1
|
Chi Y, Liu C, Liu W, Tian X, Hu J, Wang B, Liu D, Liu Y. Population genetic variation and geographic distribution of suitable areas of Coptis species in China. FRONTIERS IN PLANT SCIENCE 2024; 15:1341996. [PMID: 38567137 PMCID: PMC10985201 DOI: 10.3389/fpls.2024.1341996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
Introduction The rhizomes of Coptis plants have been used in traditional Chinese medicine over 2000 years. Due to increasing market demand, the overexploitation of wild populations, habitat degradation and indiscriminate artificial cultivation of Coptis species have severely damaged the native germplasms of species in China. Methods Genome-wide simple-sequence repeat (SSR) markers were developed using the genomic data of C. chinensis. Population genetic diversity and structure of 345 Coptis accessions collected from 32 different populations were performed based on these SSRs. The distribution of suitable areas for three taxa in China was predicted and the effects of environmental variables on genetic diversity in relation to different population distributions were further analyzed. Results 22 primer pairs were selected as clear, stable, and polymorphic SSR markers. These had an average of 16.41 alleles and an average polymorphism information content (PIC) value of 0.664. In the neighbor-joining (N-J) clustering analysis, the 345 individuals clustered into three groups, with C. chinensis, C. chinensis var. brevisepala and C. teeta being clearly separated. All C. chinensis accessions were further divided into four subgroups in the population structure analysis. The predicted distributions of suitable areas and the environmental variables shaping these distributions varied considerably among the three species. Discussion Overall, the amount of solar radiation, precipitation and altitude were the most important environmental variables influencing the distribution and genetic variation of three species. The findings will provide key information to guide the conservation of genetic resources and construction of a core reserve for species.
Collapse
Affiliation(s)
- Yujie Chi
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Changli Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Wei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xufang Tian
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Juan Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Bo Wang
- Hubei Institute for Drug Control, Wuhan, China
| | - Di Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Hubei Key Laboratory of Chinese Medicine Resource and Chemistry, Hubei University of Chinese Medicine, Wuhan, China
| |
Collapse
|
2
|
Tian X, Sang Z, Lan Z, Liu W, Feng Y, Hu J, Chen F, Liu Y. Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation. BMC PLANT BIOLOGY 2023; 23:426. [PMID: 37710158 PMCID: PMC10500821 DOI: 10.1186/s12870-023-04442-1] [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: 10/06/2022] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Galla chinensis is a traditional Chinese medicine (TCM) produced due to the interaction between the Fordinae aphids and the Rhus plant species. Horned galls with high tannin content are the most widely cultivated gall type, and Wufeng county of Hubei province in China is the center of cultivation. However, long-term artificial cultivation and domestication of horned galls to meet the increasing production demand have led to quality degradation. Understanding the reasons underlying quality degradation is urgent for horned gall production and application. The present study used a combination of metabolic, genetic, and ecological analyses to investigate the quality and genetic differentiation of the horned galls under long-term domestication as well as the potential relationships between them. RESULTS Analysis of gallic acid content and other three phenotypic traits (fresh weight, gall size, and wall thickness) revealed quality differentiation of horned galls collected from five locations in Wufeng, in which the cultivated samples from Wang Jiaping (WJP) showed the highest degradation. Genetic differentiation between the cultivated and wild Rhus chinensis trees in WJP, and between WJP and the other populations was detected based on SSR molecular markers, however, no significant difference in genetic structure was seen for the aphid populations. Among the various ecological factors examined, temperature was identified as the primary one affecting the quality of horned galls. CONCLUSIONS Both genetic and ecological factors caused quality differentiation of horned galls. The collection of diverse germplasm of host trees and aphids will help reduce the quality degradation of horned galls in Wufeng.
