA B Resour 2024; 9:605-609. [PMID: 38720906 PMCID: PMC11078073 DOI: 10.1080/23802359.2024.2349138] [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: 02/05/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
This study aims to report the complete chloroplast genome of Solidago altissima L., a globally recognized invasive plant. The complete genome length of S. altissima is 152,961 bp; S. altissima has a typical quadripartite structure (including a large single copy of 84,829 bp, a small single copy of 18,084 bp, and two inverted repeat regions of 25,024 bp), which is commonly found in angiosperms. The genome contains 129 genes, consisting of 85 coding sequences, 36 tRNA genes, and 8 rRNA genes. To understand the phylogenetic relationship between S. altissima and its related species, maximum likelihood analysis was performed. The results revealed that S. altissima is closely related to Symphyotrichum subulatum. The findings of the present study could provide fundamental data for the future phylogenetic and evolutionary studies, while also research on species invasion and resolving complexity of S. altissima.
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Affiliation(s)
- Eun Su Kang
- Forest Biodiversity Division, Korea National Arboretum, Gyeonggi-do, Republic of Korea
| | - Dong Chan Son
- Forest Biodiversity Division, Korea National Arboretum, Gyeonggi-do, Republic of Korea
| | - Sang-Chul Kim
- Forest Biodiversity Division, Korea National Arboretum, Gyeonggi-do, Republic of Korea
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Kim JH, Doh EJ, Kim HY, Lee G. Chemical Relationship among Genetically Authenticated Medicinal Species of Genus Angelica. PLANTS (BASEL, SWITZERLAND) 2024; 13:1252. [PMID: 38732467 PMCID: PMC11085054 DOI: 10.3390/plants13091252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024]
Abstract
The genus Angelica comprises various species utilized for diverse medicinal purposes, with differences attributed to the varying levels or types of inherent chemical components in each species. This study employed DNA barcode analysis and HPLC analysis to genetically authenticate and chemically classify eight medicinal Angelica species (n = 106) as well as two non-medicinal species (n = 14) that have been misused. Nucleotide sequence analysis of the nuclear internal transcribed spacer (ITS) region revealed differences ranging from 11 to 117 bp, while psbA-trnH showed variances of 3 to 95 bp, respectively. Phylogenetic analysis grouped all samples except Angelica sinensis into the same cluster, with some counterfeits forming separate clusters. Verification using the NCBI database confirmed the feasibility of species identification. For chemical identification, a robust quantitative HPLC analysis method was developed for 46 marker compounds. Subsequently, two A. reflexa-specific and seven A. biserrata-specific marker compounds were identified, alongside non-specific markers. Moreover, chemometric clustering analysis reflecting differences in chemical content between species revealed that most samples formed distinct clusters according to the plant species. However, some samples formed mixed clusters containing different species. These findings offer crucial insights for the standardization and quality control of medicinal Angelica species.
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Affiliation(s)
- Jung-Hoon Kim
- Division of Pharmacology, School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea;
| | - Eui-Jeong Doh
- Research Center of Traditional Korean Medicine, Wonkwang University, Iksan 54538, Republic of Korea;
| | - Han-Young Kim
- School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea;
| | - Guemsan Lee
- Research Center of Traditional Korean Medicine, Wonkwang University, Iksan 54538, Republic of Korea;
- Department of Herbology, College of Korean Medicine, Wonkwang University, Iksan 54538, Republic of Korea
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Zhang L, Yi C, Xia X, Jiang Z, Du L, Yang S, Yang X. Solanum aculeatissimum and Solanum torvum chloroplast genome sequences: a comparative analysis with other Solanum chloroplast genomes. BMC Genomics 2024; 25:412. [PMID: 38671394 PMCID: PMC11046870 DOI: 10.1186/s12864-024-10190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/05/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Solanum aculeatissimum and Solanum torvum belong to the Solanum species, and they are essential plants known for their high resistance to diseases and adverse conditions. They are frequently used as rootstocks for grafting and are often crossbred with other Solanum species to leverage their resistance traits. However, the phylogenetic relationship between S. aculeatissimum and S. torvum within the Solanum genus remains unclear. Therefore, this paper aims to sequence the complete chloroplast genomes of S. aculeatissimum and S. torvum and analyze them in comparison with 29 other previously published chloroplast genomes of Solanum species. RESULTS We observed that the chloroplast genomes of S. aculeatissimum and S. torvum possess typical tetrameric structures, consisting of one Large Single Copy (LSC) region, two reverse-symmetric Inverted Repeats (IRs), and one Small Single Copy (SSC) region. The total length of these chloroplast genomes ranged from 154,942 to 156,004 bp, with minimal variation. The highest GC content was found in the IR region, while the lowest was in the SSC region. Regarding gene content, the total number of chloroplast genes and CDS genes remained relatively consistent, ranging from 128 to 134 and 83 to 91, respectively. Nevertheless, there was notable variability in the number of tRNA genes and rRNAs. Relative synonymous codon usage (RSCU) analysis revealed that both S. aculeatissimum and S. torvum preferred codons that utilized A and U bases. Analysis of the IR boundary regions indicated that contraction and expansion primarily occurred at the junction between SSC and IR regions. Nucleotide polymorphism analysis and structural variation analysis demonstrated that chloroplast variation in Solanum species mainly occurred in the LSC and SSC regions. Repeat sequence analysis revealed that A/T was the most frequent base pair in simple repeat sequences (SSR), while Palindromic and Forward repeats were more common in long sequence repeats (LSR), with Reverse and Complement repeats being less frequent. Phylogenetic analysis indicated that S. aculeatissimum and S. torvum belonged to the same meristem and were more closely related to Cultivated Eggplant. CONCLUSION These findings enhance our comprehension of chloroplast genomes within the Solanum genus, offering valuable insights for plant classification, evolutionary studies, and potential molecular markers for species identification.
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Affiliation(s)
- Longhao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Chengqi Yi
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Xin Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Lihui Du
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Shixin Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China
| | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, 225009, Yangzhou, China.
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Kang ES, Kim SC, Lee SR, Park BK, Son DC. The complete chloroplast genome assembly of Commelina caroliniana Walter (Commelinaceae). Mitochondrial DNA B Resour 2024; 9:546-550. [PMID: 38665929 PMCID: PMC11044756 DOI: 10.1080/23802359.2024.2345126] [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: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
We sequenced and published the chloroplast genome of Commelina caroliniana Walter, which was previously misidentified as C. diffusa owing to their morphological similarities until 1989. The genome of C. caroliniana is 160,857 bp long [large single copy region: 88,064 bp; a small single copy region: 18,549 bp; two inverted repeat regions: 27,122 bp] and has a GC content of 35.7%. The genome comprises 133 genes, including 87 coding sequences (CDSs), 38 tRNAs, and eight rRNAs. The phylogenetic relationship between C. caroliniana and related species was analyzed using the maximum likelihood method based on the 79 CDSs of the chloroplast genome. Phylogenetic analysis revealed that C. caroliniana is closely related to C. communis. Our findings will contribute to studies on species identification and phylogenetic and evolutionary research. These results enhance our understanding of the Commelina genus.
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Affiliation(s)
- Eun Su Kang
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Gyeonggi-do, Republic of Korea
| | - Sang-Chul Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Gyeonggi-do, Republic of Korea
| | - Se Ryeong Lee
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Gyeonggi-do, Republic of Korea
| | - Beom Kyun Park
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Gyeonggi-do, Republic of Korea
| | - Dong Chan Son
- Forest Biodiversity Division, Korea National Arboretum, Pocheon-si, Gyeonggi-do, Republic of Korea
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Zhang S, Han S, Bi D, Yang J, Ge W, Ye Y, Gao J, Dai C, Kan X. Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective. Genes (Basel) 2024; 15:444. [PMID: 38674379 PMCID: PMC11049395 DOI: 10.3390/genes15040444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.
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Affiliation(s)
- Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China; (S.Z.); (S.H.); (J.Y.); (Y.Y.); (J.G.)
| | - Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China; (S.Z.); (S.H.); (J.Y.); (Y.Y.); (J.G.)
| | - De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China;
| | - Jianke Yang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China; (S.Z.); (S.H.); (J.Y.); (Y.Y.); (J.G.)
