51
|
Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review. DIVERSITY 2022. [DOI: 10.3390/d14121054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.
Collapse
|
52
|
Microsatellite Analysis Revealed Potential DNA Markers for Gestation Length and Sub-Population Diversity in Kari Sheep. Animals (Basel) 2022; 12:ani12233292. [PMID: 36496813 PMCID: PMC9736151 DOI: 10.3390/ani12233292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Kari sheep inhabiting the Chitral district of Pakistan show variation in gestation length. In this study, we have analyzed the genetic differences between the three subtypes of Kari sheep (based on variation in gestation length) using microsatellite markers. Kari sheep samples were collected from their breeding tract and were characterized for gestation length and genetic diversity using microsatellite markers. A total of 78 Kari ewes were grouped into three categories based on gestation length (GL), i.e., Kari-S (with a shorter GL), Kari-M (with a medium GL), and Kari-L (with a longer GL). DNA from these samples was used to amplify 31 ovine-specific microsatellite loci through PCR. Of the total 78 Kari specimens, 24 were grouped in Kari-S (GL = 100.7 ± 1.8), 26 were from the Kari-M subtype (GL = 123.1 ± 1.0), and 28 were Kari-L (GL = 143.8 ± 1.5). Microsatellite analysis revealed an association of genotypes at two marker sites (MAF214 and ILSTS5) with variation in GL. A total of 158 alleles were detected across the 22 polymorphic loci with an average of 7.18 alleles per locus. Unique alleles were found in all three subtypes. The highest number of unique alleles was observed in Kari-L (15), followed by Kari-S (10) and Kari-M (8). The results indicated that Kari-S is a genetically distinct subtype (with higher genetic differentiation and distance) from Kari-M and Kari-L. The genetic uniqueness of Kari-S is important for further exploration of the genetic basis for shorter gestation length, and exploitation of their unique values.
Collapse
|
53
|
High genetic diversity in American chestnut (Castanea dentata) despite a century of decline. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01473-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
54
|
Boiko SM. Identification of novel SSR markers for predicting the geographic origin of fungus Schizophyllum commune Fr. Fungal Biol 2022; 126:764-774. [PMID: 36517144 DOI: 10.1016/j.funbio.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/07/2023]
Abstract
The fungus Schizophyllum commune is a cosmopolitan basidiomycete, which is popular as an edible, medical mushroom. It causes wood rot and often used as a model object in research. In this study, we analyzed thirty-two genomes of S. commune strains from the NCBI database and designed forty-seven unique SSR DNA markers. The detailed analysis revealed the enrichment of the S. commune genome for CG, GC, CTC, GAG, and TCG motifs. Principal components analysis confirmed the effectiveness of novel SSR DNA markers that preserve the initial heterogeneity of populations. The construction of a network between strains showed single one at a maximum similarity of 38%, and increasing the similarity to 55% breaks the linkage between large groups while separating two new groups containing strains of the population Ru and test cultures S. commune. The amplicons' presence was identified as a sufficient sign of relation of the culture to a specific population. Testing the novel SSR markers allowed to establish a clear delimitation of all groups by geographic location and to differentiate the H4-8 (GCA_000143185.1) strain from the USA population. This research is the basis for the further analysis of S. commune populations and improvement of approaches to determine its genetic diversity.
Collapse
Affiliation(s)
- Sergiy M Boiko
- Department of Phytoecology, Institute for Evolutionary Ecology National Academy of Sciences of Ukraine, 37 Lebedeva Str., 03143, Kyiv, Ukraine.
| |
Collapse
|
55
|
Kerry RG, Montalbo FJP, Das R, Patra S, Mahapatra GP, Maurya GK, Nayak V, Jena AB, Ukhurebor KE, Jena RC, Gouda S, Majhi S, Rout JR. An overview of remote monitoring methods in biodiversity conservation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80179-80221. [PMID: 36197618 PMCID: PMC9534007 DOI: 10.1007/s11356-022-23242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.
Collapse
Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | | | - Rajeswari Das
- Department of Soil Science and Agricultural Chemistry, School of Agriculture, GIET University, Gunupur, Rayagada, Odisha 765022 India
| | - Sushmita Patra
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | | | - Ganesh Kumar Maurya
- Zoology Section, Mahila MahaVidyalya, Banaras Hindu University, Varanasi, 221005 India
| | - Vinayak Nayak
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | - Atala Bihari Jena
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Ram Chandra Jena
- Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Sushanto Gouda
- Department of Zoology, Mizoram University, Aizawl, 796009 India
| | - Sanatan Majhi
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Jyoti Ranjan Rout
- School of Biological Sciences, AIPH University, Bhubaneswar, Odisha 752101 India
| |
Collapse
|
56
|
Pham T, Nguyen QT, Tran DM, Nguyen H, Le HT, Hoang QTH, Van YT, Tran TN. Phylogenetic Analysis Based on DNA Barcoding and Genetic Diversity Assessment of Morinda officinalis How in Vietnam Inferred by Microsatellites. Genes (Basel) 2022; 13:1938. [PMID: 36360175 PMCID: PMC9689669 DOI: 10.3390/genes13111938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 09/19/2023] Open
Abstract
Morinda officinalis How is well-known as a valuable medicinal plant found in some regions of Vietnam. This species is mainly used for treating male impotence, irregular menstruation, and rheumatoid arthritis. This study aimed to identify the species of and genetic diversity in three M. officinalis populations: one each in Quang Binh (QB), Thua Thien Hue (TTH), and Quang Nam (QN). In this study, four DNA barcoding markers (ITS1, ITS2, matK, and rbcL) were used to identify the species and 22 microsatellite markers were applied for population structure and diversity analyses. The results showed that the sequences of gene regions studied in M. officinalis had a high similarity (>95%) to the ITS1, ITS2, matK, and rbcL sequences of M. officinalis on BLAST. Of the four DNA barcoding markers used, ITS1 and ITS2 showed higher efficiency in DNA amplification of M. officinalis. From this study, 27 GenBank codes were published on BLAST. The results also revealed high levels of genetic diversity in populations. The average observed and expected heterozygosity values were HO = 0.513 and HE = 0.612, respectively. The average FST value was 0.206. Analysis of molecular variance (AMOVA) showed 70% variation within populations and 30% among populations. The population structure of M. officinalis inferred in STRUCTURE revealed that the optimum number of genetic groups for the admixture model was K = 2. These findings provided vital background information for future studies in the conservation of M. officinalis in both ex situ and in situ plans.
