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Sharma R, Ahlawat S, Pundir RK, Arora R, Tantia MS. Genetic diversity and differentiation of Thutho cattle from northeast India using microsatellite markers. Anim Biotechnol 2023; 34:5016-5027. [PMID: 37300558 DOI: 10.1080/10495398.2023.2221704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cattle are losing maximum breeds among the world's livestock. Genetic variability data is essentially required for conservation decision-making. Thutho is a recently registered Indian cattle breed (INDIA_CATTLE_1400_THUTHO_03047) from the northeast region (NE), a biodiversity hotspot. Genetic diversity in the Thutho population and its differentiation from the only other cattle breed of NE (Siri) and cattle (Bachaur) of the neighboring region was established using highly polymorphic, FAO-recommended microsatellite markers. Numerous alleles (253) were detected across the 25 loci. The mean observed and expected numbers of alleles in the population were 10.12 ± 0.5 and 4.5 ± 0.37, respectively. The observed heterozygosity (0.67 ± 0.04) was lower than the expected heterozygosity (0.73 ± 0.03) which indicated a departure from the Hardy-Weinberg equilibrium. A positive FIS value (0.097) confirmed the heterozygote deficiency in the Thutho population. Genetic distance, phylogenetic relationships, differentiation parameters, population assignment, and Bayesian analysis explicitly ascertained the unique genetic identity of the Thutho cattle. The population did not suffer any bottlenecks in the past. Thutho has minimum diversity among the three populations; hence, its scientific management needs to be initiated immediately. Interestingly, genetic variation is enough for formulating breeding programs for managing, improving, and conserving this precious indigenous cattle germplasm.
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Affiliation(s)
- Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - R K Pundir
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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Reichel K, Herklotz V, Smolka A, Nybom H, Kellner A, De Riek J, Smulders MJM, Wissemann V, Ritz CM. Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L. PLoS One 2023; 18:e0292634. [PMID: 37797054 PMCID: PMC10553836 DOI: 10.1371/journal.pone.0292634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.
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Affiliation(s)
- Katja Reichel
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Alisia Smolka
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Alexandra Kellner
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jan De Riek
- Flanders Research Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Melle, Belgium
| | | | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
- International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Technical University Dresden, Zittau, Germany
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Nemati Z, Dadkhodaie A, Mostowfizadeh-Ghalamfarsa R, Mehrabi R, Cacciola SO. Genetic Variation of Puccinia triticina Populations in Iran from 2010 to 2017 as Revealed by SSR and ISSR Markers. J Fungi (Basel) 2023; 9:jof9030388. [PMID: 36983556 PMCID: PMC10056552 DOI: 10.3390/jof9030388] [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: 01/22/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study.
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Affiliation(s)
- Zahra Nemati
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | | | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 81431-53784, Iran
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy
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Skolotneva ES, Kosman E, Kelbin VN, Morozova EV, Laprina YV, Baranova OA, Kolomiets TM, Kiseleva MI, Sergeeva EM, Salina EA. SSR Variability of Stem Rust Pathogen on Spring Bread Wheat in Russia. PLANT DISEASE 2023; 107:493-499. [PMID: 36265157 DOI: 10.1094/pdis-10-22-2373-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, which used to be a harmful disease of winter wheat in the southern part of Russia, has been largely affecting the yield of spring bread wheat in the territories of the temperate climate zone since 2009. In total, 222 P. graminis f. sp. tritici isolates were obtained from samples of susceptible cultivars of spring bread wheat in Central and Volga regions and Omsk and Novosibirsk provinces in 2019. Genotyping of the isolates was carried out at 16 simple-sequence repeat (SSR) loci. Number of alleles, proportion of heterozygotes, and deviation from Hardy-Weinberg equilibrium were determined at each SSR locus. Based on genetic variability of SSR genotypes, it was shown that the P. graminis f. sp. tritici population is subdivided into two large clusters in the territory of the Russian temperate climate zone: the "European" population (the Central region) and the "Asian" one (the Volga region and two main wheat provinces of Western Siberia). Both of the P. graminis f. sp. tritici populations are characterized by a mixed mode of reproduction (sexual and clonal) but different sources of inoculum seem to shape a genotype structure within them. A group of P. graminis f. sp. tritici genotypes with high variability, the inbreeding coefficient closed to zero, and low observed heterozygosity was revealed among samples from Omsk. Moreover, two singular SSR genotypes identified among the Asian samples of P. graminis f. sp. tritici isolates should attract special attention in the monitoring of stem rust in order to disclose unexpected rapid changes of the pathogen in the corresponding regions and to prevent disease outbreak.
