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Ali R, Chaluvadi SR, Wang X, Hazzouri KM, Sudalaimuthuasari N, Rafi M, Al-Nuaimi M, Sasi S, Antepenko E, Bennetzen JL, Amiri KMA. Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree. Microbiol Spectr 2024; 12:e0361723. [PMID: 38624222 PMCID: PMC11237379 DOI: 10.1128/spectrum.03617-23] [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: 10/09/2023] [Accepted: 03/14/2024] [Indexed: 04/17/2024] Open
Abstract
We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.
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Affiliation(s)
- Rashid Ali
- Mitrix Bio., Inc., Farmington, Connecticut, USA
| | | | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | | | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Mariam Al-Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Eric Antepenko
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | | | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE
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Bhandari MS, Meena RK, Shamoon A, Saroj S, Kant R, Pandey S. First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora. Mol Biol Rep 2020; 47:6997-7008. [PMID: 32930932 DOI: 10.1007/s11033-020-05758-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/28/2020] [Indexed: 11/29/2022]
Abstract
Salvadoraceae constitutes ecologically imperative desert families of 3 genera-Azima, Dobera and Salvadora. Under genus Salvadora of this family, S. oleoides is a keystone species of socio-economic and medicinal value. This species naturally grows in the arid zones but currently experiencing severe fragmentation due to land use change and reduced regeneration, which may have resulted in the depletion of genetic diversity. Hence, it is up-most important to develop genomic resources for studying the population genetics in S. oleoides. This study aims to develop robust microsatellites markers, which were not yet reported in genus Salvodora due to lack of genome sequence information. We developed novel microsatellites markers in S. oleoides using Illumina paired-end sequencing technology. In total, 14,552 simple sequence repeat (SSR) markers were successfully designed from 21,055 microsatellite repeats detected in the 13 Gb raw sequence data. Afterwards, a subset of 101 SSRs were randomly selected and validated, 94 primers were successfully amplified and 34 showed polymorphisms. These SSRs were used to estimate the measures of genetic diversity in three natural populations of state Rajasthan and Gujarat. Importantly, average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were recorded as 2.4, 0.529, 0.357, and 0.326, respectively. Furthermore, 15 primers were evaluated in S. persica for cross-transferability, and all were successfully amplified but only eight showed polymorphisms. This study has been conducted first time for S. oleoides and pioneer among the native species of arid-zone in India.
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Affiliation(s)
- Maneesh S Bhandari
- 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
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Shanti Saroj
- 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
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Meena B, Singh N, Mahar KS, Sharma YK, Rana TS. Molecular analysis of genetic diversity and population genetic structure in Ephedra foliata: an endemic and threatened plant species of arid and semi-arid regions of India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:753-764. [PMID: 31168237 PMCID: PMC6522567 DOI: 10.1007/s12298-019-00648-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 05/06/2023]
Abstract
Studies on the genetic diversity and structure in endangered and threatened species are of utmost importance to design and promote effective conservation and management programs. Ephedra foliata, an endemic and threatened species growing naturally in arid and semi-arid regions of north western India, was investigated to estimate genetic variability and population structure using inter-simple sequence repeats (ISSR) and directed amplification of mini-satellite DNA (DAMD) markers. Twenty-five (ISSR 15; DAMD 10) markers produced 449 fragments, of which 382 were polymorphic in nature, revealing 84.59% polymorphism. ISSR markers revealed higher levels of polymorphism, polymorphic information content, marker index, diversity index and effective multiplex ratio than DAMD markers. Higher values of polymorphism, genetic diversity and Shannon information index at species level than at population level revealed that E. foliata possess high genetic diversity. AMOVA revealed much higher variance within populations than among the populations. The three clustering approaches viz., UPGMA, PCoA, and STRUCTURE, grouped the eleven investigated populations into two clusters revealing two genetic populations and the patterns of clustering of populations was in accordance with their geographic distribution, suggesting that these populations have evolved in response to their local environments. The high level of genetic differentiation (G ST = 0.31) and moderate gene flow (N m = 1.11) among populations could be due to geographic isolation, regional climatic conditions, over-exploitation and improper seed setting. To the best of our knowledge, this study is the first endeavour to estimate genetic diversity and population structure of E. foliata using molecular markers.
