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Türkoğlu A, Haliloğlu K, Mohammadi SA, Öztürk A, Bolouri P, Özkan G, Bocianowski J, Pour-Aboughadareh A, Jamshidi B. Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats (SSR) Markers. Genes (Basel) 2023; 14:1182. [PMID: 37372362 DOI: 10.3390/genes14061182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses.
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Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, 42310 Konya, Turkey
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Seyyed Abolgahasem Mohammadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz 5166616471, Iran
| | - Ali Öztürk
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Parisa Bolouri
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, 06100 Ankara, Turkey
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31585-854, Iran
| | - Bita Jamshidi
- Department of Food Security and Public Health, Khabat Technical Institute, Erbil Polytechnic University, Erbil 44001, Iraq
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Sah RP, Nayak AK, Chandrappa A, Behera S, Azharudheen Tp M, Lavanya GR. cgSSR marker-based genome-wide association study identified genomic regions for panicle characters and yield in rice (Oryza sativa L.). J Sci Food Agric 2023; 103:720-728. [PMID: 36054367 DOI: 10.1002/jsfa.12183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/03/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND To improve production efficiency, positive alleles corresponding to yield-related attributes must be accumulated in a single elite background. We designed and used cgSSR markers, which are superior to random SSR markers in genome-wide association study, to identify genomic regions that contribute to panicle characters and grain yield in this study. RESULTS As evidenced by the high polymorphic information content value and gene diversity coefficient, the new cgSSR markers were determined to be highly informative. These cgSSR markers were employed to generate genotype data for an association panel evaluated for four panicle characters and grain yield over three seasons. For five traits, 17 significant marker-trait associations on six chromosomes were discovered. The percentage of phenotypic variance that could be explained ranged from 4% to 13%. Unrelated gene-derived markers had a strong association with target traits as well. CONCLUSION Trait-associated cgSSR markers derived from corresponding or related genes ensure their utility in direct allele selection, while other linked markers aid in allele selection indirectly by altering the phenotype of interest. Through a marker-assisted breeding approach, these marker-trait associations can be leveraged to accumulate favourable alleles for yield enhancement in rice. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Rameswar Prasad Sah
- Crop Improvement Division, ICAR - National Rice Research Institute, Cuttack, India
| | - Amrit Kumar Nayak
- Department of Genetics and Plant breeding, Naini Agricultural Institute, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Prayagraj, India
| | - Anilkumar Chandrappa
- Crop Improvement Division, ICAR - National Rice Research Institute, Cuttack, India
| | - Sasmita Behera
- Crop Improvement Division, ICAR - National Rice Research Institute, Cuttack, India
| | | | - G Roopa Lavanya
- Department of Genetics and Plant breeding, Naini Agricultural Institute, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Prayagraj, India
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Mukherjee S, Horka P, Zdenkova K, Cermakova E. Parvalbumin: A Major Fish Allergen and a Forensically Relevant Marker. Genes (Basel) 2023; 14. [PMID: 36672964 DOI: 10.3390/genes14010223] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Parvalbumins (PVALBs) are low molecular weight calcium-binding proteins. In addition to their role in many biological processes, PVALBs play an important role in regulating Ca2+ switching in muscles with fast-twitch fibres in addition to their role in many biological processes. The PVALB gene family is divided into two gene types, alpha (α) and beta (β), with the β gene further divided into two gene types, beta1 (β1) and beta2 (β2), carrying traces of whole genome duplication. A large variety of commonly consumed fish species contain PVALB proteins which are known to cause fish allergies. More than 95% of all fish-induced food allergies are caused by PVALB proteins. The authentication of fish species has become increasingly important as the seafood industry continues to grow and the growth brings with it many cases of food fraud. Since the PVALB gene plays an important role in the initiation of allergic reactions, it has been used for decades to develop alternate assays for fish identification. A brief review of the significance of the fish PVALB genes is presented in this article, which covers evolutionary diversity, allergic properties, and potential use as a forensic marker.
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Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, Chen G, Ng WL, Islam MN, Punnarak P, Zheng H, Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea. Front Plant Sci 2023; 13:1075353. [PMID: 36684775 PMCID: PMC9845719 DOI: 10.3389/fpls.2022.1075353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
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Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuchen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qianying Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Luzhen Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Md Nazrul Islam
- Forestry and Wood Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Tian R, Widel M, Imanian B. The Light Chain Domain and Especially the C-Terminus of Receptor-Binding Domain of the Botulinum Neurotoxin (BoNT) Are the Hotspots for Amino Acid Variability and Toxin Type Diversity. Genes (Basel) 2022; 13. [PMID: 36292800 DOI: 10.3390/genes13101915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 01/15/2023] Open
Abstract
Botulinum neurotoxins (BoNT) are the most potent toxins in the world. They are produced by a few dozens of strains within several clostridial species. The toxin that they produce can cause botulism, a flaccid paralysis in humans and other animals. With seven established serologically different types and over 40 subtypes, BoNTs are among the most diverse known toxins. The toxin, its structure, its function and its physiological effects on the neural cell and animal hosts along with its diversity have been the subjects of numerous studies. However, many gaps remain in our knowledge about the BoNT toxin and the species that produce them. One of these gaps involves the distribution and extent of variability along the full length of the gene and the protein as well as its domains and subdomains. In this study, we performed an extensive analysis of all of the available 143 unique BoNT-encoding genes and their products, and we investigated their diversity and evolution. Our results indicate that while the nucleotide variability is almost uniformly distributed along the entire length of the gene, the amino acid variability is not. We found that most of the differences were concentrated along the protein's light chain (LC) domain and especially, the C-terminus of the receptor-binding domain (HCC). These two regions of the protein are thus identified as the main source of the toxin type differentiation, and consequently, this toxin's versatility to bind different receptors and their isoforms and act upon different substrates, thus infecting different hosts.
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Brhane H, Haileselassie T, Tesfaye K, Ortiz R, Hammenhag C, Abreha KB, Geleta M. Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses. Front Genet 2022; 13:848627. [PMID: 35559011 PMCID: PMC9090224 DOI: 10.3389/fgene.2022.848627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/21/2022] [Indexed: 12/04/2022] Open
Abstract
Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09–0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.
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Affiliation(s)
- Haftom Brhane
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.,Ethiopian Biotechnology Institute, Ministry of Science and Technology, Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kibrom B Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Antonova EV, Röder MS. Evaluation of the genetic structure of Bromus inermis populations from chemically and radioactively polluted areas using microsatellite markers from closely related species. Int J Radiat Biol 2021; 98:1289-1300. [PMID: 34855571 DOI: 10.1080/09553002.2022.2013569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Hypothesis The ecotoxicological and radiobiological effects can be manifested in a decrease in genetic diversity with an increase in toxic and radiation load, in an increase in the frequencies of rare and/or unique (private) alleles in impact samples, and in a decrease in the differentiation of B. inermis populations within each pollution area.Materials and methods We have selected a collection of primers for Bromus inermis, consisting of 21 microsatellite (SSR) loci from B. sterilis, B. tectorum and Triticum aestivum. The level of toxic load (chemically polluted area) was 4-19 conventional units, and the absorbed dose rate (the Kyshtym accident area) varied from 0.153 to 21.5 μGy h-1, which is up to two orders higher than the natural background radiation level (≈ 0.1 μGy h-1).Results Only eight of 21 (38%) of SSR primers showed good transferability and were used for B. inermis population studies from areas of technogenic pollution (heavy metals and radionuclides). We revealed 42 alleles at eight loci, and the number of alleles per locus varied from one to 13 in B. inermis populations. The percentage of polymorphic loci in B. inermis populations was 48.44%, the polymorphism information content (PIC) value was 0.556, and Shannon information index was 0.69 ± 0.3. A total of 22 rare, 14 private and 9 both rare and private alleles were reported for all B. inermis populations. There were no correlations between geographic and genetic distances. Only 6.8% of the genetic variability was distributed among B. inermis populations.Conclusion There was no decrease in genetic diversity ("genetic erosion") found in B. inermis populations growing for a long time under anthropogenic stress. No significant differences in the number of rare and private alleles in the background and impact populations of B. inermis were found. The smooth brome is characterized by low differentiation of the populations. Possible reasons for this phenomenon are discussed.