- School of Basic Medical Sciences, Wannan Medical College, Wuhu 241002, China
| | - Wen Ge
- School of Food and Bioengineering, Wuhu Institute of Technology, Wuhu 241003, China;
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China; (S.Z.); (S.H.); (J.Y.); (Y.Y.); (J.G.)
| | - Jinming Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China; (S.Z.); (S.H.); (J.Y.); (Y.Y.); (J.G.)
| | - Chenwei Dai
- Anhui Academy of Medical Sciences, Anhui Medical College, Hefei 230061, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China; (S.Z.); (S.H.); (J.Y.); (Y.Y.); (J.G.)
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Huang L, Xu Y, Valcárcel V, Lutz S, Wen J, Ren Z. Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae. BMC Genom Data 2024; 25:30. [PMID: 38491489 PMCID: PMC10943888 DOI: 10.1186/s12863-024-01200-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/30/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy. RESULTS The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship. CONCLUSIONS Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.
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Affiliation(s)
- Lan Huang
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Yujie Xu
- School of Geosciences, Qinghai Normal University, 810008, Xining, Qinghai, China
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidady Cambio Global (CIBC-UAM) , Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Sue Lutz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA.
| | - Zhumei Ren
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China.
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Wang D, Wei J, Yuan X, Chen Z, Wang L, Geng Y, Zhang J, Wang Y. Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield. Heliyon 2024; 10:e27223. [PMID: 38455575 PMCID: PMC10918223 DOI: 10.1016/j.heliyon.2024.e27223] [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: 07/06/2023] [Revised: 02/10/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Paclitaxel is a potent anti-cancer drug that is mainly produced through semi-synthesis, which still requires plant materials as precursors. The content of paclitaxel and 10-deacetyl baccatin III (10-DAB) in Taxus yunnanensis has been found to differ from that of other Taxus species, but there is little research on the mechanism underlying the variation in paclitaxel content in T. yunnanensis of different provenances. In this experiment, the contents of taxoids and precursors in twigs between a high paclitaxel-yielding individual (TG) and a low paclitaxel-yielding individual (TD) of T. yunnanensis were compared, and comparative analyses of transcriptomes as well as chloroplast genomes were performed. High-performance liquid chromatography (HPLC) detection showed that 10-DAB and baccatin III contents in TG were 18 and 47 times those in TD, respectively. Transcriptomic analysis results indicated that genes encoding key enzymes in the paclitaxel biosynthesis pathway, such as taxane 10-β-hydroxylase (T10βH), 10-deacetylbaccatin III 10-O-acetyltransferase (DBAT), and debenzoyl paclitaxel N-benzoyl transferase (DBTNBT), exhibited higher expression levels in TG. Additionally, qRT-PCR showed that the relative expression level of T10βH and DBAT in TG were 29 and 13 times those in TD, respectively. In addition, six putative transcription factors were identified that may be involved in paclitaxel biosynthesis from transcriptome data. Comparative analysis of plastid genomes showed that the TD chloroplast contained a duplicate of rps12, leading to a longer plastid genome length in TD relative to TG. Fifteen mutation hotspot regions were identified between the two plastid genomes that can serve as candidate DNA barcodes for identifying high-paclitaxel-yield individuals. This experiment provides insight into the difference in paclitaxel accumulation among different provenances of T. yunnanensis individuals.
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Affiliation(s)
- Dong Wang
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Jiansheng Wei
- Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau, Diqing, 674402, China
| | - Xiaolong Yuan
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Zhonghua Chen
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Lei Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Yunfen Geng
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Jinfeng Zhang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
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Gao Y, Chen T, Long J, Shen G, Tian Z. Complete chloroplast genome and comparison of herbicides toxicity on Aeschynomene indica (Leguminosae) in upland direct-seeding paddy field. BMC Genomics 2024; 25:277. [PMID: 38486176 PMCID: PMC10938726 DOI: 10.1186/s12864-024-10102-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: 12/07/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Indian jointvetch (Aeschynomene indica) is a common and pernicious weed found in the upland direct-seeding rice fields in the lower reaches of the Yangtze River in China. However, there are few reports on the degree of harm, genetic characteristics, and management methods of this weed. The purpose of this study is to clarify the harm of Indian jointvetch to upland direct-seeding rice, analyze the genetic characteristics of this weed based on chloroplast genomics and identify its related species, and screen herbicides that are effective in managing this weed in upland direct-seeding rice fields. RESULTS In a field investigation in upland direct-seeding rice paddies in Shanghai and Jiangsu, we determined that the plant height and maximum lateral distance of Indian jointvetch reached approximately 134.2 cm and 57.9 cm, respectively. With Indian jointvetch present at a density of 4/m2 and 8/m2, the yield of rice decreased by approximately 50% and 70%, respectively. We further obtained the first assembly of the complete chloroplast (cp.) genome sequence of Indian jointvetch (163,613 bp). There were 161 simple sequence repeats, 166 long repeats, and 83 protein-encoding genes. The phylogenetic tree and inverted repeat region expansion and contraction analysis based on cp. genomes demonstrated that species with closer affinity to A. indica included Glycine soja, Glycine max, and Sesbania cannabina. Moreover, a total of 3281, 3840, and 3838 single nucleotide polymorphisms were detected in the coding sequence regions of the cp. genomes of S. cannabina voucher IBSC, G. soja, and G. max compared with the A. indica sequence, respectively. A greenhouse pot experiment indicated that two pre-emergence herbicides, saflufenacil and oxyfluorfen, and two post-emergence herbicides, florpyrauxifen-benzyl and penoxsulam, can more effectively manage Indian jointvetch than other common herbicides in paddy fields. The combination of these two types of herbicides is recommended for managing Indian jointvetch throughout the entire growth period of upland direct-seeding rice. CONCLUSIONS This study provides molecular resources for future research focusing on the identification of the infrageneric taxa, phylogenetic resolution, and biodiversity of Leguminosae plants, along with recommendations for reliable management methods to control Indian jointvetch.
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Affiliation(s)
- Yuan Gao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, 201403, Shanghai, China
| | - TianYu Chen
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 201418, Shanghai, China
| | - Jiaqi Long
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 201418, Shanghai, China
| | - Guohui Shen
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, 201403, Shanghai, China.
| | - Zhihui Tian
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, 201403, Shanghai, China.
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Park H, Park JH, Kang YJ. Characterization of the complete chloroplast genome of Wolffia arrhiza and comparative genomic analysis with relative Wolffia species. Sci Rep 2024; 14:5873. [PMID: 38467810 PMCID: PMC10928178 DOI: 10.1038/s41598-024-56394-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
Lemnoideae, commonly referred to as the duckweed, are aquatic plants found worldwide. Wolffia species are known for their extreme reduction in size and complexity, lacking both roots and leaves, and they hold the distinction of being the smallest plants among angiosperms. Interestingly, it belongs to the Araceae family, despite its apparent morphological differences from land plants in the same family. Traditional morphological methods have limitations in classifying these plants, making molecular-level information essential. The chloroplast genome of Wolffia arrhiza is revealed that a total length of 169,602 bp and a total GC content of 35.78%. It follows the typical quadripartite structure, which includes a large single copy (LSC, 92,172 bp) region, a small single copy (SSC, 13,686 bp) region, and a pair of inverted repeat (IR, 31,872 bp each) regions. There are 131 genes characterized, comprising 86 Protein-Coding Genes, 37 Transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Moreover, 48 simple sequence repeats and 32 long repeat sequences were detected. Comparative analysis between W. arrhiza and six other Lemnoideae species identified 12 hotspots of high nucleotide diversity. In addition, a phylogenetic analysis was performed using 14 species belonging to the Araceae family and one external species as an outgroup. This analysis unveiled W. arrhiza and Wolffia globosa as closely related sister species. Therefore, this research has revealed the complete chloroplast genome data of W. arrhiza, offering a more detailed understanding of its evolutionary position and phylogenetic categorization within the Lemnoideae subfamily.
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Affiliation(s)
- Halim Park
- Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | | | - Yang Jae Kang
- Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, Jinju, 52828, Republic of Korea.
