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Meena RK, Kashyap P, Shamoon A, Dhyani P, Sharma H, Bhandari MS, Barthwal S, Ginwal HS. Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus. Funct Integr Genomics 2023; 23:103. [PMID: 36973584 DOI: 10.1007/s10142-023-01033-z] [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: 02/06/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (FST = 0.119), severe inbreeding (FIS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.
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Affiliation(s)
- Rajendra K Meena
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India.
| | - Priyanka Kashyap
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Payal Dhyani
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Hansraj Sharma
- ICFRE - Bamboo & Rattan Centre, Aizawl, 796007, Mizoram, India
- ICFRE-Rain Forest Research Institute, Jorhat, 785001, Assam, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Santan Barthwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Harish S Ginwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
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Mishra G, Meena RK, Kant R, Pandey S, Ginwal HS, Bhandari MS. Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta. Funct Integr Genomics 2023; 23:51. [PMID: 36707443 PMCID: PMC9883139 DOI: 10.1007/s10142-023-00975-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/29/2023]
Abstract
Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta. Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae.
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Affiliation(s)
- Garima Mishra
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand Dehradun, India
| | - Rajendra K. Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand Dehradun, India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand Dehradun, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun - 248 006, Uttarakhand Dehradun, India
| | - Harish S. Ginwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand Dehradun, India
| | - Maneesh S. Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand Dehradun, India
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Wang P, Bai J, Li X, Liu T, Yan Y, Yang Y, Li H. Phylogenetic relationship and comparative analysis of the main Bupleuri Radix species in China. PeerJ 2023; 11:e15157. [PMID: 37077311 PMCID: PMC10108860 DOI: 10.7717/peerj.15157] [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: 06/23/2022] [Accepted: 03/10/2023] [Indexed: 04/21/2023] Open
Abstract
Background Bupleuri Radix (Chaihu) is a famous traditional Chinese medicine derived from Bupleurum, Apiaceae. The origin of cultivated Chaihu germplasm in China is unclear, which has led to unstable Chaihu quality. In this study, we reconstructed the phylogeny of the main Chaihu germplasm species in China and identified potential molecular markers to authenticate its origin. Methods Three Bupleurum species (eight individuals), B. bicaule, B. chinense, and B. scorzonerifolium, were selected for genome skimming. Published genomes from B. falcatum and B. marginatum var. stenophyllum were used for comparative analysis. Results Sequences of the complete plastid genomes were conserved with 113 identical genes ranging from 155,540 to 155,866 bp in length. Phylogenetic reconstruction based on complete plastid genomes resolved intrageneric relationships of the five Bupleurum species with high support. Conflicts between the plastid and nuclear phylogenies were observed, which were mainly ascribed to introgressive hybridization. Comparative analysis showed that noncoding regions of the plastomes had most of the variable sequences. Eight regions (atpF-atpH, petN-psbM, rps16-psbK, petA-psbJ, ndhC-trnV/UAC and ycf1) had high divergence values in Bupleurum species and could be promising DNA barcodes for Chaihu authentication. A total of seven polymorphic cpSSRs and 438 polymorphic nSSRs were detected across the five Chaihu germplasms. Three photosynthesis-related genes were under positive selection, of which accD reflected the adaptation fingerprint of B. chinense to different ecological habitats. Our study provides valuable genetic information for phylogenetic investigation, germplasm authentication, and molecular breeding of Chaihu species.
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Affiliation(s)
- Ping Wang
- Xianyang Normal University, Xianyang, China
| | - Jiqing Bai
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Xue Li
- Xianyang Food and Drug Administration, Xianyang, China
| | | | - Yumeng Yan
- Xianyang Normal University, Xianyang, China
| | | | - Huaizhu Li
- Xianyang Normal University, Xianyang, China
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Tyagi P, Singh D, Mathur S, Singh A, Ranjan R. Upcoming progress of transcriptomics studies on plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:1030890. [PMID: 36589087 PMCID: PMC9798009 DOI: 10.3389/fpls.2022.1030890] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.