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Affiliation(s)
- Elena V Antonova
- Laboratory of Population Radiobiology, Institute of Plant & Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta str. 202, Ekaterinburg 620144, Russia
| | - Marion S Röder
- Group of Gene and Genome Mapping, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Stadt Seeland OT Gatersleben 06466, Germany
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Liu M, Findlay W, Dettman J, Wyka SA, Broders K, Shoukouhi P, Dadej K, Kolařík M, Basnyat A, Menzies JG. Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 Claviceps Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model. Toxins (Basel) 2021; 13:toxins13110799. [PMID: 34822583 PMCID: PMC8625505 DOI: 10.3390/toxins13110799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
Ergot fungi (Claviceps spp.) are infamous for producing sclerotia containing a wide spectrum of ergot alkaloids (EA) toxic to humans and animals, making them nefarious villains in the agricultural and food industries, but also treasures for pharmaceuticals. In addition to three classes of EAs, several species also produce paspaline-derived indole diterpenes (IDT) that cause ataxia and staggers in livestock. Furthermore, two other types of alkaloids, i.e., loline (LOL) and peramine (PER), found in Epichloë spp., close relatives of Claviceps, have shown beneficial effects on host plants without evidence of toxicity to mammals. The gene clusters associated with the production of these alkaloids are known. We examined genomes of 53 strains of 19 Claviceps spp. to screen for these genes, aiming to understand the evolutionary patterns of these genes across the genus through phylogenetic and DNA polymorphism analyses. Our results showed (1) varied numbers of eas genes in C. sect. Claviceps and sect. Pusillae, none in sect. Citrinae, six idt/ltm genes in sect. Claviceps (except four in C. cyperi), zero to one partial (idtG) in sect. Pusillae, and four in sect. Citrinae, (2) two to three copies of dmaW, easE, easF, idt/ltmB, itd/ltmQ in sect. Claviceps, (3) frequent gene gains and losses, and (4) an evolutionary hourglass pattern in the intra-specific eas gene diversity and divergence in C. purpurea.
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Affiliation(s)
- Miao Liu
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (W.F.); (J.D.); (P.S.); (K.D.); (A.B.)
- Correspondence: ; Tel.: +1-613-759-1385
| | - Wendy Findlay
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (W.F.); (J.D.); (P.S.); (K.D.); (A.B.)
| | - Jeremy Dettman
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (W.F.); (J.D.); (P.S.); (K.D.); (A.B.)
| | - Stephen A. Wyka
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University St., Peoria, IL 61604, USA;
| | - Parivash Shoukouhi
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (W.F.); (J.D.); (P.S.); (K.D.); (A.B.)
| | - Kasia Dadej
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (W.F.); (J.D.); (P.S.); (K.D.); (A.B.)
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences CAS, 14220 Prague, Czech Republic;
| | - Arpeace Basnyat
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (W.F.); (J.D.); (P.S.); (K.D.); (A.B.)
| | - Jim G. Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada;
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Zhao QB, López-Cortegano E, Oyelami FO, Zhang Z, Ma PP, Wang QS, Pan YC. Conservation Priorities Analysis of Chinese Indigenous Pig Breeds in the Taihu Lake Region. Front Genet 2021; 12:558873. [PMID: 33747032 PMCID: PMC7966724 DOI: 10.3389/fgene.2021.558873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
Most indigenous pig resources are known to originate from China. Thus, establishing conservation priorities for these local breeds is very essential, especially in the case of limited conservation funds. Therefore, in this study, we analyzed 445 individuals belonging to six indigenous breeds from the Taihu Lake Region, using a total of 131,300 SNPs. In order to determine the long-term guidelines for the management of these breeds, we analyzed the level of diversity in the metapopulation following a partition of diversity within and between breed subpopulations, using both measures of genic and allelic diversity. From the study, we found that the middle Meishan (MMS) pig population contributes the most (22%) to the total gene diversity while the Jiaxing black (JX) pig population contributes the most (27%) to the gene diversity between subpopulations. Most importantly, when we consider one breed is removed from the meta-population, the first two breeds prioritized should be JX pig breed and Fengjing pig breed followed by small Meishan (SMS), Mizhu (MI), and Erhualian (EH) if we pay more attention to the gene diversity between subpopulations. However, if the priority focus is on the total gene diversity, then the first breed to be prioritized would be the Shawutou (SW) pig breed followed by JX, MI, EH, and Fengjing (FJ). Furthermore, we noted that if conservation priority is to be based on the allelic diversity between subpopulations, then the MI breed should be the most prioritized breed followed by SW, Erhuanlian, and MMS. Summarily, our data show that different breeds have different contributions to the gene and allelic diversity within subpopulations as well as between subpopulations. Our study provides a basis for setting conservation priorities for indigenous pig breeds with a focus on different priority criteria.
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Affiliation(s)
- Qing-Bo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Eugenio López-Cortegano
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pei-Pei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qi-Shan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yu-Chun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
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Hua Y, Zhang J, Jernberg C, Chromek M, Hansson S, Frykman A, Xiong Y, Wan C, Matussek A, Bai X. Molecular Characterization of the Enterohemolysin Gene ( ehxA) in Clinical Shiga Toxin-Producing Escherichia coli Isolates. Toxins (Basel) 2021; 13:71. [PMID: 33477906 DOI: 10.3390/toxins13010071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 12/04/2022] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) is an important foodborne pathogen with the ability to cause bloody diarrhea (BD) and hemolytic uremic syndrome (HUS). Little is known about enterohemolysin-encoded by ehxA. Here we investigated the prevalence and diversity of ehxA in 239 STEC isolates from human clinical samples. In total, 199 out of 239 isolates (83.26%) were ehxA positive, and ehxA was significantly overrepresented in isolates carrying stx2a + stx2c (p < 0.001) and eae (p < 0.001). The presence of ehxA was significantly associated with BD and serotype O157:H7. Five ehxA subtypes were identified, among which, ehxA subtypes B, C, and F were overrepresented in eae-positive isolates. All O157:H7 isolates carried ehxA subtype B, which was related to BD and HUS. Three ehxA groups were observed in the phylogenetic analysis, namely, group Ⅰ (ehxA subtype A), group Ⅱ (ehxA subtype B, C, and F), and group Ⅲ (ehxA subtype D). Most BD- and HUS-associated isolates were clustered into ehxA group Ⅱ, while ehxA group Ⅰ was associated with non-bloody stool and individuals ≥10 years of age. The presence of ehxA + eae and ehxA + eae + stx2 was significantly associated with HUS and O157:H7 isolates. In summary, this study showed a high prevalence and the considerable genetic diversity of ehxA among clinical STEC isolates. The ehxA genotypes (subtype B and phylogenetic group Ⅱ) could be used as risk predictors, as they were associated with severe clinical symptoms, such as BD and HUS. Furthermore, ehxA, together with stx and eae, can be used as a risk predictor for HUS in STEC infections.