Collapse
Affiliation(s)
- Thanh Pham
- Department of Biology, University of Education, Hue University, 34 Le Loi, Hue 530000, Vietnam
| | - Quynh Thi Nguyen
- Department of Biology, University of Education, Hue University, 34 Le Loi, Hue 530000, Vietnam
| | - Duc Minh Tran
- Faculty of Forestry, University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam
| | - Hoi Nguyen
- Faculty of Forestry, University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam
| | - Hung Thai Le
- Faculty of Forestry, University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam
| | - Que Thi Hong Hoang
- Faculty of Forestry, University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam
| | - Yen Thi Van
- Faculty of Forestry, University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam
| | - Thang Nam Tran
- Faculty of Forestry, University of Agriculture and Forestry, Hue University, 102 Phung Hung, Hue 530000, Vietnam
| |
Collapse
|
57
|
Moya-Moraga MR, Pérez-Ruíz C. Application of MaxEnt Modeling and HRM Analysis to Support the Conservation and Domestication of Gevuina avellana Mol. in Central Chile. PLANTS (BASEL, SWITZERLAND) 2022; 11:2803. [PMID: 36297827 PMCID: PMC9607360 DOI: 10.3390/plants11202803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
The Chilean hazelnut (Gevuina avellana Mol., Proteaceae) is a native tree of Chile and Argentina of edible fruit-type nut. We applied two approaches to contribute to the development of strategies for mitigation of the effects of climate change and anthropic activities in G. avellana. It corresponds to the first report where both tools are integrated, the MaxEnt model to predict the current and future potential distribution coupled with High-Resolution Melting Analysis (HRM) to assess its genetic diversity and understand how the species would respond to these changes. Two global climate models: CNRM-CM6-1 and MIROC-ES2L for four Shared Socioeconomic Pathways: 126, 245, 370, and 585 (2021−2040; 2061−2080) were evaluated. The annual mean temperature (43.7%) and water steam (23.4%) were the key factors for the distribution current of G. avellana (AUC = 0.953). The future prediction model shows to the year 2040 those habitat range decreases at 50% (AUC = 0.918). The genetic structure was investigated in seven natural populations using eight EST-SSR markers, showing a percentage of polymorphic loci between 18.69 and 55.14% and low genetic differentiation between populations (Fst = 0.052; p < 0.001). According to the discriminant analysis of principal components (DAPC) we identified 10 genetic populations. We conclude that high-priority areas for protection correspond to Los Avellanos and Punta de Águila populations due to their greater genetic diversity and allelic richness.
Collapse
Affiliation(s)
- Mario René Moya-Moraga
- Doctoral Program in Biotechnology and Genetic Resources of Plants and Associated Microorganisms (02E4), Polytechnic University of Madrid (UPM), University City, 28040 Madrid, Spain
- Department of Biotechnology, Faculty of Natural Sciences, Mathematics and the Environment (FCNMM), Metropolitan Technological University (UTEM), Ñuñoa 7750000, Chile
| | - César Pérez-Ruíz
- Department of Biotechnology and Plant Biology, School of Agricultural, Food and Biosystems Engineering, Polytechnic University of Madrid (UPM), University City, 28040 Madrid, Spain
| |
Collapse
|
58
|
Liu K, Xie N. Pipeline for developing polymorphic microsatellites in species without reference genomes. 3 Biotech 2022; 12:248. [PMID: 36039078 PMCID: PMC9418399 DOI: 10.1007/s13205-022-03313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/01/2022] Open
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are the preferred type of marker for many genetic applications. In conjunction with the ongoing development of next-generation sequencing, several bioinformatic tools have been developed for identifying SSRs from genomic or transcriptomic sequences. Although these tools are handy for generating polymorphic SSRs, their application almost always depends on an existing reference genome or self-assembly of the reference genome. With this in mind, we propose a pipeline for developing polymorphic SSRs that may be applied to species without reference genomes. Using a species without a reference genome (black Amur bream; Megalobrama terminalis Richardson, 1846) as a model, our pipeline was able to effectively discover polymorphic SSRs. Under different R parameters of a reference-free single nucleotide polymorphisms (SNPs) caller (ebwt2InDel), a total of 258, 208, 102, and 11 polymorphic SSRs were mined. To quantify the accuracy of the polymorphic SSRs detected using our pipeline, we analyzed 25 SSRs with PCR experiments. All primers were successfully amplified, and most SSRs (23 SSRs, 92%) were polymorphic. From the 36 individual black Amur bream, we acquired an average of 3.36 alleles per locus, ranging from one to 11. This demonstrates the effectiveness of our pipeline in identifying polymorphic SSRs and designing primers for SSR genotyping. Ultimately, our pipeline can effectively mine polymorphic SSRs for species without reference genomes, complementing SSR mining approaches based on reference genomes and helping to resolve biological issues that accompany these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03313-0.
Collapse
Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| |
Collapse
|
59
|
Pérez-Nicolás M, Ramírez-Corona F, Colinas-León T, Peña-Ortega G, Ontiveros-Capurata RE, Alia-Tejacal I, González-Andrés F. Diversity and Genetic Structure of Scarlet Plume (Euphorbia fulgens), an Endemic Plant of Mexico. PLANTS 2022; 11:plants11192542. [PMID: 36235408 PMCID: PMC9572564 DOI: 10.3390/plants11192542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022]
Abstract
Euphorbia fulgens is an ornamental species cultivated in Europe and endemic to Mexico; its ecological, genetic, and evolutionary aspects are not known. The objectives of this study were to determine its distribution, describe the places it inhabits, and analyze the diversity and genetic structures of wild populations of E. fulgens. A bibliographic review of the herbarium specimens and a field evaluation were carried out to develop a potential distribution map based on a multi-criteria analysis of the climatic and topographic variables. Three populations (forty-five individuals) from pine–oak and cloud forests located in the Southern Sierra of Oaxaca were analyzed using ten microsatellite loci. The analysis was conducted using Arlequin v. 3.5, Mega v. 10, and Structure v. 2.3 programs. Eight loci were polymorphic, and a total of thirty-eight alleles were obtained. The average number of alleles per polymorphic locus was 4.6. The average heterozygosity of the three populations was high (Ho = 0.5483), and genetic differentiation between populations were low, with a high genetic flow, suggesting that it could be an ancestral population that became fragmented and was just beginning to differentiate genetically. The information generated on this restricted distribution species can be used in conservation programs pertaining to human activities that endanger the habitats where it is found.