- Division of Life Science Department at Gyeongsang National University, Jinju, Republic of Korea.
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11
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Jiang Y, Yang J, Folk RA, Zhao J, Liu J, He Z, Peng H, Yang S, Xiang C, Yu X. Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes. BMC PLANT BIOLOGY 2024; 24:181. [PMID: 38468197 PMCID: PMC10926627 DOI: 10.1186/s12870-024-04882-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group. RESULTS Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters. CONCLUSION This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.
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Affiliation(s)
- Yinzi Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, 39762, MS, USA
| | - Jianli Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, Yunnan, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhengshan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Shixiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Chunlei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xiangqin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Zhao S, Gao X, Yu X, Yuan T, Zhang G, Liu C, Li X, Wei P, Li X, Liu X. Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation. Int J Mol Sci 2024; 25:2193. [PMID: 38396871 PMCID: PMC10888623 DOI: 10.3390/ijms25042193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.
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Affiliation(s)
- Shuqi Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoman Gao
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Xiaolei Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tao Yuan
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Guiyu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xinzhong Li
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan 430072, China;
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
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13
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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14
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Thongjued K, Garcia K, Scott D, Gonthier DJ, Dupuis JR. DNA metabarcoding diet analysis in a generalist omnivore: feeding trials reveal the efficacy of extraction kits and a multi-locus approach for identifying diverse diets. Integr Zool 2024. [PMID: 38297429 DOI: 10.1111/1749-4877.12806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Metabarcoding-based diet analysis is a valuable tool for understanding the feeding behavior of a wide range of species. However, many studies using these methods for wild animals assume accuracy and precision without experimental evaluation with known positive control food items. Here, we conducted a feeding trial experiment with a positive control community in pasture-raised chickens and assessed the efficacy of several commonly used DNA extraction kits and primer sets. We hand-fed 22 known food items, including insects and plants, to six backyard laying hens and collected their excreta for eight h. We evaluated the efficacy of three DNA extraction kits, three primer sets for plant identification (targeting rbcL, trnL, and internal transcribed spacer 2 [ITS2]), and three primer sets for arthropod identification (targeting cytochrome oxidase subunit I [COI]). The detection success rate of our positive control food items was highly variable, ranging from 2.04% to 93.88% for all kit/primer combinations and averaging 37.35% and 43.57% for the most effective kit/primer combination for plants and insects, respectively. Extraction kits using bead-based homogenization positively affected the recovery proportion of plant and insect DNA in excreta samples. The minimum time to detect known food items was 44 min post-feeding. Two COI primer sets significantly outperformed the third, and both recovery proportion and taxonomic resolution from ITS2 were significantly higher than those from rbcL and trnL. Taken together, these results display the potential variability that can be inherently present in DNA-based diet analyses and highlight the utility of experimental feeding trials in validating such approaches, particularly for omnivores with diverse diets.
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Affiliation(s)
- Kantima Thongjued
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Karina Garcia
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Delia Scott
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - David J Gonthier
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
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15
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Quaresma A, Ankenbrand MJ, Garcia CAY, Rufino J, Honrado M, Amaral J, Brodschneider R, Brusbardis V, Gratzer K, Hatjina F, Kilpinen O, Pietropaoli M, Roessink I, van der Steen J, Vejsnæs F, Pinto MA, Keller A. Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. Sci Data 2024; 11:129. [PMID: 38272945 PMCID: PMC10810873 DOI: 10.1038/s41597-024-02962-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.
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Affiliation(s)
- Andreia Quaresma
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, S/N, Edifício FC4, 4169-007, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Vila do Conde, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Vila do Conde, Portugal
| | - Markus J Ankenbrand
- Center for Computational and Theoretical Biology, Faculty of Biology, Julius-Maximilians-Universität Würzburg, Klara-Oppenheimer-Weg 32, 97074, Würzburg, Germany
| | - Carlos Ariel Yadró Garcia
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - José Rufino
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Research Centre in Digitalization and Intelligent Robotics (CeDRI), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Mónica Honrado
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Joana Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Robert Brodschneider
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Valters Brusbardis
- Latvian Beekeepers' Association (LBA), Rigas iela 22, LV-3004, Jelgava, Latvia
| | - Kristina Gratzer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Fani Hatjina
- Ellinikos Georgikos Organismos DIMITRA (ELGO- DIMITRA), Kourtidou 56-58, GR-11145, Athina, Greece
| | - Ole Kilpinen
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - Marco Pietropaoli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri" (IZSLT), Via Appia Nuova 1411, IT-00178, Roma, Italy
| | - Ivo Roessink
- Wageningen Environmental Research, WageningenUniversity&Research, Droevendaalsesteeg 3, 6700 AA, Wageningen, Netherlands
| | | | - Flemming Vejsnæs
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Alexander Keller
- Cellular and Organismic Interactions, Biocenter, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany.
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Song BN, Liu CK, Zhao AQ, Tian RM, Xie DF, Xiao YL, Chen H, Zhou SD, He XJ. Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses. BMC PLANT BIOLOGY 2024; 24:70. [PMID: 38263006 PMCID: PMC10807117 DOI: 10.1186/s12870-024-04750-0] [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: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution. RESULTS In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074-86,197 bp), a small single copy region (SSC: 17,047-17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176-26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33-52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68-25.28 Ma). CONCLUSION The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.
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Affiliation(s)
- Bo-Ni Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - An-Qi Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Rong-Ming Tian
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yu-Lin Xiao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huai Chen
- 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, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Hou D, Lin H, Feng Y, Zhou K, Li X, Yang Y, Wang S, Yang X, Wang J, Zhao H, Zhang X, Fan J, Lu S, Wang D, Zhu L, Ju D, Chen YZ, Zeng X. CMAUP database update 2024: extended functional and association information of useful plants for biomedical research. Nucleic Acids Res 2024; 52:D1508-D1518. [PMID: 37897343 PMCID: PMC10767869 DOI: 10.1093/nar/gkad921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/23/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023] Open
Abstract
Knowledge of the collective activities of individual plants together with the derived clinical effects and targeted disease associations is useful for plant-based biomedical research. To provide the information in complement to the established databases, we introduced a major update of CMAUP database, previously featured in NAR. This update includes (i) human transcriptomic changes overlapping with 1152 targets of 5765 individual plants, covering 74 diseases from 20 027 patient samples; (ii) clinical information for 185 individual plants in 691 clinical trials; (iii) drug development information for 4694 drug-producing plants with metabolites developed into approved or clinical trial drugs; (iv) plant and human disease associations (428 737 associations by target, 220 935 reversion of transcriptomic changes, 764 and 154121 associations by clinical trials of individual plants and plant ingredients); (v) the location of individual plants in the phylogenetic tree for navigating taxonomic neighbors, (vi) DNA barcodes of 3949 plants, (vii) predicted human oral bioavailability of plant ingredients by the established SwissADME and HobPre algorithm, (viii) 21-107% increase of CMAUP data over the previous version to cover 60 222 chemical ingredients, 7865 plants, 758 targets, 1399 diseases, 238 KEGG human pathways, 3013 gene ontologies and 1203 disease ontologies. CMAUP update version is freely accessible at https://bidd.group/CMAUP/index.html.