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Tan Y, Hu H, Li C, Luo X, Tan Y, Dai L. [Research progress and applications of strain analysis based on metagenomic data]. Sheng Wu Gong Cheng Xue Bao 2021; 36:2610-2621. [PMID: 33398958 DOI: 10.13345/j.cjb.200380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.
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Affiliation(s)
- Yuxiang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
| | - Han Hu
- Shenzhen Xbiome Biotech Co., Ltd, Shenzhen 518000, Guangdong, China
| | - Chenhao Li
- Genome Institute of Singapore, Singapore 138672
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
| | - Yan Tan
- Shenzhen Xbiome Biotech Co., Ltd, Shenzhen 518000, Guangdong, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
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12
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Hua Y, Bai X, Zhang J, Jernberg C, Chromek M, Hansson S, Frykman A, Yang X, Xiong Y, Wan C, Matussek A. Molecular characteristics of eae-positive clinical Shiga toxin-producing Escherichia coli in Sweden. Emerg Microbes Infect 2020; 9:2562-2570. [PMID: 33179570 PMCID: PMC7733975 DOI: 10.1080/22221751.2020.1850182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/08/2020] [Indexed: 12/19/2022]
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) can cause a wide range of symptoms from asymptomatic carriage, mild diarrhea to bloody diarrhea (BD) and hemolytic uremic syndrome (HUS). Intimin, encoded by the eae gene, also plays a critical role in STEC pathogenesis. Herein, we investigated the prevalence and genetic diversity of eae among clinical STEC isolates from patients with diarrhea, BD, HUS as well as from asymptomatic STEC-positive individuals in Sweden with whole-genome sequencing. We found that 173 out of 239 (72.4%) of clinical STEC strains were eae positive. Six eae subtypes (ϵ1, γ1, β3, θ, ζ and ρ) were identified eae and its subtype γ1 were significantly overrepresented in O157:H7 strains isolated from BD and HUS patients. ϵ1 was associated with O121:H19 and O103:H2 strains, and β3 to O26:H11 strains. The combination of eae subtype γ1 and stx subtype (stx 2 or stx 1+stx 2) is more likely to cause severe disease, suggesting the possibility of using eae genotypes in risk assessment of STEC infection. In summary, this study demonstrated a high prevalence of eae in clinical STEC strains and considerable genetic diversity of eae in STEC strains in Sweden from 1994 through 2018, and revealed association between eae subtypes and disease severity.
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Affiliation(s)
- Ying Hua
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Xiangning Bai
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Ji Zhang
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | | | - Milan Chromek
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sverker Hansson
- Department of Pediatrics, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anne Frykman
- Department of Pediatrics, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Xi Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Chengsong Wan
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
| | - Andreas Matussek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
- Laboratory Medicine, Jönköping Region County, Jönköping, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
- Division of Laboratory Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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13
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Peters SO, Hussain T, Adenaike AS, Hazzard J, Morenikeji OB, De Donato M, Paul S, Babar M, Yakubu A, Imumorin IG. Evolutionary Pattern of Interferon Alpha Genes in Bovidae and Genetic Diversity of IFNAA in the Bovine Genome. Front Immunol 2020; 11:580412. [PMID: 33117386 PMCID: PMC7561390 DOI: 10.3389/fimmu.2020.580412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Interferons are secretory proteins induced in response to specific extracellular stimuli which stimulate intra- and intercellular networks for regulating innate and acquired immunity, resistance to viral infections, and normal and tumor cell survival and death. Type 1 interferons plays a major role in the CD8 T-cell response to viral infection. The genomic analysis carried out here for type I interferons within Bovidae family shows that cattle, bison, water buffalo, goat, and sheep (all Bovidae), have different number of genes of the different subtypes, with a large increase in the numbers, compared to human and mouse genomes. A phylogenetic analysis of the interferon alpha (IFNA) proteins in this group shows that the genes do not follow the evolutionary pattern of the species, but rather a cycle of duplications and deletions in the different species. In this study we also studied the genetic diversity of the bovine interferon alpha A (IFNAA), as an example of the IFNA genes in cattle, sequencing a fragment of the coding sequence in 18 breeds of cattle from Pakistan, Nigeria and USA. Similarity analysis allowed the allocation of sequences into 22 haplotypes. Bhagnari, Brangus, Sokoto Gudali, and White Fulani, had the highest number of haplotypes, while Angus, Hereford and Nari Master had the least. However, when analyzed by the average haplotype count, Angus, Bhagnari, Hereford, Holstein, Muturu showed the highest values, while Cholistani, Lohani, and Nari Master showed the lowest values. Haplotype 4 was found in the highest number of individuals (74), and in 15 breeds. Sequences for yak, bison, and water buffalo, were included within the bovine haplotypes. Medium Joining network showed that the sequences could be divided into 4 groups: one with highly similar haplotypes containing mostly Asian and African breeds, one with almost all of the Bos taurus American breeds, one mid-diverse group with mostly Asian and African sequences, and one group with highly divergent haplotypes with five N'Dama sequences and one from each of White Fulani, Dhanni, Tharparkar, and Bhagnari. The large genetic diversity found in IFNAA could be a very good indication of the genetic variation among the different genes of IFNA and could be an adaptation for these species in response to viral challenges they face.
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Affiliation(s)
- Sunday O. Peters
- Department of Animal Science, Berry College, Mount Berry, GA, United States
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Adeyemi S. Adenaike
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Jordan Hazzard
- Department of Animal Science, Berry College, Mount Berry, GA, United States
| | - Olanrewaju B. Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
- Department of Biology, Hamilton College, Clinton, NY, United States
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Sujay Paul
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Masroor Babar
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | | | - Ikhide G. Imumorin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
- Department of Biological Sciences, First Technical University, Ibadan, Nigeria
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Lefèvre F, Gallais A. Partitioning heterozygosity in subdivided populations: Some misuses of Nei's decomposition and an alternative probabilistic approach. Mol Ecol 2020; 29:2957-2962. [PMID: 32594582 DOI: 10.1111/mec.15527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/05/2023]
Abstract
Nei's decomposition of total expected heterozygosity in subdivided populations into within- and between-subpopulation components, HS and DST , respectively, is a classical tool in the conservation and management of genetic resources. Reviewing why this is not a decomposition into independent terms of within- and between-subpopulation gene diversity, we illustrate how this approach can be misleading because it overemphasizes the within-subpopulation component compared to Jost's nonadditive decomposition based on gene diversity indices. Using probabilistic partitioning of the total expected heterozygosity into independent within- and between-subpopulation contributions, we show that the contribution of the within-subpopulation expected heterozygosity to the total expected heterozygosity is not HS , as suggested by Nei's decomposition, but HS /s, with s being the number of subpopulations. Finally, we compare three possible approaches of decomposing total heterozygosity in subdivided populations (i.e., Nei's decomposition, Jost's approach, and probabilistic partitioning) with regard to independence between terms and sensitivity to unequal subpopulation sizes. For the conservation and management of genetic resources, we recommend using probabilistic partitioning and Jost's differentiation parameter rather than Nei's decomposition.
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Affiliation(s)
- François Lefèvre
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
| | - André Gallais
- UMR Génétique Quantitative et Evolution, INRAE-UPS-CNRS, Gif-sur-Yvette, France
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15
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Dauphin B, Wüest RO, Brodbeck S, Zoller S, Fischer MC, Holderegger R, Gugerli F, Rellstab C. Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine. Mol Ecol 2020; 29:1972-1989. [PMID: 32395881 DOI: 10.1111/mec.15467] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 01/27/2023]
Abstract
It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at > 17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, FST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (He ) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.