Collapse
Affiliation(s)
- Mónica Pérez-Nicolás
- Departamento de Fitotecnia, Universidad Autónoma Chapingo, Texcoco 56230, Mexico
| | - Fabiola Ramírez-Corona
- Taller de Sistemática y Biogeografía, Departamento de Biología Evolutiva, Facultad de Ciencias de la UNAM, Ciudad de México 04510, Mexico
| | - Teresa Colinas-León
- Departamento de Fitotecnia, Universidad Autónoma Chapingo, Texcoco 56230, Mexico
- Correspondence:
| | - Gisela Peña-Ortega
- Departamento de Fitotecnia, Universidad Autónoma Chapingo, Texcoco 56230, Mexico
| | | | - Iran Alia-Tejacal
- Facultad de Ciencias Agropecuarias, Universidad Autónoma del Estado de Morelos, Cuernavaca 62210, Mexico
| | - Fernando González-Andrés
- Instituto de Medio Ambiente, Recusos Naturales y Biodiversidad, Universidad de León, 24009 León, Spain
| |
Collapse
|
60
|
Cohen O, Ram Y, Hadany L, Geffen E, Gafny S. The effect of habitat and climatic on microsatellite diversity and allele length variation. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.893856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microsatellite loci have been shown to vary according to environment. We studied allelic length variation and diversity in eight microsatellite loci along a sharp climatic and habitat gradient in Israel, using the eastern spadefoot toad (Pelobates syriacus) as our model system. We found a gradual increase in allele lengths from north to south. We used a distance-based redundancy analysis (dbRDA) to associate between allele length and habitat and climatic measures and found that geography and annual climate explained the significant variation in allele length. We also used additional measurements pertaining to demography, heterozygosity and allelic diversity to explore four different hypotheses that might explain the variations in allele length. Our results suggest that the changes we observed in allele lengths may not be purely random but could be influenced by the differential mutation rate and/or local environmental conditions operating at the different locations.
Collapse
|
61
|
Pinheiro KDC, Gois BVA, Nogueira WG, Araújo FA, Queiroz ALC, Cardenas-Alegria O, da Silva ALDC, Júnior AMGM, Ramos RTJ. In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes. FRONTIERS IN BIOINFORMATICS 2022; 2:931583. [PMID: 36304273 PMCID: PMC9580864 DOI: 10.3389/fbinf.2022.931583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Corynebacterium pseudotuberculosis is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic markers known as microsatellites, or simple sequence repeats (SSRs), that can be used to characterize the genome, to study possible polymorphisms existing among strains, and to verify the effects of such polymorphic markers in coding regions and regions associated with VFs. In this study, several SSRs were identified within coding regions throughout the 54 genomes of this species, revealing possible polymorphisms associated with coding regions that could be used as strain-specific or serotype-specific identifiers of C. pseudotuberculosis. The similarities associated with SSRs amongst the different serum variants of C. pseudotuberculosis, biovars equi and ovis, were also evaluated, and it was possible to identify SSRs located in coding regions responsible for a VF enrolled in pathogenesis known to mediate bacterial adherence (SpaH-type pili virulence factor). Phylogenetic analyses revealed that strains sharing SSR patterns, including the possible polymorphisms identified in the same position of gene-coding regions, were displayed by strains with a common ancestor, corroborating with the Genome Tree Report of the NCBI. Statistical analysis showed that the microsatellite groups belonging to equi and ovis biovars have a significance of 0.006 (p-value) in similarity, thus indicating them as good biomarker candidates for C. pseudotuberculosis.
Collapse
Affiliation(s)
| | | | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | - Artur Luiz da Costa da Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil
| | | | - Rommel Thiago Jucá Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
- *Correspondence: Rommel Thiago Jucá Ramos,
| |
Collapse
|
62
|
Zhang ZR, Yang X, Li WY, Peng YQ, Gao J. Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions. FRONTIERS IN PLANT SCIENCE 2022; 13:965335. [PMID: 36186045 PMCID: PMC9521400 DOI: 10.3389/fpls.2022.965335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.
Collapse
Affiliation(s)
- Zheng-Ren Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Wei-Ying Li
- Southwest Research Center for Landscape Architecture Engineering Technology, State Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yan-Qiong Peng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| |
Collapse
|
63
|
Bhattacharya P, Patel TN. Looking beyond the cytogenetics in haematological malignancies: decoding the role of tandem repeats in DNA repair genes. Mol Biol Rep 2022; 49:10293-10305. [PMID: 36097110 DOI: 10.1007/s11033-022-07761-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/30/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND In cancer research, one of the most significant findings was to characterize the DNA repair deficiency as carcinogenic. Amongst the various repair mechanisms, mismatch repair (MMR) and direct reversal of DNA damage systems are designated as multilevel safeguards in the human genome. Defects in these elevate the rate of mutations and results in dire consequences like cancer. Of the several molecular signatures in human genome, tandem repeats (TRs) appear at various frequencies in the exonic, intronic, and regulatory regions of the DNA. Hypervariability among these repeats in the coding and non-coding regions of the genes is well characterized for solid tumours, but its significance in haematologic malignancies remains to be explored. The purpose of our study was to elucidate the role of nucleotide repeat instability in the coding and non-coding regions of 10 different repair genes in myeloid and lymphoid cell lines compared to the control samples. METHODS AND RESULTS We selected MMR deficient extensively studied microsatellite instable colorectal cancer (HCT116), and MMR proficient breast cancer (MCF-7) cells along with underemphasized haematologic cancer cell lines to decipher the hypermutability of tandem repeats. A statistically significant TR variation was observed for MSH2 and MSH6 genes in 4 and 3 of the 6 cell lines respectively. KG1 (AML) and Daudi (Burkitt's lymphoma) were found to have compromised DNA repair competency with highly unstable nucleotide repeats. CONCLUSION Taken together, the results suggest that mutable TRs in intronic and non-intronic regions of repair genes in blood cancer might have a tumorigenic role. Since this is a pilot study on cell lines, high throughput research in large cohorts can be undertaken to reveal novel diagnostic markers for unexplained blood cancer patients with normal karyotypes or otherwise with karyotypic defects.
Collapse
Affiliation(s)
| | - Trupti N Patel
- Department of Integrative Biology, Vellore Institute of Technology, Vellore, India.
| |
Collapse
|
64
|
Ahmed L, Al-Najjar Y, Cramer ERA, Thareja G, Suhre K, Chen KC. Development and characterization of microsatellite primers for Triops granarius (Branchiopoda: Notostraca) using MiSeq technology. Mol Biol Rep 2022; 49:10121-10125. [PMID: 36057875 PMCID: PMC9515016 DOI: 10.1007/s11033-022-07804-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/15/2022] [Indexed: 12/03/2022]
Abstract
Background Next-generation sequencing technology has allowed for the rapid development of microsatellites, neutral polymorphic markers that can be used for the analysis of population structure. Methods and Results In this study, we performed whole-genome sequencing using the Illumina MiSeq system and de novo assembly to design microsatellite primers for Triops granarius populations in Qatar. The developed microsatellites are suitable for future studies of genetic structuring among geographically isolated freshwater pools. A total of 23 different primer pairs produced typical microsatellite results, with each pair successfully amplified in up to 40 individuals. Only five of the loci produced a significant departure from Hardy-Weinberg equilibrium. Conclusions Some of the underlying mechanisms regarding the few loci that deviated from HWE may be further investigated to determine the source of deviation. As T. granarius is the most widely distributed species of the family, the development of these molecular markers would be useful for conducting population genetics and biogeographical studies broadly.