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Affiliation(s)
- Dongyue Hou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hanbo Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuhan Feng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Kaicheng Zhou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xingxiu Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuan Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Shuaiqi Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xue Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiayu Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hui Zhao
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiajun Fan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - SongLin Lu
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Dan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Lyuhan Zhu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yu Zong Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
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Choudhary A, Shekhawat D, Pathania J, Sita K, Sharma S, Chawla A, Jaiswal V. Exploring DNA barcode for accurate identification of threatened Aconitum L. species from Western Himalaya. Mol Biol Rep 2024; 51:75. [PMID: 38175298 DOI: 10.1007/s11033-023-08927-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Aconitum species, belonging to Ranunculaceae, have high medicinal importance but due to their overexploitation come under IUCN (International Union for Conservation of Nature) red list. The precise identification of the Aconitum species is equally important because they are used in herbal formulations. The present study aimed to develop an efficient DNA barcode system for the authentic identification of Aconitum species. METHODS AND RESULTS A set of 92 barcode gene sequences (including 12 developed during the present study and 80 retrieved from NCBI) of 5 Aconitum species (A. heterophyllum, A. vialoceum, A. japonicum, A. napellus, and A. stapfianum) were analyzed using three methods (tree-based, distance-based, and similarity-based) for species discrimination. The PWG-distance method was found most effective for species discrimination. The discrimination rate of PWG- distance ranged from 33.3% (rbcL + trnH-psbA) to 100% (ITS, rbcL + ITS, ITS + trnH-psbA and rbcL + ITS + trnH-psbA). Among DNA barcodes and their combinations, the ITS marker had the highest degree of species discrimination (NJ-40%, PWG-100% and BLAST-40%), followed by trnH-psbA (NJ-20%, PWG-60% and BLAST-20%). ITS also had higher barcoding gap as compared to other individual barcodes and their combinations. Further, we also analyzed six Aconitum species (A. balfourii, A. ferox, A. heterophyllum, A. rotundifolium, A. soongaricum and A. violaceum) existing in Western Himalaya. These species were distinguished clearly through tree-based method using the ITS barcode gene with 100% species resolution. CONCLUSION ITS showed the best species discrimination power and was used to develop species-specific barcodes for Aconitum species. DNA barcodes developed during the present study can be used to identify Aconitum species.
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Affiliation(s)
- Anita Choudhary
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Deepika Shekhawat
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Jyotsna Pathania
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Kumari Sita
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shailika Sharma
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Amit Chawla
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Vandana Jaiswal
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Elwick KE, Damaso N, Robertson JM. DNA Barcoding and Metabarcoding Protocols for Species Identification. Methods Mol Biol 2024; 2744:155-169. [PMID: 38683317 DOI: 10.1007/978-1-0716-3581-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.
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Affiliation(s)
- Kyleen E Elwick
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA
| | - Natalie Damaso
- Counter WMD Systems, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, MA, USA
| | - James M Robertson
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA.
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20
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Wasti QZ, Sabar MF, Farooq A, Khan MU. Stepping towards pollen DNA metabarcoding: A breakthrough in forensic sciences. Forensic Sci Med Pathol 2023:10.1007/s12024-023-00770-8. [PMID: 38147285 DOI: 10.1007/s12024-023-00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
This review is engaged in determining the capability of plant pollen as a significant source of evidence for the linkage between suspects and crime location in forensic sciences. Research and review articles were collected from Google Scholar, the Web of Science, and PubMed. Articles were searched using specific keywords such as "Forensic Palynology," "Pollen metabarcoding," "Plant forensics," and "Pollen" AND "criminal investigation." Boolean logic was also utilized to narrow the articles to be included in this review article. Through the literature and exploratory research, it has been observed in the current study that with advancements in technology, forensic palynology has found its application in creating an association between the crime scene and suspected individuals to have a link to it, as pollen DNA is a long-lasting investigative tool that can effectively help forensic investigations. Moreover, the literature shows that the DNA of pollen and spores has helped forensic scientists link suspects to crime scenes, and the introduction of pollen DNA metabarcoding tools has eased the efforts of palynologists to analyze pollen DNA. The introduction of DNA metabarcoding techniques to analyze pollen from plants has helped identify the geological locations of the plants and ultimately identify the culprit.
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Affiliation(s)
- Qandeel Zaineb Wasti
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Abeera Farooq
- Punjab University College of Pharmacy, University of the Punjab, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
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21
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Hu H, Wang Q, Hao G, Zhou R, Luo D, Cao K, Yan Z, Wang X. Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome. PeerJ 2023; 11:e16642. [PMID: 38099308 PMCID: PMC10720482 DOI: 10.7717/peerj.16642] [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: 05/17/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Abstract
Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.
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Affiliation(s)
- Huan Hu
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Qian Wang
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Guoqian Hao
- School of Life Science and Food Engineering, Yibin University, Yibin, China
| | - Ruitao Zhou
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Dousheng Luo
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Kejun Cao
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Zhimeng Yan
- School of Medical Information Engineering, Zunyi Medical University, Zunyi, China
| | - Xinyu Wang
- Key Laboratory of Medical Electrophysiology, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Krawczyk K, Paukszto Ł, Maździarz M, Sawicki J. The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1275377. [PMID: 38143577 PMCID: PMC10739336 DOI: 10.3389/fpls.2023.1275377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023]
Abstract
Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Liu DK, Zhou CY, Tu XD, Zhao Z, Chen JL, Gao XY, Xu SW, Zeng MY, Ma L, Ahmad S, Li MH, Lan S, Liu ZJ. Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes. BMC Genomics 2023; 24:749. [PMID: 38057701 DOI: 10.1186/s12864-023-09847-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that is mainly distributed in tropical or subtropical forest canopies. This rare and threatened orchid lacks molecular resources for phylogenetic and barcoding analysis. Therefore, we sequenced and assembled seven complete plastomes of Chiloschista to analyse the plastome characteristics and phylogenetic relationships and conduct a barcoding investigation. RESULTS We are the first to publish seven Chiloschista plastomes, which possessed the typical quadripartite structure and ranged from 143,233 bp to 145,463 bp in size. The plastomes all contained 120 genes, consisting of 74 protein-coding genes, 38 tRNA genes and eight rRNA genes. The ndh genes were pseudogenes or lost in the genus, and the genes petG and psbF were under positive selection. The seven Chiloschista plastomes displayed stable plastome structures with no large inversions or rearrangements. A total of 14 small inversions (SIs) were identified in the seven Chiloschista plastomes but were all similar within the genus. Six noncoding mutational hotspots (trnNGUU-rpl32 > rpoB-trnCGCA > psbK-psbI > psaC-rps15 > trnEUUC-trnTGGU > accD-psaI) and five coding sequences (ycf1 > rps15 > matK > psbK > ccsA) were selected as potential barcodes based on nucleotide diversity and species discrimination analysis, which suggested that the potential barcode ycf1 was most suitable for species discrimination. A total of 47-56 SSRs and 11-14 long repeats (> 20 bp) were identified in Chiloschista plastomes, and they were mostly located in the large single copy intergenic region. Phylogenetic analysis indicated that Chiloschista was monophyletic. It was clustered with Phalaenopsis and formed the basic clade of the subtribe Aeridinae with a moderate support value. The results also showed that seven Chiloschista species were divided into three major clades with full support. CONCLUSION This study was the first to analyse the plastome characteristics of the genus Chiloschista in Orchidaceae, and the results showed that Chiloschista plastomes have conserved plastome structures. Based on the plastome hotspots of nucleotide diversity, several genes and noncoding regions are suitable for phylogenetic and population studies. Chiloschista may provide an ideal system to investigate the dynamics of plastome evolution and DNA barcoding investigation for orchid studies.
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Affiliation(s)
- Ding-Kun Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cheng-Yuan Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiong-De Tu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhuang Zhao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jin-Liao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu-Yong Gao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shao-Wei Xu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng-Yao Zeng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liang Ma
- Fujian Health College, Fuzhou, 350101, Fujian, China
| | - Sagheer Ahmad
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ming-He Li
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Khemira H, Mahdhi M, Afzal M, Oteef MD, Tounekti T, AL-Faifi Z, Alsolami W. Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding. PeerJ 2023; 11:e16486. [PMID: 38025745 PMCID: PMC10680449 DOI: 10.7717/peerj.16486] [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: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.
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Affiliation(s)
- Habib Khemira
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
| | - Mosbah Mahdhi
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
- Laboratory of Biodiversity and Valorization of Bioresources in Arid Zones, Faculty of Sciences of Gabes, University of Gabes, Gabes, Tunisia
| | - Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed D.Y. Oteef
- Department of Chemistry, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Taieb Tounekti
- Laboratory of Process Engineering & Industrial Systems (LR11ES54), National Engineering School of Gabes, University of Gabes, Gabes, Tunisia
| | - Zarraq AL-Faifi
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Wail Alsolami
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
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25
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Jin L, Shi HY, Li T, Zhao N, Xu Y, Xiao TW, Song F, Ma CX, Li QM, Lin LX, Shao XN, Li BH, Mi XC, Ren HB, Qiao XJ, Lian JY, Du H, Ge XJ. A DNA barcode library for woody plants in tropical and subtropical China. Sci Data 2023; 10:819. [PMID: 37993453 PMCID: PMC10665436 DOI: 10.1038/s41597-023-02742-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.