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Affiliation(s)
| | - Rafael O Wüest
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Sabine Brodbeck
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Martin C Fischer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Rolf Holderegger
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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16
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Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe 2019; 26:283-295.e8. [PMID: 31415755 PMCID: PMC6716383 DOI: 10.1016/j.chom.2019.07.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/01/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023]
Abstract
Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.
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Affiliation(s)
- Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA; Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Christina Baek
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
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17
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Sultana S, Kitajima M, Kobayashi H, Nakagawa H, Shimizu M, Kageyama K, Suga H. A Natural Variation of Fumonisin Gene Cluster Associated with Fumonisin Production Difference in Fusarium fujikuroi. Toxins (Basel) 2019; 11:toxins11040200. [PMID: 30987138 PMCID: PMC6521250 DOI: 10.3390/toxins11040200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/14/2019] [Accepted: 03/21/2019] [Indexed: 12/03/2022] Open
Abstract
Fusarium fujikuroi, a member of the Fusarium fujikuroi species complex, stands out as a rice bakanae disease pathogen with a high production of gibberellic acid. Not all, but some F. fujikuroi strains are known to produce a carcinogenic mycotoxin fumonisin. Fumonisin biosynthesis is dependent on the FUM cluster composed of 16 FUM genes. The FUM cluster was detected not only from a fumonisin producing strain, but also from a fumonisin nonproducing strain that does not produce a detectable level of fumonisin. Genetic mapping indicated the causative mutation(s) of fumonisin nonproduction is present in the FUM cluster of the fumonisin nonproducing strain. Comparative analyses of FUM genes between the fumonisin producing and the nonproducing strains and gene complementation indicated that causative mutation of fumonisin nonproduction is not a single occurrence and the mutations are distributed in FUM21 and FUM7. Our research revealed a natural variation in the FUM cluster involving fumonisin production difference in F. fujikuroi.
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Affiliation(s)
- Sharmin Sultana
- The United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan.
| | - Miha Kitajima
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Hironori Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Hiroyuki Nakagawa
- Faculty of National Food Research Institute, NARO, Tsukuba 305-8642, Japan.
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan.
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan.
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18
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Schmidt DJ, Fallon S, Roberts DT, Espinoza T, McDougall A, Brooks SG, Kind PK, Bond NR, Kennard MJ, Hughes JM. Monitoring age-related trends in genomic diversity of Australian lungfish. Mol Ecol 2018; 27:3231-3241. [PMID: 29989297 DOI: 10.1111/mec.14791] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 11/28/2022]
Abstract
An important challenge for conservation science is to detect declines in intraspecific diversity so that management action can be guided towards populations or species at risk. The lifespan of Australian lungfish (Neoceratodus forsteri) exceeds 80 years, and human impacts on breeding habitat over the last half century may have impeded recruitment, leaving populations dominated by old postreproductive individuals, potentially resulting in a small and declining breeding population. Here, we conduct a "single-sample" evaluation of genetic erosion within contemporary populations of the Australian lungfish. Genetic erosion is a temporal decline in intraspecific diversity due to factors such as reduced population size and inbreeding. We examined whether young individuals showed signs of reduced genetic diversity and/or inbreeding using a novel bomb radiocarbon dating method to age lungfish nonlethally, based on 14 C ratios of scales. A total of 15,201 single nucleotide polymorphic (SNP) loci were genotyped in 92 individuals ranging in age from 2 to 77 years old. Standardized individual heterozygosity and individual inbreeding coefficients varied widely within and between riverine populations, but neither was associated with age, so perceived problems with recruitment have not translated into genetic erosion that could be considered a proximate threat to lungfish populations. Conservation concern has surrounded Australian lungfish for over a century. However, our results suggest that long-lived threatened species can maintain stable levels of intraspecific variability when sufficient reproductive opportunities exist over the course of a long lifespan.
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Affiliation(s)
- Daniel J Schmidt
- Australian Rivers Institute, Griffith University, Nathan, Qld, Australia
| | - Stewart Fallon
- Radiocarbon Facility, Research School of Earth Sciences, The Australian National University, Canberra, ACT, Australia
| | | | - Thomas Espinoza
- Department of Natural Resources and Mines, Bundaberg, Qld, Australia
| | - Andrew McDougall
- Department of Natural Resources and Mines, Bundaberg, Qld, Australia
| | - Steven G Brooks
- Queensland Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
| | - Peter K Kind
- Queensland Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
| | - Nick R Bond
- Australian Rivers Institute, Griffith University, Nathan, Qld, Australia
- The Murray-Darling Basin Freshwater Research Centre, Latrobe University, Albury-Wodonga, Vic, Australia
| | - Mark J Kennard
- Australian Rivers Institute, Griffith University, Nathan, Qld, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Nathan, Qld, Australia
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19
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Xu C, Fu J, Ai J, Zhang J, Liu C, Huo X, Bao C, Zhu Y. Phylogenetic analysis of human G9P[8] rotavirus strains circulating in Jiangsu, China between 2010 and 2016. J Med Virol 2018; 90:1461-1470. [PMID: 29719060 DOI: 10.1002/jmv.25214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/30/2018] [Indexed: 12/27/2022]
Abstract
Rotavirus A (RVA) is the leading cause of acute viral gastroenteritis in children under 5 years of age worldwide. G9P[8] is a common RVA genotype that has been persistently prevalent in Jiangsu, China. To determine the genetic diversity of G9P[8] RVAs, 7 representative G9P[8] strains collected from Suzhou Children's Hospital between 2010 and 2016 (named JS2010-JS2016) were analyzed through whole-genome sequencing. All evaluated strains showed the Wa-like constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Furthermore, phylogenetic analysis revealed that the VP7 genes of all strains clustered into lineage G9-III and G9-VI. With the exception of strain JS2012 (P[8]-4), the VP4 sequences of all strains belonged to the P[8]-3 lineage. Sequencing further revealed that amino acid substitutions were present in the antigenic regions of the VP7 and VP4 genes of all strains. Moreover, there were multiple substitutions in antigenic sites I and II of the nonstructural protein 4 (NSP4) genes, whereas the other NSP genes were relatively conserved. In conclusion, our phylogenetic analysis of these 7 G9P[8] strains suggests that RVA varied across regions and time. Therefore, our findings suggest that continued surveillance is necessary to explore the molecular evolutionary characteristics of RVA for better prevention and treatment of acute viral gastroenteritis.
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Affiliation(s)
- Cheng Xu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianguang Fu
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jing Ai
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jun Zhang
- Department of Acute Infectious Disease Control and Prevention, Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Cheng Liu
- Department of Acute Infectious Disease Control and Prevention, Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Xiang Huo
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Key Lab of Enteric Pathogenic Microbiology, Ministry of Health, Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yefei Zhu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Lstibůrek M, El-Kassaby YA, Skrøppa T, Hodge GR, Sønstebø JH, Steffenrem A. Dynamic Gene-Resource Landscape Management of Norway Spruce: Combining Utilization and Conservation. Front Plant Sci 2017; 8:1810. [PMID: 29093732 PMCID: PMC5651282 DOI: 10.3389/fpls.2017.01810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
Traditional gene-resource management programs for forest trees are long-term endeavors requiring sustained organizational commitment covering extensive landscapes. While successful in maintaining adaptation, genetic diversity and capturing traditional growth attributes gains, these programs are dependent on rigid methods requiring elaborate mating schemes, thus making them slow in coping with climate change challenges. Here, we review the significance of Norway spruce in the boreal region and its current management practices. Next, we discuss opportunities offered by novel technologies and, with the use of computer simulations, we propose and evaluate a dynamic landscape gene-resource management in Norway. Our suggested long-term management approach capitalizes on: (1) existing afforestation activities, natural crosses, and DNA-based pedigree assembly to create structured pedigree for evaluation, thus traditional laborious control crosses are avoided and (2) landscape level genetic evaluation, rather than localized traditional progeny trials, allowing for screening of adapted individuals across multiple environmental gradients under changing climate. These advantages lead to greater genetic response to selection in adaptive traits without the traditional breeding and testing scheme, facilitating conservation of genetic resources within the breeding population of the most important forest tree species in Norway. The use of in situ selection from proven material exposed to realistic conditions over vast territories has not been conducted in forestry before. Our proposed approach is in contrast to worldwide current programs, where genetic evaluation is constrained by the range of environments where testing is conducted, which may be insufficient to capture the broad environmental variation necessary to tackle adaptation under changing climate.