Collapse
Affiliation(s)
- Lina Ahmed
- Department of Medical Education Education City, Qatar Foundation, Weill Cornell Medicine - Qatar, 24144, Doha, Qatar
| | - Yousef Al-Najjar
- Department of Medical Education Education City, Qatar Foundation, Weill Cornell Medicine - Qatar, 24144, Doha, Qatar
| | - Emily R A Cramer
- Natural History Museum, University of Oslo, Sars Gate 1, 0562, Oslo, Norway
| | - Gaurav Thareja
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar Education City, Qatar Foundation, P.O. Box 24144, Doha, Qatar
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar Education City, Qatar Foundation, P.O. Box 24144, Doha, Qatar
| | - Kuei-Chiu Chen
- Department of Premedical Education, Weill Cornell Medicine-Qatar Education City, Qatar Foundation, P.O. Box 24144, Doha, Qatar.
| |
Collapse
|
65
|
The Predominance of a Specific Genotype of Cryptococcus neoformans var. Grubii in China and Japan. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8162096. [PMID: 36035289 PMCID: PMC9410922 DOI: 10.1155/2022/8162096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022]
Abstract
Background The extensive deployment of molecular genotyping methods is the top reliable keyword to characterize the population genetic structure of C. neoformans in the past decade. However, studies involving genotypic analysis of C. neoformans var. grubii from China and Japan are limited. Objectives We address this challenge to determine the genotype distribution of C. neoformans var. grubii strains from China and Japan. Methods Genotypic analysis of 52 C. neoformans var. grubii isolates was performed using multilocus microsatellite typing (MLMT) based on the sequence analysis of 3 functional genes. In order to place the herein-studied strains into the global picture, 22 strains randomly selected from the 52 strains studied by MLMT were also analyzed by restriction fragment length polymorphism analysis of the orotidine monophosphate pyrophosphorylase gene (URA5-RFLP), M13 PCR-fingerprinting, and multilocus sequence typing (MLST). Results MLMT classified 46 (88.5%) of the 52 strains as genotype MLMT-17. The high prevalence of the MLMT-17 type was observed for environmental and clinical isolates from China and Japan. URA5-RFLP analysis, M13 PCR-fingerprinting, and MLST showed that most of these belong to the VNI/ST5 (M5) genotype. Conclusions Our study suggests the predominance of a specific genotype of C. neoformans var. grubii in China and Japan.
Collapse
|
66
|
Jamasbi E, Hamelian M, Hossain MA, Varmira K. The cell cycle, cancer development and therapy. Mol Biol Rep 2022; 49:10875-10883. [PMID: 35931874 DOI: 10.1007/s11033-022-07788-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/11/2022] [Indexed: 10/16/2022]
Abstract
The process of cell division plays a vital role in cancer progression. Cell proliferation and error-free chromosomes segregation during mitosis are central events in life cycle. Mistakes during cell division generate changes in chromosome content and alter the balances of chromosomes number. Any defects in expression of TIF1 family proteins, SAC proteins network, mitotic checkpoint proteins involved in chromosome mis-segregation and cancer development. Here we discuss the function of organelles deal with the chromosome segregation machinery, proteins and correction mechanisms involved in the accurate chromosome segregation during mitosis.
Collapse
Affiliation(s)
- Elaheh Jamasbi
- Research Center of Oils and Fats (RCOF), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mona Hamelian
- Research Center of Oils and Fats (RCOF), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammed Akhter Hossain
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Kambiz Varmira
- Research Center of Oils and Fats (RCOF), Kermanshah University of Medical Sciences, Kermanshah, Iran.
| |
Collapse
|
67
|
de Carvalho JA, Monteiro RC, Hagen F, de Camargo ZP, Rodrigues AM. Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species. J Fungi (Basel) 2022; 8:jof8080809. [PMID: 36012797 PMCID: PMC9409836 DOI: 10.3390/jof8080809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Sporotrichosis is the most important subcutaneous mycosis that affects humans and animals worldwide. The mycosis is caused after a traumatic inoculation of fungal propagules into the host and may follow an animal or environmental transmission route. The main culprits of sporotrichosis are thermodimorphic Sporothrix species embedded in a clinical clade, including S. brasiliensis, S. schenckii, S. globosa, and S. luriei. Although sporotrichosis occurs worldwide, the etiological agents are not evenly distributed, as exemplified by ongoing outbreaks in Brazil and China, caused by S. brasiliensis and S. globosa, respectively. The gold standard for diagnosing sporotrichosis has been the isolation of the fungus in vitro. However, with the advance in molecular techniques, molecular assays have complemented and gradually replaced the classical mycological tests to quickly and accurately detect and/or differentiate molecular siblings in Sporothrix. Nearly all techniques available for molecular diagnosis of sporotrichosis involve PCR amplification, which is currently moving towards detecting Sporothrix DNA directly from clinical samples in multiplex qPCR assays. From an epidemiological perspective, genotyping is key to tracing back sources of Sporothrix infections, detecting diversity in outbreak areas, and thus uncovering finer-scale epidemiological patterns. Over the past decades, molecular epidemiological studies have provided essential information to policymakers regarding outbreak management. From high-to-low throughput genotyping methods, MLSA, AFLP, SSR, RAPD, PCR-RFLP, and WGS are available to assess the transmission dynamics and sporotrichosis expansion. This review discusses the trends in the molecular diagnosis of sporotrichosis, genotyping techniques applied in molecular epidemiological studies, and perspectives for the near future.
Collapse
Affiliation(s)
- Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ruan Campos Monteiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
| |
Collapse
|
68
|
Francisconi AF, Cauz-Santos LA, Morales Marroquín JA, van den Berg C, Alves-Pereira A, Delmondes de Alencar L, Picanço-Rodrigues D, Zanello CA, Ferreira Costa M, Gomes Lopes MT, Veasey EA, Zucchi MI. Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes. PLoS One 2022; 17:e0266304. [PMID: 35901127 PMCID: PMC9333295 DOI: 10.1371/journal.pone.0266304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.