Collapse
Affiliation(s)
- Xufang Tian
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Ziyang Sang
- Forestry Science Research Institute of Wufeng County, Yichang, 443400, People's Republic of China
| | - Zhaohui Lan
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Wei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Ying Feng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Juan Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China
| | - Faju Chen
- Biotechnology Research Center, China Three Gorges University, Yichang, 443002, People's Republic of China
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, People's Republic of China.
| |
Collapse
|
3
|
Shen Y, Li W, Zeng Y, Li Z, Chen Y, Zhang J, Zhao H, Feng L, Ma D, Mo X, Ouyang P, Huang L, Wang Z, Jiao Y, Wang HB. Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli. Nat Commun 2022; 13:3511. [PMID: 35717499 PMCID: PMC9206139 DOI: 10.1038/s41467-022-31121-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/06/2022] [Indexed: 12/26/2022] Open
Abstract
Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development. The ploidy level of patchouli, an aromatic plant in the Lamiaceae family, remain unclear. Here, the authors assemble a chromosome-level and haplotype-resolved genome for patchouli and reveal that it is tetraploid hybrid as well as compensated aneuploidy.
Collapse
Affiliation(s)
- Yanting Shen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China. .,State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
| | - Wanying Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Zeng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhipeng Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yiqiong Chen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jixiang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lingfang Feng
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China
| | - Dongming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China
| | - Xiaolu Mo
- School of Traditional Chinese Medicine, Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Puyue Ouyang
- School of Traditional Chinese Medicine, Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Lili Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zheng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Bin Wang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China. .,Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China. .,State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
| |
Collapse
|
4
|
Full-Length SMRT Transcriptome Sequencing and SSR Analysis of Bactrocera dorsalis (Hendel). INSECTS 2021; 12:insects12100938. [PMID: 34680707 PMCID: PMC8537375 DOI: 10.3390/insects12100938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022]
Abstract
Simple Summary In this study, a full-length transcriptome was analyzed with single-molecule real-time (SMRT) sequencing, which was first used to discover simple sequence repeat (SSR) genetic markers from B. dorsalis. Moreover, SSR markers from isoforms were screened for the identification of species diversity. These results could provide molecular biology methods for further population research. Abstract Bactrocera dorsalis (Hendel), as one of the most notorious and destructive invasive agricultural pests in the world, causes damage to over 250 different types of fruits and vegetables throughout tropical and subtropical areas. PacBio single-molecule real-time (SMRT) sequencing was used to generate the full-length transcriptome data of B. dorsalis. A total of 40,319,890 subreads (76.6 Gb, clean reads) were generated, including 535,241 circular consensus sequences (CCSs) and 386,916 full-length non-concatemer reads (FLNCs). Transcript cluster analysis of the FLNC reads revealed 22,780 high-quality reads (HQs). In total, 12,274 transcripts were functionally annotated based on four different databases. A total of 1978 SSR loci were distributed throughout 1714 HQ transcripts, of which 1926 were complete SSRs and 52 were complex SSRs. Among the total SSR loci, 2–3 nucleotide repeats were dominant, occupying 83.62%, of which di- and tri- nucleotide repeats were 39.38% and 44.24%, respectively. We detected 105 repeat motifs, of which AT/AT (50.19%), AC/GT (39.15%), CAA/TTG (32.46%), and ACA/TGT (10.86%) were the most common in di- and tri-nucleotide repeats. The repeat SSR motifs were 12–190 bp in length, and 1638 (88.02%) were shorter than 20 bp. According to the randomly selected microsatellite sequence, 80 pairs of primers were designed, and 174 individuals were randomly amplified by PCR using primers. The number of primers that had amplification products with clear bands and showed good polymorphism came to 41, indicating that this was a feasible way to explore SSR markers from the transcriptomic data of B. dorsalis. These results lay a foundation for developing highly polymorphic microsatellites for researching the functional genomics, population genetic structure, and genetic diversity of B. dorsalis.