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Affiliation(s)
- Lu Jin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hao-You Shi
- Central South Academy of Inventory and Planning of NFGA, Changsha, 410014, China
| | - Ting Li
- Yiyang Forestry Bureau, Yiyang, 413000, China
| | - Nan Zhao
- Hunan Police Academy, Changsha, 410138, China
| | - Yong Xu
- Conghua Middle School, Guangzhou, 510900, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Feng Song
- College of Forestry, Central South University of Forestry & Technology, Changsha, 410004, China
| | - Chen-Xin Ma
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650201, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiao-Na Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bu-Hang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Bao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiu-Juan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ju-Yu Lian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hu Du
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Lee M, Lee HY, Kang JS, Lee H, Park KJ, Park JY, Yang TJ. Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA. PLoS One 2023; 18:e0294457. [PMID: 37983242 PMCID: PMC10659177 DOI: 10.1371/journal.pone.0294457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Allium ulleungense (AU) and A. microdictyon (AM) are valuable medicinal and edible vegetables, referred to as mountain garlic in Korea. The identification of AU, AM and a neighboring species A. ochotense (AO) is difficult because of their morphological similarities. We collected samples from three species and 46 cultivated collections to understand the genetic diversity of these valuable Allium species. Among them, we sequenced six collections, including three species and three cultivating collections to obtain data from the plastid genome (plastome) and nuclear 45S ribosomal DNA (nrDNA) for super-barcoding. The AM and AO showed around 60 single nucleotide polymorphisms (SNPs) and 39 Insertion/Deletion (InDels) in the plastome but no variations in the nrDNA sequences. Conversely, the AU and AM showed more than 170 SNPs and 80 InDels in the plastomes, and 20 SNPs and 1 InDel were found in the 45S nrDNA sequences. Among the three cultivating collections, one TB collection was determined to be the AU type in both plastome and nrDNA sequences. However, the other two collections, JB and SA, showed the AM type plastome but were heterozygous in the 45S nrDNA sequences, indicating both AU and AM types (putative AM x AU hybrid). Ten molecular markers were developed based on sequence variations to identify these three species and assess their genetic diversity. A total of 49 collections were genotyped using the ten developed markers and classified into five groups: 14 AU, 22 AM, 1 AO, 3 putative AM x AU hybrids, and 9 putative AU x AM hybrid collections. Super-barcoding with plastomes and nrDNAs revealed the genetic diversity of the three Allium species and putative hybrids between species. The newly developed markers will facilitate species and hybrid identification, thereby benefiting marker-assisted molecular breeding of Allium species.
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Affiliation(s)
- Minyoung Lee
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyo Young Lee
- Gangwondo State Agricultural Research & Extension Services, Wild Vegetable Research Institute, Pyeongchang-gun, Gangwon State, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeji Lee
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ki-Jin Park
- Gangwondo State Agricultural Research & Extension Services, Wild Vegetable Research Institute, Pyeongchang-gun, Gangwon State, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
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Dziedzic E, Sidlauskas B, Cronn R, Anthony J, Cornwell T, Friesen TA, Konstantinidis P, Penaluna BE, Stein S, Levi T. Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA. Mol Ecol Resour 2023; 23:1880-1904. [PMID: 37602732 DOI: 10.1111/1755-0998.13855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
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Affiliation(s)
- Emily Dziedzic
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brian Sidlauskas
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Cronn
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - James Anthony
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Trevan Cornwell
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Thomas A Friesen
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Peter Konstantinidis
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brooke E Penaluna
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - Staci Stein
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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Chen X, Li B, Zhang X. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Sci Rep 2023; 13:18731. [PMID: 37907468 PMCID: PMC10618267 DOI: 10.1038/s41598-023-45421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
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Affiliation(s)
- Xiaoli Chen
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Buyu Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
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Su H, Ding X, Liao B, Zhang D, Huang J, Bai J, Xu S, Zhang J, Xu W, Qiu X, Gong L, Huang Z. Comparative chloroplast genomes provided insights into the evolution and species identification on the Datureae plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1270052. [PMID: 37941675 PMCID: PMC10628451 DOI: 10.3389/fpls.2023.1270052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Generally, chloroplast genomes of angiosperms are always highly conserved but carry a certain number of variation among species. In this study, chloroplast genomes of 13 species from Datureae tribe that are of importance both in ornamental gardening and medicinal usage were studied. In addition, seven chloroplast genomes from Datureae together with two from Solanaceae species retrieved from the National Center for Biotechnology Information (NCBI) were integrated into this study. The chloroplast genomes ranged in size from 154,686 to 155,979 and from 155,497 to 155,919 bp for species of Datura and Brugmansia, respectively. As to Datura and Brugmansia, a total of 128 and 132 genes were identified, in which 83 and 87 protein coding genes were identified, respectively; Furthermore, 37 tRNA genes and 8 rRNA genes were both identified in Datura and Brugmansia. Repeats analysis indicated that the number and type varied among species for Simple sequence repeat (SSR), long repeats, and tandem repeats ranged in number from 53 to 59, 98 to 99, and 22 to 30, respectively. Phylogenetic analysis based on the plastid genomes supported the monophyletic relationship among Datura and Brugmansia and Trompettia, and a refined phylogenic relationships among each individual was resolved. In addition, a species-specific marker was designed based on variation spot that resulted from a comparative analysis of chloroplast genomes and verified as effective maker for identification of D. stramonium and D. stramonium var. inermis. Interestingly, we found that 31 genes were likely to be under positive selection, including genes encoding ATP protein subunits, photosystem protein subunit, ribosome protein subunits, NAD(P)H dehydrogenase complex subunits, and clpP, petB, rbcL, rpoCl, ycf4, and cemA genes. These genes may function as key roles in the adaption to diverse environment during evolution. The diversification of Datureae members was dated back to the late Oligocene periods. These chloroplast genomes are useful genetic resources for taxonomy, phylogeny, and evolution for Datureae.
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Affiliation(s)
- He Su
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaoxia Ding
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Baosheng Liao
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danchun Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juan Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Junqi Bai
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Subing Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jing Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Wen Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaohui Qiu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Lu Gong
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Zhihai Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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Mehmetoğlu E, Kaymaz Y, Ateş D, Kahraman A, Tanyolaç MB. The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species. Sci Rep 2023; 13:17871. [PMID: 37857674 PMCID: PMC10587350 DOI: 10.1038/s41598-023-44599-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The Cicer reticulatum is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of C. reticulatum consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of C. reticulatum was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between C. reticulatum and C. arietinum. Phylogenetic analysis further indicated that the closest evolutionary relative to C. arietinum was C. reticulatum, whereas the previously sequenced wild Cicer species displayed slight distinctions across their entire coding regions. Several genomic regions, such as clpP and ycf1, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the Cicer genus. The first complete cp genome sequence of C. reticulatum will provide novel insights for future genetic research on Cicer crops.
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Affiliation(s)
- Ezgi Mehmetoğlu
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Yasin Kaymaz
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Duygu Ateş
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Abdullah Kahraman
- Faculty of Agriculture, Department of Field Crops, Harran University, S. Urfa, 64000, Şanlıurfa, Turkey
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Zhang SD, Ling LZ. Comparative and phylogenetic analyses of the chloroplast genomes of Filipendula species (Rosoideae, Rosaceae). Sci Rep 2023; 13:17748. [PMID: 37853204 PMCID: PMC10584953 DOI: 10.1038/s41598-023-45040-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023] Open
Abstract
Genus Filipendula (Rosoideae, Rosaceae) comprises about 15 species and mainly distributed in Northern Hemisphere. The phylogenetic relationships based on the nrITS marker are not consistent with the traditional taxonomic systems of the genus. Here, we first analysed the complete chloroplast (cp) genomes of seven Filipendula species (including two varieties of F. palmate). Our results indicated that the cp genomes of Filipendula species had few changes in size, ranging from 154,205 bp to 154,633 bp and the average of 36.63% GC content. A total of 126 annotated genes had the identical order and orientation, implying that the cp genome structure of Filipendula species was rather conserved. However, the cp genomes of Filipendula species exhibited structural differences, including gene loss, transposition and inversion when compared to those of other genera of Rosoideae. Moreover, SSRs with the different number were observed in the cp genome of each Filipendula species and sequence divergence mainly occurred in noncoding regions, in which four mutational hotspots were identified. In contrast, only two positive selection genes (matK and rps8) were found. Phylogenetic and molecular-dating analysis indicated that Filipendula species were divergent from other genera of Rosoideae at about 82.88 Ma. Additionally, Filipendula species from East Asia were split at about 9.64 Ma into two major clades. These results provide a basis for further studying the infrageneric classification of Filipendula.