Collapse
Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
| | | | | | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brasil
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Luciano Delmondes de Alencar
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | | | - Cesar Augusto Zanello
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Marcones Ferreira Costa
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Campus Amílcar Ferreira Sobral, Universidade Federal do Piauí, Floriano, Piauí, Brasil
| | - Maria Teresa Gomes Lopes
- Departamento de Produção Animal e Vegetal, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Maria Imaculada Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
| |
Collapse
|
69
|
Xiong Y, Yang J, Xiong Y, Zhao J, Liu L, Liu W, Sha L, Zhou J, You M, Li D, Lei X, Bai S, Ma X. Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera. FRONTIERS IN PLANT SCIENCE 2022; 13:959042. [PMID: 35958193 PMCID: PMC9358441 DOI: 10.3389/fpls.2022.959042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2023]
Abstract
As a typical psammophyte of the Triticeae, Kengyilia melanthera possesses high feeding potential and great utilization values in desertification control in the Qinghai-Tibet Plateau. However, few gene function and genetic studies have been performed in K. melanthera. In this study, single-molecule real-time sequencing technology was used to obtain the full-length transcriptome sequence of K. melanthera, following the functional annotation of transcripts and prediction of coding sequences (CDSs), transcription factors (TFs), and long noncoding RNA (lncRNA) sequences. Meanwhile, a total of 42,433 SSR loci were detected, with 5'-UTRs having the most SSR loci and trinucleotide being the most abundant type. In total, 108,399 SSR markers were designed, and 300 SSR markers were randomly selected for diversity verification of K. melanthera. A total of 49 polymorphic SSR markers were used to construct the genetic relationships of 56 K. melanthera accessions, among which 21 SSR markers showed good cross-species transferability among the related species. In conclusion, the full-length transcriptome sequence of the K. melanthera will assist gene prediction and promote molecular biology and genomics research, and the polymorphic SSR markers will promote molecular-assisted breeding and related research of K. melanthera and its relatives.
Collapse
Affiliation(s)
- Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lin Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiqiong Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
70
|
Developing microsatellite duplex PCR reactions for sterlet (Acipenser ruthenus) and their application in parentage identification. Sci Rep 2022; 12:12036. [PMID: 35835817 PMCID: PMC9283521 DOI: 10.1038/s41598-022-16194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022] Open
Abstract
The sterlet (Acipenser ruthenus) is one of the 27 sturgeon species and is well-known for its wide distribution and small body size in comparison to other sturgeons. For assessing the population genetics and parentage identification of sterlet, ten microsatellites developed for Chinese sturgeon and cross-amplified in sterlet were tested by 40 individuals of sterlet. The ten microsatellites were developed using transcriptome sequencing of Chinese sturgeon. The expected heterozygosity (HE), observed heterozygosity (HO), Shannon-Weiner diversity indices (H') and polymorphic information content (PIC) of the 10 microsatellites ranged from 0.466 to 0.751, from 0.438 to 0.938, from 0.66 to 1.51 and from 0.368 to 0.716, respectively. Combined exclusion probability based on the genotype of pair parent known (CE-PP), one parent known (CE-2P), and no parent known (CE-1P) of the 10 microsatellites were 99.99%, 99.96%, and 99.49%, respectively. These result showed that the 10 microsatellites should be helpful for assessing the population genetics and parentage identification of sterlet.
Collapse
|
71
|
Varga F, Liber Z, Jakše J, Turudić A, Šatović Z, Radosavljević I, Jeran N, Grdiša M. Development of Microsatellite Markers for Tanacetum cinerariifolium (Trevis.) Sch. Bip., a Plant with a Large and Highly Repetitive Genome. PLANTS 2022; 11:plants11131778. [PMID: 35807729 PMCID: PMC9269103 DOI: 10.3390/plants11131778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022]
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevis.) Sch. Bip.) is an outcrossing plant species (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repeatability and large genome (1C-value = 9.58 pg) our previous attempts to develop microsatellite markers using the traditional method were unsuccessful. Now we have used Illumina paired-end whole genome sequencing and developed a specific procedure to obtain useful microsatellite markers. A total of 796,130,142 high-quality reads (approx. 12.5× coverage) were assembled into 6,909,675 contigs using two approaches (de novo assembly and joining of overlapped pair-end reads). A total of 31,380 contigs contained one or more microsatellite sequences, of which di-(59.7%) and trinucleotide (25.9%) repeats were the most abundant. Contigs containing microsatellites were filtered according to various criteria to achieve better yield of functional markers. After two rounds of testing, 17 microsatellite markers were developed and characterized in one natural population. Twelve loci were selected for preliminary genetic diversity analysis of three natural populations. Neighbor-joining tree, based on the proportion of shared alleles distances, grouped individuals into clusters according to population affiliation. The availability of codominant SSR markers will allow analysis of genetic diversity and structure of natural Dalmatian pyrethrum populations as well as identification of breeding lines and cultivars.
Collapse
Affiliation(s)
- Filip Varga
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
| | - Zlatko Liber
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-4898-092
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
| | - Ante Turudić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
| | - Zlatko Šatović
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
| | - Ivan Radosavljević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
| | - Nina Jeran
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
| | - Martina Grdiša
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia; (F.V.); (Z.Š.); (N.J.); (M.G.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia; (A.T.); (I.R.)
| |
Collapse
|
72
|
Antunes AM, Nunes Stival JG, Targueta CP, de Campos Telles MP, Soares TN. A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data. Curr Genomics 2022; 23:175-181. [PMID: 36777003 PMCID: PMC9878831 DOI: 10.2174/1389202923666220428101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusion: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.
Collapse
Affiliation(s)
- Adriana Maria Antunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil;,Address correspondence to this author at the Department of Genetics, Institute of Biological Sciences, Goias Federal University, Goiânia, Brazil; Tel/Fax: +55 62 981660987; E-mail:
| | - Júlio Gabriel Nunes Stival
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Mariana Pires de Campos Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brasil
| | - Thannya Nascimentos Soares
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil
| |
Collapse
|
73
|
Mahapatra S, Sureja AK, Behera TK, Verma M. Assessment of genetic diversity of ninety-one bottle gourd [Lagenaria siceraria (Mol.) Standl.] genotypes from fourteen different agro-climatic zones of India using agro-morphological traits and SSR markers. Mol Biol Rep 2022; 49:6367-6383. [PMID: 35435602 DOI: 10.1007/s11033-022-07446-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND The evaluation of the magnitude of genetic diversity present in the germplasm collection is prerequisite for bottle gourd improvement programme. The characterization of the diversity pattern of Indian bottle gourd accessions will facilitate the optimal use of genetic resources for breeding improved cultivars. METHODS In the present study, the magnitude of genetic diversity was evaluated in ninety-one genotypes of bottle gourd collected across fourteen different agro-climatic zones of India. RESULTS Significant variations were observed for all the studied ten quantitative and nine qualitative traits. The ninety-one genotypes were grouped into nine clusters based on cluster analysis of morphological characteristics. Eigen value from principal component analysis depicted first seven quantitative traits accounted for more than 97.5 cumulative percent of the total variations. The first two components accounted for 50 cumulative percent of the total variation, which signifies a high degree of correlation between the analyzed traits. Molecular diversity with the 40 SSR markers screened revealed 11 polymorphic markers in the genotypes studied. Population structure analysis divulged five populations, conforming to the Principal Coordinate Analysis. Molecular analysis revealed genetically diverse genotypes along with the morphologically divergent genotypes from the quantitative traits and highest inter-cluster distance would be the most appropriate parents for exploiting heterosis. CONCLUSIONS The results of this study will facilitate the optimal use of genetic resources for breeding improved cultivars of bottle gourd and the adoption of the identified superior genotypes directly by the breeders.