Collapse
|
5
|
Poursalavati A, Rashidi-Monfared S, Ebrahimi A. Toward understanding of the methoxylated flavonoid biosynthesis pathway in Dracocephalum kotschyi Boiss. Sci Rep 2021; 11:19549. [PMID: 34599246 PMCID: PMC8486745 DOI: 10.1038/s41598-021-99066-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/05/2021] [Indexed: 01/26/2023] Open
Abstract
Nowadays, with the development and advancement of next-generation sequencing technologies, a new path has been provided for transcriptomic studies. In this study, the transcriptome of Dracocephalum kotschyi Boiss., as an endemic and endangered plant which is contained a large amount of valuable secondary metabolites with antioxidant and anticancer properties, was sequenced. Then functional annotation and gene ontology analysis for 165,597 assembled transcripts were performed, most were associated with the metabolic pathways. This might be because there are various active biochemical pathways in this plant. Furthermore, after comprehensive transcript annotation, the putative genes involved in the main metabolic pathways of D. kotschyi were identified. Then, the biosynthetic pathway of its valuable methoxylated flavones was proposed. Finally, the accumulations of important methoxylated-flavone metabolites in three different tissues were quantified by HPLC. The relative expression of the genes involved in the proposed pathway was investigated by qRT-PCR, which indicated high expression levels in the bud tissue. The present results may lead to the design strategies to preserve the genetic diversity of endangered D. kotschyi plants and apply the new methods for engineering its valuable methoxylated-flavones pathway.
Collapse
Affiliation(s)
- Abdonaser Poursalavati
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.,Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, QC, Canada.,Department of Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Sajad Rashidi-Monfared
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran
| |
Collapse
|
6
|
Shen Y, Wang J, Shaw RK, Yu H, Sheng X, Zhao Z, Li S, Gu H. Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli ( Brassica oleracea L. var. italica) in China. FRONTIERS IN PLANT SCIENCE 2021; 12:655254. [PMID: 34149754 PMCID: PMC8213352 DOI: 10.3389/fpls.2021.655254] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.
Collapse
Affiliation(s)
- Yusen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ranjan K. Shaw
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
7
|
Genome survey of Zanthoxylum bungeanum and development of genomic-SSR markers in congeneric species. Biosci Rep 2021; 40:225368. [PMID: 32558907 PMCID: PMC7322109 DOI: 10.1042/bsr20201101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 01/13/2023] Open
Abstract
Zanthoxylum bungeanum, a spice and medicinal plant, is cultivated in many parts of China and some countries in Southeast Asia; however, data on its genome are lacking. In the present study, we performed a whole-genome survey and developed novel genomic-SSR markers of Z. bungeanum. Clean data (∼197.16 Gb) were obtained and assembled into 11185221 scaffolds with an N50 of 183 bp. K-mer analysis revealed that Z. bungeanum has an estimated genome size of 3971.92 Mb, and the GC content, heterozygous rate, and repeat sequence rate are 37.21%, 1.73%, and 86.04%, respectively. These results indicate that the genome of Z. bungeanum is complex. Furthermore, 27153 simple sequence repeat (SSR) loci were identified from 57288 scaffolds with a minimum length > 1 kb. Mononucleotide repeats (19706) were the most abundant type, followed by dinucleotide repeats (5154). The most common motifs were A/T, followed by AT/AT; these SSRs accounted for 71.42% and 11.84% of all repeats, respectively. A total of 21243 non-repeating primer pairs were designed, and 100 were randomly selected and validated by PCR analysis using DNA from 10 Z. bungeanum individuals and 5 Zanthoxylum armatum individuals. Finally, 36 polymorphic SSR markers were developed with polymorphism information content (PIC) values ranging from 0.16 to 0.75. Cluster analysis revealed that Z. bungeanum and Z. armatum could be divided into two major clusters, suggesting that these newly developed SSR markers are useful for genetic diversity and germplasm resource identification in Z. bungeanum and Z. armatum.