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Affiliation(s)
- Ekaterina S Skolotneva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Evsey Kosman
- Institute for Cereal Crops Research, School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vasiliy N Kelbin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Eugenia V Morozova
- Branch of Institute of Cytology and Genetics SB RAS, Siberian Research Institute of Plant Industry and Breeding, Krasnoobsk 630501, Russia
| | - Yulia V Laprina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga A Baranova
- All-Russian Institute of Plant Protection, St. Petersburg-Pushkin 196608, Russia
| | | | - Marina I Kiseleva
- All-Russian Research Institute of Phytopathology, Moscow 143050, Russia
| | - Ekaterina M Sergeeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena A Salina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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Fu C, Ai Q, Cai L, Qiu F, Yao L, Wu H. Genetic Diversity and Population Dynamics of Leptobrachium leishanense (Anura: Megophryidae) as Determined by Tetranucleotide Microsatellite Markers Developed from Its Genome. Animals (Basel) 2021; 11:3560. [PMID: 34944336 PMCID: PMC8698065 DOI: 10.3390/ani11123560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Persisting declination of amphibians around the world has resulted in the public attaching importance to the conservation of their biodiversity. Genetic data can be greatly helpful in conservation planning and management, especially in species that are small in size and hard to observe. It is essential to perform genetic assessments for the conservation of Leptobrachium leishanense, an endangered toad and receiving secondary protection on the list of state-protected wildlife in China. However, current molecular markers with low reliability and efficiency hinder studies. Here, we sampled 120 adult toes from the population in the Leishan Mountain, 23 of which were used to develop tetranucleotide microsatellite markers based on one reference L. leishanense genome. After primer optimization, stability detection, and polymorphism detection, we obtained 12 satisfactory microsatellite loci. Then, we used these loci to evaluate the genetic diversity and population dynamics of the 120 individuals. Our results show that there is a low degree of inbreeding in the population, and it has a high genetic diversity. Recently, the population has not experienced population bottlenecks, and the estimated effective population size was 424.3. Accordingly, stabilizing genetic diversity will be key to population sustainability. Recovering its habitat and avoiding intentional human use will be useful for conservation of this species.
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Affiliation(s)
| | | | | | | | | | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (C.F.); (Q.A.); (L.C.); (F.Q.); (L.Y.)
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Gultyaeva EI, Shaydayuk EL, Kazartsev IA, Kosman E. Race Characterization and Molecular Genotyping of Puccinia triticina Populations from Durum Wheat in Russia. PLANT DISEASE 2021; 105:1495-1504. [PMID: 33797936 DOI: 10.1094/pdis-09-20-1927-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Variability of the Russian population of Puccinia triticina from durum wheat was studied with virulence and simple sequence repeat (SSR) markers. The pathogen was sampled during 2017 to 2019 in all regions with sizable durum wheat (Triticum durum) growing areas from winter (North Caucasus) and spring (Middle Volga, Ural, and West Siberia) wheat. A total of 474 isolates were tested on a set of 20 Lr-gene lines. Molecular genotypes for 105 selected isolates were determined at 11 SSR loci. Variable virulence/avirulence reaction was observed only on three Lr-gene lines, whereas just five SSR loci were polymorphic with two alleles at each. Seven different virulence phenotypes and 11 SSR genotypes were found among 474 and 105 isolates, respectively, indicating a very low variability of the pathogen. One virulence phenotype and three SSR genotypes occurred in all Russian regions. However, two phenotypes were specific to the European regions of Russia (North Caucasus and Middle Volga), while another two were found only in the Asian part of Russia (Ural and West Siberia). Significant differentiation between six populations of P. triticina from durum wheat in the Asian and European (mainly North Caucasus) regions was also shown with numerous metrics and approaches for data with and without clone correction. Relationships among the regional populations of P. triticina from durum wheat established with virulence phenotypes significantly associated with those for SSR genotypes and was similar to the relationships among the regional populations of the pathogen from common wheat.
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Affiliation(s)
- Elena I Gultyaeva
- All-Russian Institute of Plant Protection, St. Petersburg-Pushkin 196608, Russia
| | | | - Igor A Kazartsev
- All-Russian Institute of Plant Protection, St. Petersburg-Pushkin 196608, Russia
| | - Evsey Kosman
- Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Wolf KKE, Hoppe CJM, Leese F, Weiss M, Rost B, Neuhaus S, Gross T, Kühne N, John U. Revealing environmentally driven population dynamics of an Arctic diatom using a novel microsatellite PoolSeq barcoding approach. Environ Microbiol 2021; 23:3809-3824. [PMID: 33559305 DOI: 10.1111/1462-2920.15424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/28/2022]
Abstract
Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms, it is challenging to follow intraspecific dynamics over space and time. We propose a new method, microsatellite PoolSeq barcoding (MPB), for tracing allele frequency changes in protist populations. We successfully applied this method to experimental community incubations and field samples of the diatom Thalassiosira hyalina from the Arctic, a rapidly changing ecosystem. Validation of the method found compelling accuracy in comparison with established genotyping approaches within different diversity contexts. In experimental and environmental samples, we show that MPB can detect meaningful patterns of population dynamics, resolving allelic stability and shifts within a key diatom species in response to experimental treatments as well as different bloom phases and years. Through our novel MPB approach, we produced a large dataset of populations at different time-points and locations with comparably little effort. Results like this can add insights into the roles of selection and plasticity in natural protist populations under stable experimental but also variable field conditions. Especially for organisms where genotype sampling remains challenging, MPB holds great potential to efficiently resolve eco-evolutionary dynamics and to assess the mechanisms and limits of resilience to environmental stressors.