Collapse
Affiliation(s)
- Sourav Mahapatra
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Amish Kumar Sureja
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India.
| | | | - Manjusha Verma
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
| |
Collapse
|
74
|
The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.
Collapse
|
75
|
Maibam A, Lone SA, Ningombam S, Gaikwad K, Amitha Mithra SV, Singh MP, Singh SP, Dalal M, Padaria JC. Transcriptome Analysis of Pennisetum glaucum (L.) R. Br. Provides Insight Into Heat Stress Responses. Front Genet 2022; 13:884106. [PMID: 35719375 PMCID: PMC9201763 DOI: 10.3389/fgene.2022.884106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Pennisetum glaucum (L.) R. Br., being widely grown in dry and hot weather, frequently encounters heat stress at various stages of growth. The crop, due to its inherent capacity, efficiently overcomes such stress during vegetative stages. However, the same is not always the case with the terminal (flowering through grain filling) stages of growth, where recovery from stress is more challenging. However, certain pearl millet genotypes such as 841-B are known to overcome heat stress even at the terminal growth stages. Therefore, we performed RNA sequencing of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42°C for 6 h) at flowering stages. Over 274 million high quality reads with an average length of 150 nt were generated, which were assembled into 47,310 unigenes having an average length of 1,254 nucleotides, N50 length of 1853 nucleotides, and GC content of 53.11%. Blastx resulted in the annotation of 35,628 unigenes, and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms. A total of 13,786 unigenes were allocated to 23 Clusters of Orthologous Groups, and 4,255 unigenes were distributed to 132 functional Kyoto Encyclopedia of Genes and Genomes database pathways. A total of 12,976 simple sequence repeats and 305,759 SNPs were identified in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidate genes were selected based on log2 fold change and adjusted p value parameters for their differential gene expression by qRT-PCR. We were able to identify differentially expressed genes unique to either of the two genotypes, and also, some DEGs common to both the genotypes were enriched. The differential expression patterns suggested that 841-B 6 h has better ability to maintain homeostasis during heat stress as compared to PPMI-69 6 h. The sequencing data generated in this study, like the SSRs and SNPs, shall serve as an important resource for the development of genetic markers, and the differentially expressed heat responsive genes shall be used for the development of transgenic crops.
Collapse
Affiliation(s)
- Albert Maibam
- PG School, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Showkat Ahmad Lone
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Sunil Ningombam
- PG School, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Kishor Gaikwad
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - S. V. Amitha Mithra
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, Indian Council of Agricultural Research -Indian Agricultural Research Institute, New Delhi, India
| | - Sumer Pal Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi, India
| | - Monika Dalal
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
| | - Jasdeep Chatrath Padaria
- Indian Council of Agricultural Research -National Institute for Plant Biotechnology, New Delhi, India
- *Correspondence: Jasdeep Chatrath Padaria,
| |
Collapse
|
76
|
Zhou T, Ning K, Mo Z, Zhang F, Zhou Y, Chong X, Zhang D, El-Kassaby YA, Bian J, Chen H. Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae. PLoS One 2022; 17:e0268679. [PMID: 35588136 PMCID: PMC9119449 DOI: 10.1371/journal.pone.0268679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.
Collapse
Affiliation(s)
- Ting Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Kun Ning
- College of Horticulture, Jinling Institute of Technology, Nanjing City, Jiangsu Province, P.R. China
| | - Zhenghai Mo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Fan Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Yanwei Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinran Chong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Donglin Zhang
- Department of Horticulture, University of Georgia, Athens, GA, United States of America
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jian Bian
- Jiangsu Yufeng Tourism Development Co. Ltd., Yancheng, China
| | - Hong Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
- * E-mail:
| |
Collapse
|
77
|
Zhang C, Jia C, Liu X, Zhao H, Hou L, Li M, Cui B, Li Y. Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:903674. [PMID: 35646027 PMCID: PMC9134938 DOI: 10.3389/fpls.2022.903674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (N A), expected heterozygosity (H E), and Shannon's information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (N m = 1.252) and high genetic differentiation (F st = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.
Collapse
Affiliation(s)
- Chenxing Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chunfeng Jia
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Xinru Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Meng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Binbin Cui
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Yingyue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| |
Collapse
|
78
|
El-Ganainy SM, Iqbal Z, Awad HM, Sattar MN, Tohamy AM, Abbas AO, Squires J, Cooke DEL. Genotypic and Phenotypic Structure of the Population of Phytophthora infestans in Egypt Revealed the Presence of European Genotypes. J Fungi (Basel) 2022; 8:jof8050468. [PMID: 35628724 PMCID: PMC9147654 DOI: 10.3390/jof8050468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/10/2022] Open
Abstract
Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers David E. L. Cooke and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into two main clonal lineages. The first clonal lineage comprised 21 isolates belonging to A2 mating type and 8 self-fertile isolates. This clonal lineage was identified as Blue_13 or EU_13_A2. The second main clonal lineage comprised 55 isolates and was identified as EU_23_A1. A single isolate with a novel SSR genotype that formed a distinct genetic grouping was also identified. The effector sequencing showed good correspondence with the virulence data and highlighted differences in the presence and absence of loci as well as nucleotide polymorphism that affect gene function. This study indicated a changing population of P. infestans in Egypt and discusses the findings in the context of late blight management.