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Affiliation(s)
- Milan Lstibůrek
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | | | - Tore Skrøppa
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Gary R. Hodge
- Camcore, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
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Chen H, Yin Y, Wang Y, Wang X, Xiang C. Host Specificity of Flagellins from Segmented Filamentous Bacteria Affects Their Patterns of Interaction with Mouse Ileal Mucosal Proteins. Appl Environ Microbiol 2017; 83:e01061-17. [PMID: 28687648 DOI: 10.1128/AEM.01061-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022] Open
Abstract
Segmented filamentous bacteria (SFB) are known modulators of the mammalian immune system. Currently, the technology for investigating SFB culture in vitro is immature, and as a result, the mechanisms of SFB colonization and immune regulation are not yet fully elucidated. In this study, we investigated the gene diversity and host specificity of SFB flagellin genes. The fliC1 and fliC2 genes are relatively conserved, while the fliC3 and fliC4 genes are more variable, especially at the central and C-terminal regions. Host specificity analysis demonstrated that the fliC1 genes do not cluster together based on the host organism, whereas the fliC3 and fliC4 genes were host specific at the nucleotide and deduced amino acid levels. SFB flagellin protein expression in the ileum mucosa and cecal contents was detected by using fluorescence in situ hybridization (FISH) combined with immunohistochemical (IHC) analysis, immunoblotting, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Although the purified SFB FliC3 protein originating from both mouse and rat was able to activate Toll-like receptor 5 (TLR5)-linked NF-κB signaling, no host specificity was observed. Interestingly, the patterns of interaction with mouse ileum mucosal proteins were different for mouse FliC3 (mFliC3) and rat FliC3 (rFliC3). Gene Ontology (GO) and KEGG analyses indicated that more adherence-related proteins interacted with mFliC3, while more lysosome- and proteolysis-related proteins interacted with rFliC3. In vitro degradation experiments indicated that the stability of rFliC3 was lower than that of mFliC3 when they were incubated with mouse ileum mucosal proteins. In summary, the gene diversity and host specificity of SFB flagellin genes were investigated, and SFB flagellin expression was detected in gut samples.IMPORTANCE Since SFB genomes contain only one copy of each FliC gene, the diversity of FliC is representative of SFB strain diversity. Currently, little is known regarding the diversity and specificity of members of the group of SFB. The work presented herein demonstrates that select SFB strains, exhibiting unique FliC patterns, are present in a variety of mammalian hosts. SFB fliC genes were found to interact with a number of unique targets, providing further evidence for SFB host selection. Together, this work represents a major advancement in identifying SFB and delineating how members of the group of SFB interact with the host. Future examination of FliC genes will likely enhance our knowledge of intestinal colonization by the gut microbiota.
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Xu B, Xiong C, Deng M, Li J, Tang X, Wu Q, Zhou J, Yang Y, Ding J, Han N, Huang Z. Genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome. J Basic Microbiol 2017; 57:883-895. [PMID: 28745827 DOI: 10.1002/jobm.201700106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/25/2017] [Accepted: 06/06/2017] [Indexed: 11/07/2022]
Abstract
Catechol 1,2-dioxygenase is the key enzyme that catalyzes the cleavage of the aromatic ring of catechol. We explored the genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome by PCR with degenerate primers. A total of 35 gene fragments of C12O were retrieved from microbial DNA in the feces of pygmy loris. Based on phylogenetic analysis, most sequences were closely related to C12O sequences from Acinetobacter. A full-length C12O gene was directly cloned, heterologously expressed in Escherichia coli, and biochemically characterized. Purified catPL12 had optimum pH and temperature pH 8.0 and 25 °C and retained 31 and 50% of its maximum activity when assayed at 0 and 35 °C, respectively. The enzyme was stable at 25 and 37 °C, retaining 100% activity after pre-incubation for 1 h. The kinetic parameters of catPL12 were determined. The enzyme had apparent Km of 67 µM, Vmax of 7.3 U/mg, and kcat of 4.2 s-1 for catechol, and the cleavage activities for 3-methylcatechol, 4-methylcatechol, and 4-chlorocatechol were much less than for catechol, and no activity with hydroquinone or protocatechuate was detected. This study is the first to report the molecular and biochemical characterizations of a cold-adapted catechol 1,2-dioxygenase from a fecal microbial metagenome.
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Affiliation(s)
- Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Caiyun Xiong
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Meng Deng
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junjun Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Yunjuan Yang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
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Ramya AR, Ahamed M L, Satyavathi CT, Rathore A, Katiyar P, Raj AGB, Kumar S, Gupta R, Mahendrakar MD, Yadav RS, Srivastava RK. Towards Defining Heterotic Gene Pools in Pearl Millet [ Pennisetum glaucum (L.) R. Br.]. Front Plant Sci 2017; 8:1934. [PMID: 29552020 PMCID: PMC5841052 DOI: 10.3389/fpls.2017.01934] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/26/2017] [Indexed: 05/09/2023]
Abstract
Pearl millet is a climate resilient crop and one of the most widely grown millets worldwide. Heterotic hybrid development is one of the principal breeding objectives in pearl millet. In a maiden attempt to identify heterotic groups for grain yield, a total of 343 hybrid parental [maintainer (B-) and restorer (R-)] lines were genotyped with 88 polymorphic SSR markers. The SSRs generated a total of 532 alleles with a mean value of 6.05 alleles per locus, mean gene diversity of 0.55, and an average PIC of 0.50. Out of 532 alleles, 443 (83.27%) alleles were contributed by B-lines with a mean of 5.03 alleles per locus. R-lines contributed 476 alleles (89.47%) with a mean of 5.41, while 441 (82.89%) alleles were shared commonly between B- and R-lines. The gene diversity was higher among R-lines (0.55) compared to B-lines (0.49). The unweighted neighbor-joining tree based on simple matching dissimilarity matrix obtained from SSR data clearly differentiated B- lines into 10 sub-clusters (B1 through B10), and R- lines into 11 sub-clusters (R1 through R11). A total of 99 hybrids (generated by crossing representative 9 B- and 11 R- lines) along with checks were evaluated in the hybrid trial. The 20 parents were evaluated in the line trial. Both the trials were evaluated in three environments. Based on per se performance, high sca effects and standard heterosis, F1s generated from crosses between representatives of groups B10R5, B3R5, B3R6, B4UD, B5R11, B2R4, and B9R9 had high specific combining ability for grain yield compared to rest of the crosses. These groups may represent putative heterotic gene pools in pearl millet.