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Affiliation(s)
- Shu-Dong Zhang
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, 553004, China
| | - Li-Zhen Ling
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, 553004, China.
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Yan R, Geng Y, Jia Y, Xiang C, Zhou X, Hu G. Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1265641. [PMID: 37828930 PMCID: PMC10565954 DOI: 10.3389/fpls.2023.1265641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023]
Abstract
Introduction The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. Methods In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. Results The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Discussion Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.
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Affiliation(s)
- Rongrong Yan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yanfei Geng
- College of Tea Science, Guizhou University, Guiyang, Guizhou, China
| | - Yuhuan Jia
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Chunlei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xinxin Zhou
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Guoxiong Hu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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Wang H, Chen Y, Wang L, Liu Q, Yang S, Wang C. Advancing herbal medicine: enhancing product quality and safety through robust quality control practices. Front Pharmacol 2023; 14:1265178. [PMID: 37818188 PMCID: PMC10561302 DOI: 10.3389/fphar.2023.1265178] [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: 07/22/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
This manuscript provides an in-depth review of the significance of quality control in herbal medication products, focusing on its role in maintaining efficiency and safety. With a historical foundation in traditional medicine systems, herbal remedies have gained widespread popularity as natural alternatives to conventional treatments. However, the increasing demand for these products necessitates stringent quality control measures to ensure consistency and safety. This comprehensive review explores the importance of quality control methods in monitoring various aspects of herbal product development, manufacturing, and distribution. Emphasizing the need for standardized processes, the manuscript delves into the detection and prevention of contaminants, the authentication of herbal ingredients, and the adherence to regulatory standards. Additionally, it highlights the integration of traditional knowledge and modern scientific approaches in achieving optimal quality control outcomes. By emphasizing the role of quality control in herbal medicine, this manuscript contributes to promoting consumer trust, safeguarding public health, and fostering the responsible use of herbal medication products.
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Affiliation(s)
- Hongting Wang
- Anhui Provincial Engineering Laboratory for Screening and Re-evaluation of Active Compounds of Herbal Medicines in Southern Anhui, Anhui Provincial Engineering Research Center for Polysaccharide Drugs, Anhui Innovative Center for Drug Basic Research of Metabolic Diseases, School of Pharmacy, Wannan Medical College, Wuhu, China
| | | | | | | | | | - Cunqin Wang
- Anhui Provincial Engineering Laboratory for Screening and Re-evaluation of Active Compounds of Herbal Medicines in Southern Anhui, Anhui Provincial Engineering Research Center for Polysaccharide Drugs, Anhui Innovative Center for Drug Basic Research of Metabolic Diseases, School of Pharmacy, Wannan Medical College, Wuhu, China
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Hu HS, Mao JY, Wang X, Liang YZ, Jiang B, Zhang DQ. Plastid phylogenomics and species discrimination in the "Chinese" clade of Roscoea (Zingiberaceae). PLANT DIVERSITY 2023; 45:523-534. [PMID: 37936815 PMCID: PMC10625918 DOI: 10.1016/j.pld.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 03/30/2023] [Indexed: 11/09/2023]
Abstract
Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the "Chinese" clade and the "Himalayan" clade. Despite extensive research on the genus, Roscoea species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the "Chinese" clade of Roscoea and as DNA super barcodes for species discrimination. We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the "Chinese" clade of Roscoea can be divided into four distinct subclades. Furthermore, our analysis supported the independence of R. cautleoides var. pubescens, the recovery of Roscoea pubescens Z.Y. Zhu, and a close relationship between R. humeana and R. cautloides. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species. These limitations are likely related to the complex history of Roscoea speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.
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Affiliation(s)
- Hai-Su Hu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Jiu-Yang Mao
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Yu-Ze Liang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Bei Jiang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali 671000, Yunnan, China
| | - De-Quan Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali 671000, Yunnan, China
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Yu D, Pei Y, Cui N, Zhao G, Hou M, Chen Y, Chen J, Li X. Comparative and phylogenetic analysis of complete chloroplast genome sequences of Salvia regarding its worldwide distribution. Sci Rep 2023; 13:14268. [PMID: 37652950 PMCID: PMC10471775 DOI: 10.1038/s41598-023-41198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023] Open
Abstract
Salvia is widely used as medicine, food, and ornamental plants all over the world, with three main distribution centers, the Central and western Asia/Mediterranean (CAM), the East Aisa (EA), and the Central and South America (CASA). Along with its large number of species and world-wide distribution, Salvia is paraphyletic with multiple diversity. Chloroplast genomes (CPs) are useful tools for analyzing the phylogeny of plants at lower taxonomic levels. In this study, we reported chloroplast genomes of five species of Salvia and performed phylogenetic analysis with current available CPs of Salvia. Repeated sequence analysis and comparative analysis of Salvia CPs were also performed with representative species from different distribution centers. The results showed that the genetic characters of the CPs are related to the geographic distribution of plants. Species from CAM diverged first to form a separate group, followed by species from EA, and finally species from CASA. Larger variations of CPs were observed in species from CAM, whereas more deficient sequences and less repeated sequences in the CPs were observed in species from CASA. These results provide valuable information on the development and utilization of the worldwide genetic resources of Salvia.
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Affiliation(s)
- Dade Yu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ning Cui
- Shandong Academy of Chinese Medicine, Jinan, 250014, China
| | - Guiping Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Mengmeng Hou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Yingying Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jialei Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China.
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Xu XM, Wei Z, Sun JZ, Zhao QF, Lu Y, Wang ZL, Zhu SX. Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2023; 14:1163065. [PMID: 37583593 PMCID: PMC10425225 DOI: 10.3389/fpls.2023.1163065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.
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Affiliation(s)
| | | | | | | | | | | | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Zhang Z, Mu W, Kong W, Liu J, Zhao J, Zhao Q, Shi M, Zhao H, Liu J, Shi L. Validation of the shotgun metabarcoding approach for comprehensively identifying herbal products containing plant, fungal, and animal ingredients. PLoS One 2023; 18:e0286069. [PMID: 37399206 DOI: 10.1371/journal.pone.0286069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/08/2023] [Indexed: 07/05/2023] Open
Abstract
Identifying plant, fungal, and animal ingredients in a specific mixture remains challenging during the limitation of PCR amplification and low specificity of traditional methods. Genomic DNA was extracted from mock and pharmaceutical samples. Four type of DNA barcodes were generated from shotgun sequencing dataset with the help of a local bioinformatic pipeline. Taxa of each barcode was assigned by blast to TCM-BOL, BOLD, and GenBank. Traditional methods including microscopy, thin layer chromatography (TLC), and high-performance liquid chromatography (HPLC) were carried out according to Chinese pharmacopoeia. On average, 6.8 Gb shotgun reads were sequenced from genomic DNA of each sample. Then, 97, 11, 10, 14, and one operational taxonomic unit (OTU) were generated for ITS2, psbA-trnH, rbcL, matK, and COI, respectively. All the labeled ingredients including eight plant, one fungal, and one animal species were successfully detected in both the mock and pharmaceutical samples, in which Chebulae Fructus, Poria, and Fritilariae Thunbergia Bulbus were identified via mapping reads to organelle genomes. In addition, four unlabeled plant species were detected from pharmaceutical samples, while 30 genera of fungi, such as Schwanniomyces, Diaporthe, Fusarium were detected from mock and pharmaceutical samples. Furthermore, the microscopic, TLC, and HPLC analysis were all in accordance with the standards stipulated by Chinese Pharmacopoeia. This study indicated that shotgun metabarcoding could simultaneously identified plant, fungal, and animal ingredients in herbal products, which has the ability to serve as a valuable complement to traditional methods.