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Meena RK, Negi N, Uniyal N, Bhandari MS, Sharma R, Ginwal HS. Genome skimming-based STMS marker discovery and its validation in temperate hill bamboo Drepanostachyum falcatum. J Genet 2021. [DOI: 10.1007/s12041-021-01273-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Guo J, Huang Z, Sun J, Cui X, Liu Y. Research Progress and Future Development Trends in Medicinal Plant Transcriptomics. FRONTIERS IN PLANT SCIENCE 2021; 12:691838. [PMID: 34394145 PMCID: PMC8355584 DOI: 10.3389/fpls.2021.691838] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/29/2021] [Indexed: 05/17/2023]
Abstract
Transcriptomics is one of the most popular topics in biology in recent times. Transcriptome sequencing (RNA-Seq) is a high-throughput, high-sensitivity, and high-resolution technique that can be used to study model and non-model organisms. Transcriptome sequencing is also an important method for studying the genomes of medicinal plants, a topic on which limited information is available. The study of medicinal plants through transcriptomics can help researchers analyze functional genes and regulatory mechanisms of medicinal plants and improve breeding selection and cultivation techniques. This article analyzes and compares the applications of transcriptome sequencing in medicinal plants over the past decade and briefly introduces the methods of transcriptome sequencing and analysis, their applications in medicinal plant research, and potential development trends. We will focus on the research and application progress of transcriptome sequencing in the following four areas: the mining of functional genes in medicinal plants, development of molecular markers, biosynthetic pathways of secondary metabolites, and developmental mechanisms of medicinal plants. Our review will provide ideas for the mining of functional genes of medicinal plants and breeding new varieties.
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Affiliation(s)
- Junda Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zhen Huang
- Yuxi Walvax Biotechnology Co., Ltd., Yuxi, China
| | - Jialing Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
- Key Laboratory of Panax Notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
- Key Laboratory of Panax Notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
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Dabral A, Shamoon A, Meena RK, Kant R, Pandey S, Ginwal HS, Bhandari MS. Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1623-1638. [PMID: 34305342 PMCID: PMC8285676 DOI: 10.1007/s12298-021-01035-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Proteaceae, a largely southern hemisphere family consisting of 80 genera distributed in Australia and southern Africa as its centres of greatest diversity, also extends well in northern and southern America. Under this family, Grevillea robusta is a fast-growing species got popularity in farm and avenue plantations. Despite the ecological and economic importance, the species has not yet been investigated for its genetic improvement and genome-based studies. Only a few molecular markers are available for the species or its close relatives, which hinders genomic and population genetics studies. Genetic markers have been intensively applied for the main strategies in breeding programs, especially for the economically important traits. Hence, it is of utmost priority to develop genomic database resources and species-specific markers for studying quantitative genetics in G. robusta. Given this, the present study aimed to develop de novo genome sequencing, robust microsatellites markers, sequence annotation and their validation in different stands of G. robusta in northern India. Library preparation and sequencing were carried out using Illumina paired-end sequencing technology. Approximately, ten gigabases (Gb) sequence data with 70.87 million raw reads assembled into 425,923 contigs (read mapped to 76.48%) comprising 455 Mb genome size (23 × coverage) generated through genome skimming approach. In total, 9421 simple sequence repeat (SSR) primer pairs were successfully designed from 13,335 microsatellite repeats. Afterward, a subset of 161 primer pairs was randomly selected, synthesized and validated. All the tested primers showed successful amplification but only 13 showed polymorphisms. The polymorphic SSRs were further used to estimate the measures of genetic diversity in 12 genotypes each from the states of Punjab, Haryana, Himachal Pradesh and Uttarakhand. Importantly, the average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.69, 0.356, 0.557 and 0.388, respectively. The availability of sequence information and newly developed SSR markers could potentially be used in various genetic analyses and improvements through molecular breeding strategies for G. robusta. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01035-w.
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Affiliation(s)
- Aman Dabral
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Rajendra K. Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, Uttarakhand 248 006 India
| | - Harish S. Ginwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Maneesh S. Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
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