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Affiliation(s)
- A. Radhika Ramya
- Department of Genetics and Plant Breeding, Acharya N. G. Ranga Agricultural University, Guntur, India
- International Crops Research Institute for the Semi-Arid Crops, Patancheru, India
| | - Lal Ahamed M
- Department of Genetics and Plant Breeding, Acharya N. G. Ranga Agricultural University, Guntur, India
| | - C. Tara Satyavathi
- All India Coordinated Research Project on Pearl Millet, Indian Council of Agricultural Research, Jodhpur, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Crops, Patancheru, India
| | - Pooja Katiyar
- International Crops Research Institute for the Semi-Arid Crops, Patancheru, India
| | - A. G. Bhasker Raj
- International Crops Research Institute for the Semi-Arid Crops, Patancheru, India
| | - Sushil Kumar
- Centre of Excellence in Biotechnology, Anand Agricultural University, Anand, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Crops, Patancheru, India
| | | | - Rattan S. Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Crops, Patancheru, India
- *Correspondence: Rakesh K. Srivastava
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Vatandoost N, Salehi AR, Kazemi M, Khosravi S, Eslami G, Kamali S, Salehi R. Genetic polymorphism of 8 Y-STR loci in native population of Isfahan province in central part of Iran. Ann Hum Biol 2016; 44:175-179. [PMID: 27282193 DOI: 10.1080/03014460.2016.1200671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification and population studies. AIM Here we present the allelic and haplotype frequencies of 8 Y-STR loci most commonly used in forensic medicine in 103 unrelated native males of Isfahan province, central part of Iran. SUBJECTS AND METHODS The cases were selected on the basis of strict criteria to assure pure native populations of Isfahan origin. DNA extracted from peripheral blood samples and PCR amplified for each marker. Y-specific STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 were included in this study. RESULTS The most common alleles for each locus were: DYS19, allele 12; DYS385, allele 12; DYS389I, allele 13; DYS389II, allele 29; DYS390, allele 24; DYS391, allele 10; DYS392, allele 11; and DYS393, allele 13. Gene diversity value was calculated from the allelic frequency for each locus. The average gene diversity was 0.6518. A total of 101 haplotypes were observed in eight Y-specific STR loci, the haplotype diversity was raised to 0.986. CONCLUSION The results revealed that a set of eight Y-specific STR loci were able to discriminate most of the male individuals in the population studied. A search through the Y Haplotype Reference Database demonstrated 21 matched haplotypes to 160,693 haplotypes, exclusively with Eurasian-European, Eurasian, and Eurasian-Indo Iranian populations.
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Affiliation(s)
- Nasimeh Vatandoost
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Ahmad Reza Salehi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Mohammad Kazemi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Sharifeh Khosravi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Gilda Eslami
- b Department of Parasitology and Mycology, Faculty of Medicine , Shahid Sadoughi University of Medical Sciences , Yazd , Iran
| | - Sara Kamali
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran
| | - Rasoul Salehi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan, Iran.,c Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences , Isfahan , Iran.,d Gerfa Namayesh Azmayesh (GENAZMA) Research & Science Institute , Isfahan, Iran
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25
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Golicz AA, Batley J, Edwards D. Towards plant pangenomics. Plant Biotechnol J 2016; 14:1099-105. [PMID: 26593040 DOI: 10.1111/pbi.12499] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/18/2015] [Accepted: 10/04/2015] [Indexed: 05/05/2023]
Abstract
As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.
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Affiliation(s)
- Agnieszka A Golicz
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
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Zhao W, Chen JJ, Foley S, Wang Y, Zhao S, Basinger J, Zou W. Biomarker identification from next-generation sequencing data for pathogen bacteria characterization and surveillance. Biomark Med 2015; 9:1253-64. [PMID: 26501894 DOI: 10.2217/bmm.15.88] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIM The purpose was to develop an analytical pipeline for specific gene analysis and biomarker discovery from next generation sequencing (NGS) data. MATERIALS & METHODS As a test case, the fliC gene reference sequences of 24 Salmonella enterica strains of 13 serotypes and NGS reads of 32 serovar Newport, 48 Montevideo and 115 Enteritidis outbreak isolates were retrieved from the National Center for Biotechnology Information database. RESULTS Establishment of an analytical pipeline consisting of four steps: reference sequences retrieval and template sequence determination; NGS sequence reads retrieval; multiple sequence alignments and phylogenetic analysis; data mining and biomarker discovery. CONCLUSION The pipeline developed provides an effective bioinformatics tool for genetic diversity clarification and marker sequences discovery for pathogen characterization and surveillance.
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Affiliation(s)
- Weizhong Zhao
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - James J Chen
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Steven Foley
- Division of Microbiology, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Yuping Wang
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Shaohua Zhao
- Division of Animal & Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food & Drug Administration, Laurel, MD 20993, USA
| | - John Basinger
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Wen Zou
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
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Vilas A, Pérez-Figueroa A, Quesada H, Caballero A. Allelic diversity for neutral markers retains a higher adaptive potential for quantitative traits than expected heterozygosity. Mol Ecol 2015. [PMID: 26222582 DOI: 10.1111/mec.13334] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The adaptive potential of a population depends on the amount of additive genetic variance for quantitative traits of evolutionary importance. This variance is a direct function of the expected frequency of heterozygotes for the loci which affect the trait (QTL). It has been argued, but not demonstrated experimentally, that long-term response to selection is more dependent on QTL allelic diversity than on QTL heterozygosity. Conservation programmes, aimed at preserving this variation, usually rely on neutral markers rather than on quantitative traits for making decisions on management. Here, we address, both through simulation analyses and experimental studies with Drosophila melanogaster, the question of whether allelic diversity for neutral markers is a better indicator of a high adaptive potential than expected heterozygosity. In both experimental and simulation studies, we established synthetic populations for which either heterozygosity or allelic diversity was maximized using information from QTL (simulations) or unlinked neutral markers (simulations and experiment). The synthetic populations were selected for the quantitative trait to evaluate the evolutionary potential provided by the two optimization methods. Our results show that maximizing the number of alleles of a low number of markers implies higher responses to selection than maximizing their heterozygosity.
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Affiliation(s)
- Ana Vilas
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310, Vigo, Spain
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310, Vigo, Spain
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Sheng P, Li Y, Marshall SD, Zhang H. High Genetic Diversity of Microbial Cellulase and Hemicellulase Genes in the Hindgut of Holotrichia parallela Larvae. Int J Mol Sci 2015; 16:16545-59. [PMID: 26197317 DOI: 10.3390/ijms160716545] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this study, we used a culture-independent method based on library construction and sequencing to analyze the genetic diversity of the cellulase and hemicellulase genes of the bacterial community resident in the hindgut of Holotrichia parallela larvae. The results indicate that there is a large, diverse set of bacterial genes encoding lignocellulose hydrolysis enzymes in the hindgut of H. parallela. The total of 101 distinct gene fragments (similarity <95%) of glycosyl hydrolase families including GH2 (24 genes), GH8 (27 genes), GH10 (19 genes), GH11 (14 genes) and GH36 (17 genes) families was retrieved, and certain sequences of GH2 (10.61%), GH8 (3.33%), and GH11 (18.42%) families had <60% identities with known sequences in GenBank, indicating their novelty. Based on phylogenetic analysis, sequences from hemicellulase families were related to enzymes from Bacteroidetes and Firmicutes. Fragments from cellulase family were most associated with the phylum of Proteobacteria. Furthermore, a full-length endo-xylanase gene was obtained, and the enzyme exhibited activity over a broad range of pH levels. Our results indicate that there are large number of cellulolytic and xylanolytic bacteria in the hindgut of H. parallela larvae, and these symbiotic bacteria play an important role in the degradation of roots and other organic matter for the host insect.