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Affiliation(s)
- Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weishan Mu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jiali Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jingyi Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Qing Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Mengmeng Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Hongye Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Linchun Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Xu XM, Liu DH, Zhu SX, Wang ZL, Wei Z, Liu QR. Phylogeny of Trigonotis in China-with a special reference to its nutlet morphology and plastid genome. PLANT DIVERSITY 2023; 45:409-421. [PMID: 37601540 PMCID: PMC10435912 DOI: 10.1016/j.pld.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 08/22/2023]
Abstract
The genus Trigonotis comprises nearly 60 species mainly distributed in East and Southeast Asia. China has the largest number of Trigonotis species in the world, with a total of 44 species, of which 38 are endemic. Nutlet morphology is useful for the taxonomic delimitation of Trigonotis. However, there are still controversial circumscriptions of nutlet shape in some species. In previous studies, interspecies phylogenetic relationships were inferred using few DNA markers and very few taxa, which possibly led to erroneous or incomplete conclusions. In this study, the nutlet morphology of 39 Trigonotis taxa and the characteristics of 34 complete chloroplast genomes (29 taxa) were investigated and analyzed. Then, the phylogenetic relationships were discussed within this genus based on complete chloroplast genomes. To the best of our knowledge, this study is the first comprehensive analysis of nutlet morphology and complete chloroplast genome of Trigonotis. Based on nutlet morphology, Trigonotis can be divided into two groups: Group 1, hemispherical or oblique tetrahedron with carpopodiums, and Group 2, inverted tetrahedron without carpopodiums. The chloroplast genome of Trigonotis exhibited a typical quadripartite structure, including 84-86 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes, with a total length of 147,247-148,986 bp. Genes in the junctions were well conserved in Trigonotis, similar to those in other Boraginaceae s.str. species. Furthermore, Trigonotis chloroplast genomes showed relatively high diversity, with more conserved genic regions than intergenic regions; in addition, we detected 14 hot spots (Pi > 0.005) in non-coding regions. Phylogenetic analyses based on chloroplast genome data identified highly resolved relationships between Trigonotis species. Specifically, Trigonotis was divided into two clades with strong support: one clade included species with hemispherical or oblique tetrahedron nutlets with carpopodiums and bracts, whereas the other clade included species with inverted tetrahedron nutlets without carpopodiums or bracts. Our results may inform future taxonomic, phylogenetic, and evolutionary studies on Boraginaceae.
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Affiliation(s)
- Xue-Min Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Dan-Hui Liu
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhen-Long Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhen Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Quan-Ru Liu
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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Gao Y, Li S, Yuan G, Fang J, Shen G, Tian Z. Comparison of Biological and Genetic Characteristics between Two Most Common Broad-Leaved Weeds in Paddy Fields: Ammannia arenaria and A. multiflora (Lythraceae). BIOLOGY 2023; 12:936. [PMID: 37508367 PMCID: PMC10375975 DOI: 10.3390/biology12070936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/16/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023]
Abstract
Ammannia arenaria and A. multifloras, morphologically similar at the seedling stage, are the most common broad-leaved weeds in paddy fields. Our study showed that A. arenaria occupied more space than A. multifloras when competing with rice. However, A. multifloras germination has lower temperature adaptability. No difference in sensitivity to common herbicides between two Ammannia species was observed. Chloroplast (cp) genomes could be conducive to clarify their genetic relationship. The complete cp genome sequences of A. arenaria (158,401 bp) and A. multiflora (157,900 bp) were assembled for the first time. In A. arenaria, there were 91 simple sequence repeats, 115 long repeats, and 86 protein-encoding genes, one, sixteen, and thirty more than those in A. multiflora. Inverted repeats regions expansion and contraction and the phylogenetic tree based on cp genomes demonstrated the closely relationship between the two species. However, in A. arenaria, 20 single nucleotide polymorphisms in the CDS region were detected compared to A. multiflora, which can be used to distinguish the two species. Moreover, there was one unique gene, infA, only in A. arenaria. This study provides reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure, and biodiversity of Ammannia species.
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Affiliation(s)
- Yuan Gao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Shenghui Li
- College of Agriculture, Anshun University, Anshun 561000, China
| | - Guohui Yuan
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jiapeng Fang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guohui Shen
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Zhihui Tian
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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Zhou N, Tang L, Xie P, Miao K, Yang C, Liu H, Ji Y. Genome skimming as an efficient tool for authenticating commercial products of the pharmaceutically important Paris yunnanensis (Melanthiaceae). BMC PLANT BIOLOGY 2023; 23:344. [PMID: 37380980 DOI: 10.1186/s12870-023-04365-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Paris yunnanensis (Melanthiaceae) is a traditional Chinese medicinal plant of significant pharmaceutical importance. Due to previous taxonomic confusion, a congeneric species, Paris liiana, has been mistaken for P. yunnanensis and cultivated on a large scale, leading to the mixing of commercial products (i.e., seedlings and processed rhizomes) of P. yunnanensis with those of P. liiana. This may have adverse effects on quality control in the standardization of P. yunnanensis productions. As the lack of PCR amplifiable genomic DNA within processed rhizomes is an intractable obstacle to the authentication of P. yunnanensis products using PCR-based diagnostic tools, this study aimed to develop a PCR-free method to authenticate commercial P. yunnanensis products, by applying genome skimming to generate complete plastomes and nrDNA arrays for use as the molecular tags. RESULTS Based on a dense intraspecies sampling of P. liiana and P. yunnanensis, the robustness of the proposed authentication systems was evaluated by phylogenetic inferences and experimental authentication of commercial seedling and processed rhizome samples. The results indicate that the genetic criteria of both complete plastomes and nrDNA arrays were consistent with the species boundaries to achieve accurate discrimination of P. yunnanensis and P. liinna. Owing to its desirable accuracy and sensitivity, genome skimming can serve as an effective and sensitive tool for monitoring and controlling the trade of P. yunnanensis products. CONCLUSION This study provides a new way to solve the long-standing problem of the molecular authentication of processed plant products due to the lack of PCR amplifiable genomic DNA. The proposed authentication system will support quality control in the standardization of P. yunnanensis products in cultivation and drug production. This study also provides molecular evidence to clarify the long-standing taxonomic confusion regarding the species delimitation of P. yunnanensis, which will contribute to the rational exploration and conservation of the species.
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Affiliation(s)
- Nian Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lilei Tang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Pingxuan Xie
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengjin Yang
- Yunnan Baiyao Group, Chinese Medicinal Resources Co. LTD, Kunming, China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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Xu Q, Li Z, Wu N, Yang J, Yuan L, Zhao T, Sima Y, Xu T. Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes (Basel) 2023; 14:1262. [PMID: 37372442 DOI: 10.3390/genes14061262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The genus Houpoea belongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species of Houpoea: Houpoea officinalis var officinalis (OO), Houpoea officinalis var. biloba (OB), and Houpoea rostrata (R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these three Houpoea plants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the three Houpoea plants, it is highly conservative, with only changes between H. rostrata and the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label for Houpoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates that Houpoea is a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties of H. officinalis var. officinalis, H. rostrata, H. officinalis var. biloba, Houpoea obovate, and Houpoea tripetala, which evolved and differentiated from the ancestors of Houpoea to the present Houpoea in the above order. This study provides valuable information on the genus Houpoea, enriches the CPG information on Houpoea genus, and provides genetic resources for the further classification of and phylogenetic research on Houpoea.
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Affiliation(s)
- Qinbin Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Zhuoran Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Nannan Wu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Jing Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Lang Yuan
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Tongxing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yongkang Sima
- Kunming Arboretum, Yunnan Academy of Forestry & Grassland Science, Kunming 650201, China
| | - Tao Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
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Shi W, Hu S, Song W, Huang Y, Shi C, Wang S. Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus ( Rhamnaceae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:855-869. [PMID: 37520808 PMCID: PMC10382440 DOI: 10.1007/s12298-023-01331-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01331-7.