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Affiliation(s)
- Baleshwar Meena
- Molecular Systematics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India
| | - Niraj Singh
- Molecular Systematics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India
| | - Kamalesh Singh Mahar
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015 India
| | - Yogesh Kumar Sharma
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh 226007 India
| | - Tikam Singh Rana
- Molecular Systematics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India
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Shekhawat JK, Rai MK, Shekhawat NS, Kataria V. Exploring genetic variability in Prosopis cineraria using two gene targeted CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers. Mol Biol Rep 2018; 45:2359-2367. [PMID: 30255277 DOI: 10.1007/s11033-018-4400-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/21/2018] [Indexed: 10/28/2022]
Abstract
Two gene targeted molecular marker systems, CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism, were used to assess the genetic diversity and relatedness in Prosopis cineraria, a tree of abiotic stress tolerance, agroforestry and ethano-botanical importance. A total of ten wild populations consisting 49 individuals collected from different locations of Indian Thar Desert were examined for the genetic analysis of P. cineraria. Ten CBDP and seven SCoT primers, total 17 primers, generated 204 bands with an average of 12 bands per primer, of which 159 (76.8%) were polymorphic. The average PIC values for both CBDP and SCoT marker were 0.543 and 0.547, respectively. The cumulative data of these two markers were used to analyze different genetic diversity indices and compute pair-wise distances. The population genetic diversity analysis based on cumulative data of CBDP and SCoT markers revealed the high levels of genetic differentiation (GST = 0.341; GST > 0.15 as high), low value of gene flow (Nm = 0.966; Nm > 1 as high) and high fixation index (FST = 0. 415). The highest genetic diversity was observed among NGBAR populations followed by CHR populations, while SIK populations showed lowest genetic diversity. AMOVA revealed the percent molecular variation was higher within the populations (77%) compared to that of among populations (23%). The clustering pattern based on UPGMA and PCoA plot clearly demonstrated the genetic relationship among the genotypes collected from the different regions of Indian Thar Desert.
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Affiliation(s)
- Jatan K Shekhawat
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India
| | - Manoj K Rai
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India.,Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, 484887, India
| | - N S Shekhawat
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India
| | - Vinod Kataria
- Biotechnology Unit, Department of Botany (UGC-Centre of Advanced Study), Jai Narain Vyas University, Jodhpur, Rajasthan, 342001, India.
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Rai MK, Shekhawat JK, Kataria V, Shekhawat N. De novo assembly of leaf transcriptome, functional annotation and genomic resources development in Prosopis cineraria , a multipurpose tree of Indian Thar Desert. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Bhattacharyya P, Kumaria S, Tandon P. Applicability of ISSR and DAMD markers for phyto-molecular characterization and association with some important biochemical traits of Dendrobium nobile, an endangered medicinal orchid. PHYTOCHEMISTRY 2015; 117:306-316. [PMID: 26125940 DOI: 10.1016/j.phytochem.2015.06.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
Dendrobium nobile is an important medicinal orchid having profound importance in traditional herbal drug preparations and pharmacopeias worldwide. Due to various anthropogenic pressures the natural populations of this important orchid species are presently facing threats of extinction. In the present study, genetic and chemical diversity existing amongst 6 natural populations of D. nobile were assessed using molecular markers, and the influence of genetic factors on its phytochemical activity especially antioxidant potential was determined. Molecular fingerprinting of the orchid taxa was performed using ISSR and DAMD markers along with the estimation of total phenolics, flavonoids and alkaloid contents. Antioxidant activity was also measured using DPPH and FRAP assays which cumulatively revealed a significant level of variability across the sampled populations. The representatives from Sikkim in Northeast India revealed higher phytochemical activity whereas those from Mizoram showed lesser activity. Analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly higher than within the populations. The data generated by UPGMA and Bayesian analytical models were compared in order to estimate the genetic relationships amongst the D. nobile germplasm sampled from different geographical areas of Northeast India. Interestingly, identical grouping patterns were exhibited by both the approaches. The results of the present study detected a high degree of existing genetic and phytochemical variation amongst the populations in relation to bioclimatic and geographic locations of populations. Our results strongly establish that the cumulative marker approach could be the best suited for assessing the genetic relationships with high accuracy amongst distinct D. nobile accessions.
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Affiliation(s)
- Paromik Bhattacharyya
- Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Suman Kumaria
- Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong 793022, Meghalaya, India.
| | - Pramod Tandon
- Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong 793022, Meghalaya, India
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Nongrum I, Kumar S, Kumaria S, Tandon P. Genetic variation and gene flow estimation of Nepenthes khasiana Hook. F- A threatened insectivorous plant of India as revealed by RAPD markers. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12892-011-0070-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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