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Zhivotovsky LA. Relationships Between Wright's F ST and F IS Statistics in a Context of Wahlund Effect. J Hered 2015; 106:306-9. [PMID: 25888609 DOI: 10.1093/jhered/esv019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/20/2015] [Indexed: 11/14/2022] Open
Abstract
Waples (2015) has suggested a formula for the Wahlund effect in a case of unequal contribution of samples from genetically different populations that relates Wright's inbreeding coefficient, F IS , and normalized variance in allele frequencies between populations, F ST . I generalize this relationship to a case of multiple alleles and multiple populations not assuming Hardy-Weinberg ratios prior to mixing. This can help to evaluate the impact of a Wahlund effect on heterozygote deficiency relative to other factors such as null alleles, nonrandom mating, or selection. It is suggested that Wahlund effect cannot be an important factor of deviations from Hardy-Weinberg proportions in natural populations in the majority of instances, but it can have a substantial contribution to heterozygote deficiency in a population that has low genetic diversity compared to that among immigrants or in mixed samples that contain comparable fractions of individuals from genetically different populations.
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Affiliation(s)
- Lev A Zhivotovsky
- From the Institute of General Genetics, The Russian Academy of Sciences, Moscow 119991, Russia.
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Moaeen-ud-Din M, Bilal G. Sequence diversity and molecular evolutionary rates between buffalo and cattle. J Anim Breed Genet 2015; 132:74-84. [PMID: 25619307 DOI: 10.1111/jbg.12100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/12/2014] [Indexed: 12/19/2022]
Abstract
Identification of genes of importance regarding production traits in buffalo is impaired by a paucity of genomic resources. Choice to fill this gap is to exploit data available for cow. The cross-species application of comparative genomics tools is potential gear to investigate the buffalo genome. However, this is dependent on nucleotide sequences similarity. In this study, gene diversity between buffalo and cattle was determined using 86 gene orthologues. There was approximately 3% difference in all genes in terms of nucleotide diversity and 0.267 ± 0.134 in amino acids, indicating the possibility for successfully using cross-species strategies for genomic studies. There were significantly higher non-synonymous substitutions both in cattle and buffalo; however, there was similar difference in terms of dN- dS (4.414 versus 4.745) in buffalo and cattle, respectively. Higher rate of non-synonymous substitutions at similar level in buffalo and cattle indicated a similar positive selection pressure. Results for relative rate test were assessed with the chi-squared test. There was no significance difference on unique mutations between cattle and buffalo lineages at synonymous sites. However, there was a significance difference on unique mutations for non-synonymous sites, indicating ongoing mutagenic process that generates substitutional mutation at approximately the same rate at silent sites. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of cattle and buffalo. This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.
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Affiliation(s)
- M Moaeen-ud-Din
- Laboratories of Animal Breeding & Genetics, Faculty of Veterinary & Animal Sciences, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
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Affiliation(s)
- Akio Kanai
- Functional RNA Group, Institute for Advanced Biosciences, Keio University Tsuruoka, Japan
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Ohtsuki T, Shoda T, Kaneko Y, Setoguchi H. Development of microsatellite markers for Vitex rotundifolia (Verbenaceae), an endangered coastal plant in Lake Biwa, Japan. Appl Plant Sci 2014; 2:apps.1300100. [PMID: 25202620 PMCID: PMC4103139 DOI: 10.3732/apps.1300100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 01/25/2014] [Indexed: 06/03/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY Microsatellite loci were developed for Vitex rotundifolia, an endangered species isolated to Lake Biwa, to investigate its genetic diversity and population structure. • METHODS AND RESULTS Ten primer sets were identified in Japanese populations of V. rotundifolia. The number of alleles per locus ranged from one to six and gene diversity per locus ranged from 0.040 to 0.697 between two populations. In addition, all loci could be successfully amplified in V. trifolia. • CONCLUSIONS These markers will be useful for studies of genetic diversity and population structure of endangered species isolated to Lake Biwa of V. rotundifolia, to aid in the development of conservation strategies.
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Affiliation(s)
- Tatsuo Ohtsuki
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tasuku Shoda
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8224, Japan
| | - Yuko Kaneko
- Lake Biwa Environmental Research Institute, 5-34 Yanagasaki, Otsu-city, Shiga 520-0022, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Abstract
A canon of population genetics concerns the properties of FST, a descriptor of spatial genetic structure. Interest for FST arose from Wright's early insights linking FST to dispersal parameters as well as to his concept of effective population size (e.g., Wright 1938, 1951). Although there is continued interest in this topic, FST also serves in other applications, such as detecting selected markers in natural populations (Beaumont and Nichols 1996) and more often in routine descriptive works. Remarkably, it is the latter use that seems to attract most discussion. Alternative descriptors have been proposed. Conversely, attempts have been made to draw biological inferences from FST properties that do not depend on biological processes. A reconsideration of its properties under biological scenarios underlines the weaknesses of such approaches.
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Abstract
Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided.
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Affiliation(s)
- Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
| | - Aurora García-Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28080 Madrid, Spain
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Choi J, Kim H, Lee YH. Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing. Plant Pathol J 2013; 29:435-9. [PMID: 25288972 PMCID: PMC4174813 DOI: 10.5423/ppj.nt.04.2013.0042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/25/2013] [Accepted: 05/25/2013] [Indexed: 06/03/2023]
Abstract
Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980's. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.
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Affiliation(s)
- Jaehyuk Choi
- Center for Fungal Pathogenesis, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Hyojung Kim
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Yong-Hwan Lee
- Center for Fungal Pathogenesis, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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36
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Abstract
Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided.
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Affiliation(s)
- Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
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Sánchez-Molano E, Caballero A, Fernández J. Efficiency of conservation management methods for subdivided populations under local adaptation. ACTA ACUST UNITED AC 2013; 104:554-64. [PMID: 23526788 DOI: 10.1093/jhered/est016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Computer simulations were used to investigate the efficiency of management methods for the conservation of a structured population when local adaptation exists. A subdivided population, with subpopulations adapted to different optima for a quantitative trait under stabilizing selection, was managed in order to maintain the highest genetic diversity in a 10-generation period. Two procedures were compared. For the first, minimum coancestry contributions were carried out independently for each subpopulation, and random migration of individuals was accomplished thereafter. For the second, minimum coancestry contributions from individuals were globally implemented, including an optimal migration design. This optimal method can be adjusted to control local inbreeding to different extents. Adaptation to local optima implies a reduction in the efficiency of the management methods because of the effective failure in the established migrations. For strong selection, the optimal design can be very inefficient, even more than the random migration scheme because the intended migrants have usually low fitness in the recipient subpopulations. However, for more realistic moderate or weak selection, the optimal method is more efficient than random migration, especially if inbreeding depression on fitness is also taken into account. It is concluded that the optimal management method can be recommended in conservation programs with local adaptation of subpopulations, but this issue should be accounted for when designing the management strategies.