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Affiliation(s)
- Klara K E Wolf
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Clara J M Hoppe
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Florian Leese
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Martina Weiss
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Björn Rost
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,University of Bremen, FB2, Bremen, Germany
| | - Stefan Neuhaus
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Thilo Gross
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,University of Oldenburg, ICBM, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Nancy Kühne
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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Kosman E, Scheiner SM, Gregorius H. Severe limitations of the FEve metric of functional evenness and some alternative metrics. Ecol Evol 2021; 11:123-132. [PMID: 33437418 PMCID: PMC7790661 DOI: 10.1002/ece3.6974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 12/01/2022] Open
Abstract
The metric of functional evenness FEve is an example of how approaches to conceptualizing and measuring functional variability may go astray. This index has several critical conceptual and practical drawbacks: Different values of the FEve index for the same community can be obtained if the species have unequal species abundances; this result is highly likely if most of the traits are categorical.Very minor differences in even one pairwise distance can result in very different values of FEve.FEve uses only a fraction of the information contained in the matrix of species distances. Counterintuitively, this can cause very similar FEve scores for communities with substantially different patterns of species dispersal in trait space.FEve is a valid metric only if all species have exactly the same abundances. However, the meaning of FEve in such an instance is unclear as the purpose of the metric is to measure the variability of abundances in trait space. We recommend not using the FEve metric in studies of functional variability. Given the wide usage of FEve index over the last decade, the validity of the conclusions based on those estimates is in question. Instead, we suggest three alternative metrics that combine variability in species distances in trait space with abundance in various ways. More broadly, we recommend that researchers think about which community properties (e.g., trait distances of a focus species to the nearest neighbor or all other species, variability of pairwise interactions between species) they want to measure and pick from among the appropriate metrics.
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Affiliation(s)
- Evsey Kosman
- Institute for Cereal Crops ImprovementTel Aviv UniversityTel AvivIsrael
| | - Samuel M. Scheiner
- Division of Environmental BiologyNational Science FoundationAlexandriaVAUSA
| | - Hans‐Rolf Gregorius
- Institut für Populations‐ und ökologische GenetikGöttingenGermany
- Abteilung Forstgenetik und ForstpflanzenzüchtungUniversität GöttingenGöttingenGermany
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Barido-Sottani J, Chapman SD, Kosman E, Mushegian AR. Measuring similarity between gene interaction profiles. BMC Bioinformatics 2019; 20:435. [PMID: 31438841 PMCID: PMC6704681 DOI: 10.1186/s12859-019-3024-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 08/09/2019] [Indexed: 11/14/2022] Open
Abstract
Background Gene and protein interaction data are often represented as interaction networks, where nodes stand for genes or gene products and each edge stands for a relationship between a pair of gene nodes. Commonly, that relationship within a pair is specified by high similarity between profiles (vectors) of experimentally defined interactions of each of the two genes with all other genes in the genome; only gene pairs that interact with similar sets of genes are linked by an edge in the network. The tight groups of genes/gene products that work together in a cell can be discovered by the analysis of those complex networks. Results We show that the choice of the similarity measure between pairs of gene vectors impacts the properties of networks and of gene modules detected within them. We re-analyzed well-studied data on yeast genetic interactions, constructed four genetic networks using four different similarity measures, and detected gene modules in each network using the same algorithm. The four networks induced different numbers of putative functional gene modules, and each similarity measure induced some unique modules. In an example of a putative functional connection suggested by comparing genetic interaction vectors, we predict a link between SUN-domain proteins and protein glycosylation in the endoplasmic reticulum. Conclusions The discovery of molecular modules in genetic networks is sensitive to the way of measuring similarity between profiles of gene interactions in a cell. In the absence of a formal way to choose the “best” measure, it is advisable to explore the measures with different mathematical properties, which may identify different sets of connections between genes. Electronic supplementary material The online version of this article (10.1186/s12859-019-3024-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joëlle Barido-Sottani
- Stowers Institute for Medical Research, Kansas City, MO, USA.,École Polytechnique, Route de Saclay, Palaiseau, France.,Present Address: Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Samuel D Chapman
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Present Address: Booz Allen Hamilton, McLean, Virginia, USA
| | - Evsey Kosman
- Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Arcady R Mushegian
- Stowers Institute for Medical Research, Kansas City, MO, USA. .,Department of Microbiology, Molecular Genetics and Immunology, Kansas University Medical Center, Kansas City, Kansas, USA. .,Present Address: Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, USA.
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