Collapse
|
8
|
Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri. PLANTS 2021; 10:plants10030487. [PMID: 33807587 PMCID: PMC8000228 DOI: 10.3390/plants10030487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022]
Abstract
The Viburnum genus is of particular interest to horticulturalists, phylogeneticists, and biogeographers. Despite its popularity, there are few existing molecular markers to investigate genetic diversity in this large genus, which includes over 160 species. There are also few polymorphic molecular tools that can delineate closely related species within the genus. Viburnum farreri, a member of the Solenotinus subclade and one of the centers of diversity for Viburnum, was selected for DNA sequencing and development of genomic simple sequence repeats (gSSRs). In this study, 15 polymorphic gSSRs were developed and characterized for a collection of 19 V. farreri samples. Number of alleles per locus ranged from two- to- eight and nine loci had four or more alleles. Observed heterozygosity ranged from 0 to 0.84 and expected heterozygosity ranged from 0.10 to 0.80 for the 15 loci. Shannon diversity index values across these loci ranged from 0.21 to 1.62. The markers developed in this study add to the existing molecular toolkit for the genus and will be used in future studies investigating cross-transferability, genetic variation, and species and cultivar delimitation in the Viburnum genus and closely allied genera in the Adoxaceae and Caprifoliaceae.
Collapse
|
9
|
Development and technical application of SSR-based individual identification system for Chamaecyparis taiwanensis against illegal logging convictions. Sci Rep 2020; 10:22095. [PMID: 33328522 PMCID: PMC7744516 DOI: 10.1038/s41598-020-79061-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 11/24/2020] [Indexed: 11/23/2022] Open
Abstract
Chamaecyparis taiwanensis is an endemic plant suffering illegal logging in Taiwan for its high economic value. Lack of direct evidence to correlate stump and timber remains a hurdle for law enforcement. In this report, 23 polymorphic Genomic Simple Sequence Repeat (gSSR) and 12 Expressed Sequence Tag (EST)-SSR markers were developed and their transferability was assessed. The individual identification system built from selected non-linkage 30 SSR markers has a combined probability of identity as 5.596 × 10–12 equivalents to identifying an individual in a population of up to 18 million C. taiwanensis with 99.99% confidence level. We also applied the system in an actual criminal case by selecting 19 of these markers to correlate illegally felled timbers and victim trees. Our data demonstrate that molecular signals from three timbers hit with three victim trees with confidence level more than 99.99%. This is the first example of successfully applying SSR in C. taiwanensis as a court evidence for law enforcement. The identification system adapted advanced molecular technology and exhibits its great potential for natural resource management on C. taiwanensis.
Collapse
|
10
|
Liu M, Hu X, Wang X, Zhang J, Peng X, Hu Z, Liu Y. Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data. FRONTIERS IN PLANT SCIENCE 2020; 11:600249. [PMID: 33424898 PMCID: PMC7785966 DOI: 10.3389/fpls.2020.600249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/02/2020] [Indexed: 05/16/2023]
Abstract
Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon's information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.
Collapse
Affiliation(s)
- Man Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xin Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xu Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xubing Peng
- Hubei Kangnong Seed Co., Ltd., Yichang, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- *Correspondence: Zhigang Hu,
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
- Yifei Liu,
| |
Collapse
|
11
|
Fu L, Ding Z, Kumpeangkeaw A, Tan D, Han B, Sun X, Zhang J. De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:133-142. [PMID: 32158126 PMCID: PMC7036385 DOI: 10.1007/s12298-019-00726-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 09/11/2019] [Accepted: 10/18/2019] [Indexed: 05/12/2023]
Abstract
Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, ~ 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) > 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri- (14.9%), tetra- (4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM ≤ 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.
Collapse
Affiliation(s)
- Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Anuwat Kumpeangkeaw
- International College, Huazhong Agricultural University, Wuhan, 430070 China
- Department of Agriculture, Song Khla Agricultural Research and Development Center, Ministry of Agriculture and Cooperatives, Had Yai, Song Khla 90110 Thailand
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, 571101 China
| |
Collapse
|
12
|
Zhang C, Liu T, Yuan X, Huang H, Yao G, Mo X, Xue X, Yan H. The plastid genome and its implications in barcoding specific-chemotypes of the medicinal herb Pogostemon cablin in China. PLoS One 2019; 14:e0215512. [PMID: 30986249 PMCID: PMC6464210 DOI: 10.1371/journal.pone.0215512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/03/2019] [Indexed: 12/04/2022] Open
Abstract
Pogostemon cablin (Blanco) Benth. (Patchouli) is not only an important essential oil plant, but also a valuable medicinal plant in China. P. cablin in China can be divided into three cultivars (Shipai, Gaoyao, and Hainan) and two chemotypes (pogostone-type and patchoulol-type). The pogostone-type and patchoulol-type are, respectively, used for medicinals and perfumes. In this study, we sequenced and characterized the plastid genomes for all three Chinese cultivars and aimed to develop a chemotype-specific barcode for future quality control. The plastid genomes of P. cablin cultivars ranged from 152,461 to 152,462 bp in length and comprise 114 genes including 80 protein coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analyses suggested that P. cablin cultivars clustered with the other two Pogostemon species with strong support. Although extremely conserved in P. cablin plastid genomes, 58 cpSSRs were filtered out among the three cultivars. One single variable locus, cpSSR, was discovered. The cpSSR genotypes successfully matched the chemotypes of Chinese patchouli, which was further supported by PCR-based Sanger sequences in more Chinese patchouli samples. The barcode developed in this study is thought to be a simple and reliable quality control method for Chinese P. cablin on the market.
