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García-Meseguer AJ, Villastrigo A, Mirón-Gatón JM, Millán A, Velasco J, Muñoz I. Novel Microsatellite Loci, Cross-Species Validation of Multiplex Assays, and By-Catch Mitochondrial Genomes on Ochthebius Beetles from Supratidal Rockpools. INSECTS 2023; 14:881. [PMID: 37999080 PMCID: PMC10672297 DOI: 10.3390/insects14110881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Here we focus on designing, for the first time, microsatellite markers for evolutionary and ecological research on aquatic beetles from the genus Ochthebius (Coleoptera, Hydraenidae). Some of these non-model species, with high cryptic diversity, exclusively inhabit supratidal rockpools, extreme and highly dynamic habitats with important anthropogenic threats. We analysed 15 individuals of four species (O. lejolisii, O. subinteger, O. celatus, and O. quadricollis) across 10 localities from the Mediterranean coasts of Spain and Malta. Using next-generation sequencing technology, two libraries were constructed to interpret the species of the two subgenera present consistently (Ochthebius s. str., O. quadricollis; and Cobalius, the rest of the species). Finally, 20 markers (10 for each subgenus) were obtained and successfully tested by cross-validation in the four species under study. As a by-catch, we could retrieve the complete mitochondrial genomes of O. lejolisii, O. quadricollis, and O. subinteger. Interestingly, the mitochondrial genome of O. quadricollis exhibited high genetic variability compared to already published data. The novel SSR panels and mitochondrial genomes for Ochthebius will be valuable in future research on species identification, diversity, genetic structure, and population connectivity in highly dynamic and threatened habitats such as supratidal coastal rockpools.
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Affiliation(s)
| | - Adrián Villastrigo
- Division of Entomology, SNSB-Zoologische Staatssammlung München, 81247 Munich, Germany;
| | - Juana María Mirón-Gatón
- Ecology and Hydrology Department, University of Murcia, 30100 Murcia, Spain; (A.J.G.-M.); (J.M.M.-G.); (A.M.)
| | - Andrés Millán
- Ecology and Hydrology Department, University of Murcia, 30100 Murcia, Spain; (A.J.G.-M.); (J.M.M.-G.); (A.M.)
| | - Josefa Velasco
- Ecology and Hydrology Department, University of Murcia, 30100 Murcia, Spain; (A.J.G.-M.); (J.M.M.-G.); (A.M.)
| | - Irene Muñoz
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040 Madrid, Spain;
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Morphologic and genetic analysis for geographic populations of greenbug Schizaphis graminum (Hemiptera: Aphididae) in Egypt. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00501-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bishnoi R, Singla D. APMicroDB: A microsatellite database of Acyrthosiphon pisum. GENOMICS DATA 2017; 12:111-115. [PMID: 28413782 PMCID: PMC5384296 DOI: 10.1016/j.gdata.2017.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/23/2017] [Accepted: 03/26/2017] [Indexed: 11/28/2022]
Abstract
Pea aphids represent a complex genetic system that could be used for QTL analysis, genetic diversity and population genetics studies. Here, we described the development of first microsatellite repeat database of the pea aphid (APMicroDB), accessible at “http://deepaklab.com/aphidmicrodb”. We identified 3,40,233 SSRs using MIcroSAtellite (MISA) tool that was distributed in 14,067 (out of 23,924) scaffold of the pea aphid. We observed 89.53% simple repeats of which 73.41% were mono-nucleotide, followed by di-nucleotide repeats. This database stored information about the repeats kind, GC content, motif type (mono - hexa), genomic location etc. We have also incorporated the primer information derived from Primer3 software of the 250bp flanking region of the identified marker. Blast tool is also provided for searching the user query sequence for identified marker and their primers. This work has an immense use for scientific community working in the field of agricultural pest management, QTL mapping, and host-pathogen interaction analysis.
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Affiliation(s)
- Ritika Bishnoi
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Deepak Singla
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, India
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Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
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Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
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Hao W, Wang S, Liu H, Zhou B, Wang X, Jiang T. Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla). PLoS One 2015; 10:e0125235. [PMID: 25923698 PMCID: PMC4414481 DOI: 10.1371/journal.pone.0125235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 03/22/2015] [Indexed: 11/19/2022] Open
Abstract
In order to study genetic diversity of white birch (Betula platyphylla), 544 primer pairs were designed based on the genome-wide Solexa sequences. Among them, 215 primer pairs showed polymorphism between five genotypes and 111 primer pairs that presented clear visible bands in genotyping 41 white birch plants that were collected from 6 different geographical regions. A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus. The results of statistic analysis showed that polymorphic frequency of the alleles ranged from 17% to 100% with a mean of 55.85%; polymorphism information content (PIC) of the loci was from 0.09 to 0.58 with a mean of 0.30; and gene diversity between the tested genotypes was from 0.01 to 0.66 with a mean of 0.36. The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66. The 41 white birch genotypes at the 111 selected SSR loci showed low to moderate similarity (0.025-0.610), indicating complicated genetic diversity among the white birch collections. The UPGMA-based clustering analysis of the allelic constitution of 41 white birch genotypes at 111 SSR loci suggested that the six different geographical regions can be further separated into four clusters at a similarity coefficient of 0.22. Genotypes from Huanren and Liangshui provenances were grouped into Cluster I, genotypes from Xiaobeihu and Qingyuan provenances into Cluster II, genotypes from Finland provenance into Cluster III, and genotypes from Maoershan into Cluster IV. The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.
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Affiliation(s)
- Wei Hao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shengji Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Huajing Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinwang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Texas A&M AgriLife Research and Extension Center, Texas A&M System, Dallas, Texas, United States of America
- * E-mail: (XW); (TJ)
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- * E-mail: (XW); (TJ)
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Biswas MK, Xu Q, Mayer C, Deng X. Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis). PLoS One 2014; 9:e104182. [PMID: 25148383 PMCID: PMC4141690 DOI: 10.1371/journal.pone.0104182] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.
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Affiliation(s)
- Manosh Kumar Biswas
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | | | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
- * E-mail:
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Development and characterization of 18 novel EST-SSRs from the western flower Thrips, Frankliniella occidentalis (Pergande). Int J Mol Sci 2012; 13:2863-2876. [PMID: 22489130 PMCID: PMC3317692 DOI: 10.3390/ijms13032863] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 01/01/2023] Open
Abstract
The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy–Weinberg equilibrium (HWE). Pairwise FST analysis showed a low but significant differentiation (0.026 < FST < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies.
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Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, Huang S, Weng Y. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 2010; 11:569. [PMID: 20950470 PMCID: PMC3091718 DOI: 10.1186/1471-2164-11-569] [Citation(s) in RCA: 258] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Accepted: 10/15/2010] [Indexed: 01/19/2023] Open
Abstract
Background Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. Results A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available. Conclusions The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.
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Affiliation(s)
- Pablo F Cavagnaro
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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