Collapse
Affiliation(s)
- Sherif Mohamed El-Ganainy
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Hossam Mohamed Awad
- Agriculture Botany Department, Menofia University, Shibin El-Kom 32415, Egypt;
| | - Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Abdel Mohsen Tohamy
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
| | - Ahmed O. Abbas
- Department of Animal and Fish Production, College of Agricultural and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia;
| | | | - David E. L. Cooke
- The James Hutton Institute, Dundee DD2 5DA, UK;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
| |
Collapse
|
79
|
Yue J, Liu Y. SSR2Marker: an integrated pipeline for identification of SSR markers within any two given genome-scale sequences. MOLECULAR HORTICULTURE 2022; 2:11. [PMID: 37789487 PMCID: PMC10515269 DOI: 10.1186/s43897-022-00033-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/11/2022] [Indexed: 10/05/2023]
Affiliation(s)
- Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
| |
Collapse
|
80
|
Wang Z, Pierce NE. Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol 2022; 32:2695-2714. [PMID: 35377501 DOI: 10.1111/mec.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
Collapse
Affiliation(s)
- Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| |
Collapse
|
81
|
Mosher CM, Johnson CJ, Murray BW. Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat specialization,
Ascaphus truei
, resolved using two types of genetic markers. Ecol Evol 2022; 12:e8716. [PMID: 35342604 PMCID: PMC8931771 DOI: 10.1002/ece3.8716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Reconstruction of historical relationships between geographic regions within a species’ range can indicate dispersal patterns and help predict future responses to shifts in climate. Ascaphus truei (coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques—microsatellite and genotype‐by‐sequencing (GBS)—to compare the within‐region genetic diversity of populations near the northern extent of the species’ range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving toward the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of A. truei to climate change.
Collapse
Affiliation(s)
- Cherie M. Mosher
- University of Northern British Columbia Prince George British Columbia Canada
| | - Chris J. Johnson
- University of Northern British Columbia Prince George British Columbia Canada
| | - Brent W. Murray
- University of Northern British Columbia Prince George British Columbia Canada
| |
Collapse
|
82
|
Campello C, Lima-Silva M, de Lima E, Nunes G, Silva H, Dellalibera E, de Britto L, Lemos C, Muniz M. Genetic polymorphisms and protein levels in vocal fold leukoplakia: a systematic review. Braz J Med Biol Res 2022; 55:e11920. [PMID: 35293553 PMCID: PMC8922550 DOI: 10.1590/1414-431x2022e11920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022] Open
Abstract
Vocal fold leukoplakia (VFL) has a risk of malignant transformation. Therefore, patients can have symptoms such as dysphonia, vocal strain, difficulty breathing, and dysphagia. Additionally, there is a genetic predisposition that can be associated with genetic polymorphisms. We aimed to evaluate the influence of genetic polymorphisms and protein levels in the etiology of VFL. Our study followed the PRISMA checklist and was registered on PROSPERO database. The questions were: "Are genetic polymorphisms involved in the etiology of VFL? Are protein levels altered in patients with VFL?". Eligibility criteria were case control studies that compared the presence of polymorphisms or/and protein levels of subjects diagnosed with VFL and healthy controls. Of the 905 articles retrieved, five articles with a total of 1038 participants were included in this study. The C allele of the single nucleotide polymorphisms (SNP)-819 T/C IL-10, A allele of the SNP -592 A/C IL-10, CT genotype of the SNP rs11886868 C/T BCL11A, GG genotype of the SNP rs4671393 A/G BCL11A, LL genotype, and L allele of (GT)n repeat polymorphisms of the HO-1 were risk factors for VFL development. Nevertheless, there was a lack of association between VFL and the -1082 A/G IL-10, rs14024 CK-1, and -309 T/G Mdm2 SNPs. The concentrations of the MDM2, BCL11A, and HO-1 proteins were modified, while IL-10 levels were normally expressed in these subjects. In conclusion, most markers evaluated in this review could be potential indicators to develop effective therapies, avoiding a malignant transformation of the lesion.
Collapse
Affiliation(s)
- C.P. Campello
- Programa Associado de Pós-Graduação em Fonoaudiologia,
Universidade Federal da Paraíba, João Pessoa, PB, Brasil
- Laboratório de Biologia Molecular, Centro de Oncohematologia
Pediátrica, Hospital Universitário Oswaldo Cruz, Universidade de Pernambuco,
Recife, PE, Brasil
| | - M.F.B. Lima-Silva
- Programa Associado de Pós-Graduação em Fonoaudiologia,
Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - E.L.S. de Lima
- Laboratório de Biologia Molecular, Centro de Oncohematologia
Pediátrica, Hospital Universitário Oswaldo Cruz, Universidade de Pernambuco,
Recife, PE, Brasil
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de
Ciências Médicas, Universidade de Pernambuco, Recife, PE, Brasil
| | - G.R.S. Nunes
- Programa Associado de Pós-Graduação em Fonoaudiologia,
Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - H.A.M. Silva
- Laboratório de Biologia Molecular, Centro de Oncohematologia
Pediátrica, Hospital Universitário Oswaldo Cruz, Universidade de Pernambuco,
Recife, PE, Brasil
- Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brasil
| | - E. Dellalibera
- Laboratório de Biologia Molecular, Centro de Oncohematologia
Pediátrica, Hospital Universitário Oswaldo Cruz, Universidade de Pernambuco,
Recife, PE, Brasil
| | | | - C.A.A. Lemos
- Departamento de Odontologia, Universidade Federal de Juiz de
Fora, Governador Valadares, MG, Brasil
| | - M.T.C. Muniz
- Laboratório de Biologia Molecular, Centro de Oncohematologia
Pediátrica, Hospital Universitário Oswaldo Cruz, Universidade de Pernambuco,
Recife, PE, Brasil
- Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brasil
| |
Collapse
|
83
|
Wang H, Gao S, Liu Y, Wang P, Zhang Z, Chen D. A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data. Ecol Evol 2022; 12:e8705. [PMID: 35342577 PMCID: PMC8928897 DOI: 10.1002/ece3.8705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 01/24/2023] Open
Abstract
Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.
Collapse
Affiliation(s)
- Hui Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Yu Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life Sciences Nanjing Normal University Nanjing China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| |
Collapse
|
84
|
Ramírez-Camejo LA, Eamvijarn A, Díaz-Valderrama JR, Karlsen-Ayala E, Koch RA, Johnson E, Pruvot-Woehl S, Mejía LC, Montagnon C, Maldonado-Fuentes C, Aime MC. Global Analysis of Hemileia vastatrix Populations Shows Clonal Reproduction for the Coffee Leaf Rust Pathogen Throughout Most of Its Range. PHYTOPATHOLOGY 2022; 112:643-652. [PMID: 34428920 DOI: 10.1094/phyto-06-21-0255-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.
Collapse
Affiliation(s)
- Luis A Ramírez-Camejo
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
- Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton, Panama, Republic of Panama
| | - Amnat Eamvijarn
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Department of Agriculture, Chatuchak, Bangkok, Thailand
| | - Jorge R Díaz-Valderrama
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elena Karlsen-Ayala
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- University of Florida, Department of Plant Pathology, Gainesville, FL, U.S.A
| | - Rachel A Koch
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elizabeth Johnson
- Inter-American Institute for Cooperation on Agriculture, Hope Gardens, Kingston, Jamaica
| | | | - Luis C Mejía
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
| | | | | | - M Catherine Aime
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| |
Collapse
|
85
|
Wang N, Chen S, Xie L, Wang L, Feng Y, Lv T, Fang Y, Ding H. The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. Ecol Evol 2022; 12:e8637. [PMID: 35222983 PMCID: PMC8848467 DOI: 10.1002/ece3.8637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/07/2022] Open
Abstract
Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.