Collapse
Affiliation(s)
- Caiyun Zhang
- Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Tongjian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xun Yuan
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Huirun Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Yao
- South China Limestone Plants Research Centre, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiaolu Mo
- Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Xue Xue
- Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Haifei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
13
|
An RNA Sequencing Transcriptome Analysis and Development of EST-SSR Markers in Chinese Hawthorn through Illumina Sequencing. FORESTS 2019. [DOI: 10.3390/f10020082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chinese hawthorn (Crataegus pinnatifida) is an important ornamental and economic horticultural plant. However, the lack of molecular markers has limited the development and utilization of hawthorn germplasm resources. Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) allow precise and effective cultivar characterization and are routinely used for genetic diversity analysis. Thus, we first reported the development of polymorphic EST-SSR markers in C. pinnatifida with perfect repeats using Illumina RNA-Seq technique. In total, we investigated 14,364 unigenes, from which 5091 EST-SSR loci were mined. Di-nucleotides (2012, 39.52%) were the most abundant SSRs, followed by mono- (1989, 39.07%), and tri-nucleotides (1024, 20.11%). On the basis of these EST-SSRs, a total of 300 primer pairs were designed and used for polymorphism analysis in 70 accessions collected from different geographical regions of China. Of 239 (79.67%) pairs of primer-generated amplification products, 163 (54.33%) pairs of primers showed polymorphism. Finally, 33 primers with high polymorphism were selected for genetic diversity analysis and tested on 70 individuals with low-cost fluorescence-labeled M13 primers using capillary electrophoresis genotyping platform. A total of 108 alleles were amplified by 33 SSR markers, with the number of alleles (Na) ranging from 2 to 14 per locus (mean: 4.939), and the effective number of alleles (Ne) ranging from 1.258 to 3.214 (mean: 2.221). The mean values of gene diversity (He), observed heterozygosity (Ho), and polymorphism information content (PIC) were 0.524 (range 0.205–0.689), 0.709 (range 0.132–1.000), and 0.450 (range 0.184–0.642), respectively. Furthermore, the dendrogram constructed based on the EST-SSR separated the cultivars into two main clusters. In sum, our study was the first comprehensive study on the development and analysis of a large set of SSR markers in hawthorn. The results suggested that the use of NGS techniques for SSR development represented a powerful tool for genetic studies. Additionally, fluorescence-labeled M13 markers proved to be a valuable method for genotyping. All of these EST-SSR markers have agronomic potential and constitute a scientific basis for future studies on the identification, classification, and innovation of hawthorn germplasms.
Collapse
|
14
|
Tan J, Guo JJ, Yin MY, Wang H, Dong WP, Zeng J, Zhou SL. Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides. Molecules 2018; 23:E2963. [PMID: 30428601 PMCID: PMC6278481 DOI: 10.3390/molecules23112963] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/09/2018] [Accepted: 11/11/2018] [Indexed: 11/25/2022] Open
Abstract
Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96⁻84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.
Collapse
Affiliation(s)
- Jing Tan
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Jun-Jie Guo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Ming-Yu Yin
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Huan Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Wen-Pan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Jie Zeng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Shi-Liang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| |
Collapse
|