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Affiliation(s)
- Enrique Sánchez-Molano
- Departamento de Mejora Genética, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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Moleirinho A, Seixas S, Lopes AM, Bento C, Prata MJ, Amorim A. Evolutionary constraints in the β-globin cluster: the signature of purifying selection at the δ-globin (HBD) locus and its role in developmental gene regulation. Genome Biol Evol 2013; 5:559-71. [PMID: 23431002 PMCID: PMC3622298 DOI: 10.1093/gbe/evt029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2013] [Indexed: 12/15/2022] Open
Abstract
Human hemoglobins, the oxygen carriers in the blood, are composed by two α-like and two β-like globin monomers. The β-globin gene cluster located at 11p15.5 comprises one pseudogene and five genes whose expression undergoes two critical switches: the embryonic-to-fetal and fetal-to-adult transition. HBD encodes the δ-globin chain of the minor adult hemoglobin (HbA2), which is assumed to be physiologically irrelevant. Paradoxically, reduced diversity levels have been reported for this gene. In this study, we sought a detailed portrait of the genetic variation within the β-globin cluster in a large human population panel from different geographic backgrounds. We resequenced the coding and noncoding regions of the two adult β-globin genes (HBD and HBB) in European and African populations, and analyzed the data from the β-globin cluster (HBE, HBG2, HBG1, HBBP1, HBD, and HBB) in 1,092 individuals representing 14 populations sequenced as part of the 1000 Genomes Project. Additionally, we assessed the diversity levels in nonhuman primates using chimpanzee sequence data provided by the PanMap Project. Comprehensive analyses, based on classic neutrality tests, empirical and haplotype-based studies, revealed that HBD and its neighbor pseudogene HBBP1 have mainly evolved under purifying selection, suggesting that their roles are essential and nonredundant. Moreover, in the light of recent studies on the chromatin conformation of the β-globin cluster, we present evidence sustaining that the strong functional constraints underlying the decreased contemporary diversity at these two regions were not driven by protein function but instead are likely due to a regulatory role in ontogenic switches of gene expression.
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Affiliation(s)
- Ana Moleirinho
- Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal.
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Pradeep AR, Jingade AH, Singh CK, Awasthi AK, Kumar V, Rao GC, Prakash NBV. Genetic analysis of scattered populations of the Indian eri silkworm, Samia cynthia ricini Donovan: Differentiation of subpopulations. Genet Mol Biol 2011; 34:502-10. [PMID: 21931526 PMCID: PMC3168194 DOI: 10.1590/s1415-47572011005000033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 05/04/2011] [Indexed: 11/21/2022] Open
Abstract
Deforestation and exploitation has led to the fragmentation of habitats and scattering of populations of the economically important eri silkworm, Samia cynthia ricini, in north-east India. Genetic analysis of 15 eri populations, using ISSR markers, showed 98% inter-population, and 23% to 58% intra-population polymorphism. Nei's genetic distance between populations increased significantly with altitude (R(2) = 0.71) and geographic distance (R(2) = 0.78). On the dendrogram, the lower and upper Assam populations were clustered separately, with intermediate grouping of those from Barpathar and Chuchuyimlang, consistent with geographical distribution. The Nei's gene diversity index was 0.350 in total populations and 0.121 in subpopulations. The genetic differentiation estimate (Gst) was 0.276 among scattered populations. Neutrality tests showed deviation of 118 loci from Hardy-Weinberg equilibrium. The number of loci that deviated from neutrality increased with altitude (R(2) = 0.63). Test of linkage disequilibrium showed greater contribution of variance among eri subpopulations to total variance. D('2)IS exceeded D('2)ST, showed significant contribution of random genetic drift to the increase in variance of disequilibrium in subpopulations. In the Lakhimpur population, the peripheral part was separated from the core by a genetic distance of 0.260. Patchy habitats promoted low genetic variability, high linkage disequilibrium and colonization by new subpopulations. Increased gene flow and habitat-area expansion are required to maintain higher genetic variability and conservation of the original S. c. ricini gene pool.
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Peter M, Courty PE, Kohler A, Delaruelle C, Martin D, Tagu D, Frey-Klett P, Duplessis S, Chalot M, Podila G, Martin F. Analysis of expressed sequence tags from the ectomycorrhizal basidiomycetes Laccaria bicolor and Pisolithus microcarpus. New Phytol 2003; 159:117-129. [PMID: 33873685 DOI: 10.1046/j.1469-8137.2003.00796.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• In an effort to discover genes that are expressed in the ectomycorrhizal basidiomycetes Laccaria bicolor and Pisolithus microcarpus, and in P. microcarpus/Eucalyptus globulus ectomycorrhizas, we have sequenced 1519 and 1681 expressed sequence tags (ESTs) from L. bicolor and P. microcarpus cDNA libraries. • Contig analysis resulted in 905 and 806 tentative consensus sequences (unique transcripts) in L. bicolor and P. microcarpus, respectively. For 36% of the ESTs, significant similarities to sequences in databases were detected. The most abundant transcripts showed no similarity to previously identified genes. Sequence redundancy analysis between different developmental stages indicated that several genes were differentially expressed in free-living mycelium and symbiotic tissues of P. microcarpus. • Based on sequence similarity, 11% of L. bicolor unique transcripts were also detected in P. microcarpus. Similarly, L. bicolor and P. microcarpus shared only a low proportion of common transcripts with other basidiomycetous fungi, such as Pleurotus ostreatus and Agaricus bisporus. Such a low proportion of shared transcripts between basidiomycetes suggests, on the one hand, that the variability of expressed transcripts in different fungi and fungal tissues is considerably high. On the other hand, it might reflect the low number of GenBank entries of basidiomycetous origin and stresses the necessity of an additional sequencing effort. • The present ESTs provide a valuable resource for future research on the development and functioning of ectomycorrhizas.
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Affiliation(s)
- Martina Peter
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
- These authors contributed equally to this work
| | - Pierre-Emmanuel Courty
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
- These authors contributed equally to this work
| | - Annegret Kohler
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
| | - Christine Delaruelle
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
| | - David Martin
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
| | - Denis Tagu
- INRA Rennes, Unité Mixte de Recherche BiO3P, BP 35327, 35653 Le Rheu Cedex, France
| | - Pascale Frey-Klett
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
| | - Sébastien Duplessis
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
| | - Michel Chalot
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
| | - Gopi Podila
- Dept. of Biological Sciences, University of Alabama, Huntsville, AL 35899, USA
| | - Francis Martin
- Unité Mixte de Recherche INRA-UHP 1136 'Interactions Arbres/Microorganismes', Centre de Recherches de Nancy, 54280 Champenoux, France
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Klugbauer N, Lacinová L, Marais E, Hobom M, Hofmann F. Molecular diversity of the calcium channel alpha2delta subunit. J Neurosci 1999; 19:684-91. [PMID: 9880589 PMCID: PMC6782206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Sequence database searches with the alpha2delta subunit as probe led to the identification of two new genes encoding proteins with the essential properties of this calcium channel subunit. Primary structure comparisons revealed that the novel alpha2delta-2 and alpha2delta-3 subunits share 55.6 and 30.3% identity with the alpha2delta-1 subunit, respectively. The number of putative glycosylation sites and cysteine residues, hydropathicity profiles, and electrophysiological character of the alpha2delta-3 subunit indicates that these proteins are functional calcium channel subunits. Coexpression of alpha2delta-3 with alpha1C and cardiac beta2a or alpha1E and beta3 subunits shifted the voltage dependence of channel activation and inactivation in a hyperpolarizing direction and accelerated the kinetics of current inactivation. The kinetics of current activation were altered only when alpha2delta-1 or alpha2delta-3 was expressed with alpha1C. The effects of alpha2delta-3 on alpha1C but not alpha1E are indistinguishable from the effects of alpha2delta-1. Using Northern blot analysis, it was shown that alpha2delta-3 is expressed exclusively in brain, whereas alpha2delta-2 is found in several tissues. In situ hybridization of mouse brain sections showed mRNA expression of alpha2delta-1 and alpha2delta-3 in the hippocampus, cerebellum, and cortex, with alpha2delta-1 strongly detected in the olfactory bulb and alpha2delta-3 in the caudate putamen.
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Affiliation(s)
- N Klugbauer
- Institut für Pharmakologie und Toxikologie der Technischen Universität München, 80802 München, Germany
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