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Affiliation(s)
- Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Siqi Hu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Yahui Huang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204 China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
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Kim KR, Park SY, Kim H, Hong JM, Kim SY, Yu JN. Complete Chloroplast Genome Determination of Ranunculus sceleratus from Republic of Korea (Ranunculaceae) and Comparative Chloroplast Genomes of the Members of the Ranunculus Genus. Genes (Basel) 2023; 14:1149. [PMID: 37372329 DOI: 10.3390/genes14061149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE, ndhF, rpl23, atpF, rps4, and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses.
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Affiliation(s)
- Kang-Rae Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - So Young Park
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Heesoo Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Jeong Min Hong
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Sun-Yu Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Jeong-Nam Yu
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
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Chen J, Zhou K, Hu X. Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China. Genes (Basel) 2023; 14:genes14051083. [PMID: 37239444 DOI: 10.3390/genes14051083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
The differences in cpDNA SNPs and InDels of 13 samples from single trees of different species or populations of oil-tea camellia in South China were examined in this study, and phylogenetic trees were reconstructed based on CDSs and non-CDSs of cpDNAs to research the evolutionary relationships among all samples. The SNPs of all samples included all kinds of substitutions, and the frequency of the transition from AT to GC was highest; meanwhile, the frequencies of all kinds of transversions differed among the samples, and the SNPs exhibited polymorphism. The SNPs were distributed in all the different functional regions of cpDNAs, and approximately half of all SNPs in exons led to missense mutations and the gain or loss of termination codons. There were no InDels in the exons of any cpDNA samples, except those retrieved from Camellia gigantocarpa, although this InDel did not lead to a frame shift. The InDels of all cpDNA samples were unevenly distributed in the intergenic region and upstream and downstream of genes. The genes, regions of the same gene, sites and mutation types in the same region related to the distributions of SNPs, and InDels were inconsistent among samples. The 13 samples were divided into 2 clades and 7 or 6 subclades, and the samples of species from the same sections of the Camellia genus did not belong to the same subclades. Meanwhile, the genetic relationship between the samples of Camellia vietnamensis and the undetermined species from Hainan Province or the population of C. gauchowensis in Xuwen was closer than that between C. vietnamensis and the population of C. gauchowensis in Luchuan, and the genetic relationship among C. osmantha, C. vietnamensis and C. gauchowensis was very close. In sum, SNPs and InDels in the different cpDNAs resulted in variable phenotypes among the different species or populations, and they could be developed into molecular markers for studies on species and population identification and phylogenetic relationships. The conclusion from the identification of undetermined species from Hainan Province and the phylogenetic relationships among 13 oil-tea camellia samples based on cpCDS and cpnon-CDS sequences were the same as those from the former report.
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Affiliation(s)
- Jing Chen
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
| | - Kaibing Zhou
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
| | - Xinwen Hu
- School of Life Science, Hainan University, Haikou 570228, China
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Wang X, Bai S, Zhang Z, Zheng F, Song L, Wen L, Guo M, Cheng G, Yao W, Gao Y, Li J. Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1179009. [PMID: 37229122 PMCID: PMC10203424 DOI: 10.3389/fpls.2023.1179009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K A/K S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.
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Affiliation(s)
- Xiaomin Wang
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Shengyi Bai
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Fushun Zheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lina Song
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Lu Wen
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
| | - Meng Guo
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Guoxin Cheng
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Wenkong Yao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Yanming Gao
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jianshe Li
- College of Enology and Horticultrue, Ningxia University, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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Ahmad W, Asaf S, Al-Rawahi A, Al-Harrasi A, Khan AL. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci Rep 2023; 13:7436. [PMID: 37156827 PMCID: PMC10167353 DOI: 10.1038/s41598-023-34477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, USA.
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Zhai Y, Zhang T, Guo Y, Gao C, Zhou L, Feng L, Zhou T, Xumei W. Phylogenomics, phylogeography and germplasms authentication of the Rheum palmatum complex based on complete chloroplast genomes. JOURNAL OF PLANT RESEARCH 2023; 136:291-304. [PMID: 36808315 DOI: 10.1007/s10265-023-01440-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
As a traditional Chinese medicine, rhubarb is used to treat several diseases such as severe acute pancreatitis, sepsis and chronic renal failure. However, few studies focused on the authentication of germplasm for the Rheum palmatum complex, and no studies have been conducted to elucidate the evolutionary history of the R. palmatum complex using plastome datasets. Hence, we aim to develop the potential molecular markers to identify the elite germplasms of rhubarb and explore the divergence and biogeographic history of the R. palmatum complex based on the newly sequenced chloroplast genome datasets. Chloroplast genomes of thirty-five the R. palmatum complex germplasms were sequenced, and the length ranged from 160,858 to 161,204 bp. The structure, gene content and gene order were highly conserved across all genomes. Eight InDels and sixty-one SNPs loci could be used to authenticate the high-quality germplasms of rhubarb in specific areas. Phylogenetic analysis revealed that all rhubarb germplasms were clustered in the same clade with high bootstrap support values and Bayesian posterior probabilities. According to the molecular dating result, the intraspecific divergence of the complex occurred in the Quaternary, which might be affected by climatic fluctuation. The biogeography reconstruction indicated that the ancestor of the R. palmatum complex might originate from the Himalaya-Hengduan Mountains or/and Bashan-Qinling Mountains, and then spread to surrounding areas. Several useful molecular markers were developed to identify rhubarb germplasms, and our study will provide further understanding on speciation, divergence and biogeography of the R. palmatum complex.
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Affiliation(s)
- Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanbing Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Wang Xumei
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Gu YF, Shu JP, Lu YJ, Shen H, Shao W, Zhou Y, Sun QM, Chen JB, Liu BD, Yan YH. Insights into cryptic speciation of quillworts in China. PLANT DIVERSITY 2023; 45:284-301. [PMID: 37397601 PMCID: PMC10311115 DOI: 10.1016/j.pld.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/24/2022] [Accepted: 11/08/2022] [Indexed: 07/04/2023]
Abstract
Cryptic species are commonly misidentified because of high morphological similarities to other species. One group of plants that may harbor large numbers of cryptic species is the quillworts (Isoëtes spp.), an ancient aquatic plant lineage. Although over 350 species of Isoëtes have been reported globally, only ten species have been recorded in China. The aim of this study is to better understand Isoëtes species diversity in China. For this purpose, we systematically explored the phylogeny and evolution of Isoëtes using complete chloroplast genome (plastome) data, spore morphology, chromosome number, genetic structure, and haplotypes of almost all Chinese Isoëtes populations. We identified three ploidy levels of Isoëtes in China-diploid (2n = 22), tetraploid (2n = 44), and hexaploid (2n = 66). We also found four megaspore and microspore ornamentation types in diploids, six in tetraploids, and three in hexaploids. Phylogenetic analyses confirmed that I. hypsophila as the ancestral group of the genus and revealed that Isoëtes diploids, tetraploids, and hexaploids do not form monophyletic clades. Most individual species possess a single genetic structure; however, several samples have conflicting positions on the phylogenetic tree based on SNPs and the tree based on plastome data. All 36 samples shared 22 haplotypes. Divergence time analysis showed that I. hypsophila diverged in the early Eocene (∼48.05 Ma), and most other Isoëtes species diverged 3-20 Ma. Additionally, different species of Isoëtes were found to inhabit different water systems and environments along the Yangtze River. These findings provide new insights into the relationships among Isoëtes species in China, where highly similar morphologic populations may harbor many cryptic species.
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Affiliation(s)
- Yu-Feng Gu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jiang-Ping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yi-Jun Lu
- Zhejiang University City College, Hangzhou, 310015, China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wen Shao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yan Zhou
- Jiande Xin'anjiang Forest Farm, Jiande, 311600, China
| | - Qi-Meng Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Jian-Bing Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Bao-Dong Liu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
| | - Yue-Hong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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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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Alshegaihi RM, Mansour H, Alrobaish SA, Al Shaye NA, Abd El-Moneim D. The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis. Genes (Basel) 2023; 14:genes14050976. [PMID: 37239336 DOI: 10.3390/genes14050976] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).
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Affiliation(s)
- Rana M Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hassan Mansour
- Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Shouaa A Alrobaish
- Department of Biology, College of Science, Qassim University, Buraydah 52377, Saudi Arabia
| | - Najla A Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
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