Collapse
Affiliation(s)
- NingJie Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - ShuiFei Chen
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
| | - Lei Xie
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YueYao Feng
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Ting Lv
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YanMing Fang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Hui Ding
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
| |
Collapse
|
86
|
Divya PR, Joy L, Poulose S, Jency PME, Basheer VS, Kathirvelpandian A, Mohindra V, Lal KK. Genetic stock identification in Perna viridis (Linnaeus1758) from the Indian Peninsula by using microsatellite markers. Mol Biol Rep 2022; 49:3357-3363. [DOI: 10.1007/s11033-022-07178-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 01/19/2022] [Indexed: 11/28/2022]
|
87
|
Sun Y, Zou P, Jiang N, Fang Y, Liu G. Comparative Analysis of the Complete Chloroplast Genomes of Nine Paphiopedilum Species. Front Genet 2022; 12:772415. [PMID: 35186004 PMCID: PMC8854857 DOI: 10.3389/fgene.2021.772415] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/27/2021] [Indexed: 12/14/2022] Open
Abstract
Paphiopedilum is known as “lady’s or Venus” slipper orchids due to its prominent shoe-shaped labellum, with high ornamental value. Phylogenetic relationships among some species in Paphiopedilum genus cannot be effectively determined by morphological features alone or through the analysis of nuclear or chloroplast DNA fragments. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Paphiopedilum at chloroplast (cp) genome-scale level, the complete cp genomes of six Paphiopedilum species were newly sequenced in this study, and three other published cp genome sequences of Paphiopedilum were included in the comparative analyses. The cp genomes of the six Paphiopedilum species ranged from 154,908 bp (P. hirsutissimum) to 161,300 bp (P. victoria-mariae) in size, all constituting four-part annular structures. Analyses of the nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes were conducted. Ten highly variable regions that could serve as potential DNA barcodes or phylogenetic markers for this diverse genus were identified. Sequence variations in the non-coding regions were greater than that in the conserved protein-coding regions, as well as in the large single copy (LSC) and small single copy (SSC) regions than in the inverted repeat (IR) regions. Phylogenetic analysis revealed that all Paphiopedilum species clustered in one monophyletic clade in the Cypripedioideae subfamily and then subdivided into seven smaller branches corresponding to different subgenus or sections of the genus, with high bootstrap supports, indicate that cp genome sequencing can be an effective means in resolving the complex relationship in Paphiopedilum.
Collapse
Affiliation(s)
- Yin Sun
- Shandong Provincial Academy of Forestry, Jinan, China
| | - Peishan Zou
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Nannan Jiang
- Shandong Provincial Academy of Forestry, Jinan, China
| | - Yifu Fang
- Shandong Provincial Academy of Forestry, Jinan, China
| | - Guofeng Liu
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| |
Collapse
|
88
|
Soara AE, Talaki E, Dayo GK, Houaga I, Tona K, Bakkali M. Genetic diversity of indigenous guinea fowl ( Numida meleagris) using microsatellite markers in northern Togo. PeerJ 2022; 10:e12637. [PMID: 35116192 PMCID: PMC8784013 DOI: 10.7717/peerj.12637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/23/2021] [Indexed: 01/07/2023] Open
Abstract
Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.
Collapse
Affiliation(s)
- Aïcha Edith Soara
- Centre d’Excellence Régional sur les Sciences Aviaires, Université de Lomé, Lomé, Togo,Département Environnement et Forêts, Institut de l’Environnement et de Recherches Agricoles, Ouagadougou, Burkina Faso
| | - Essodina Talaki
- Centre d’Excellence Régional sur les Sciences Aviaires, Université de Lomé, Lomé, Togo,Ecole Supérieure d’Agronomie, Université de Lomé, Lomé, Togo
| | | | - Isidore Houaga
- Centre International de Recherche-Développement sur l’Elevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
| | - Kokou Tona
- Centre d’Excellence Régional sur les Sciences Aviaires, Université de Lomé, Lomé, Togo,Ecole Supérieure d’Agronomie, Université de Lomé, Lomé, Togo
| | - Mohammed Bakkali
- Departamento de Genética, Facultad de Ciencias, Fuentenueva, Universidad de Granada, Granada, Spain
| |
Collapse
|
89
|
Towards an in-situ non-lethal rapid test to accurately detect the presence of the nematode parasite, Anguillicoloides crassus, in European eel, Anguilla anguilla. Parasitology 2022; 149:605-611. [PMID: 35042576 PMCID: PMC10090626 DOI: 10.1017/s0031182021002146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Anguillicoloides crassus is an invasive nematode parasite of the critically endangered European eel, Anguilla anguilla, and possibly one of the primary drivers of eel population collapse, impacting many features of eel physiology and life history. Early detection of the parasite is vital to limit the spread of A. crassus, to assess its potential impact on spawning biomass. However accurate diagnosis of infection could only be achieved via necropsy. To support eel fisheries management we developed a rapid, non-lethal, minimally invasive and in situ DNA-based method to infer the presence of the parasite in the swim bladder. Screening of 131 wild eels was undertaken between 2017 and 2019 in Ireland and UK to validate the procedure. DNA extractions and PCR were conducted using both a Qiagen Stool kit and in situ using Whatman qualitative filter paper No1 and a miniPCR DNA Discovery-System™. Primers were specifically designed to target the cytochrome oxidase mtDNA gene region and in situ extraction and amplification takes approximately 3 h for up to 16 individuals. Our in-situ diagnostic procedure demonstrated positive predictive values at 96% and negative predictive values at 87% by comparison to necropsy data. Our method could be a valuable tool in the hands of fisheries managers to enable infection control and help protect this iconic but critically endangered species.
Collapse
|
90
|
Chen Q, Smit C, Pen I, Olff H. Small herbivores and abiotic heterogeneity promote trait variation of a saltmarsh plant in local communities. PeerJ 2022; 9:e12633. [PMID: 35036137 PMCID: PMC8710046 DOI: 10.7717/peerj.12633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Intraspecific trait variation (ITV) enables plants to respond to global changes. However, causes for ITV, especially from biotic components such as herbivory, are not well understood. We explored whether small vertebrate herbivores (hares and geese) impact ITV of a dominant clonal plant (Elytrigia atherica) in local communities. Moreover, we looked at the relative importance of their direct (e.g., selective grazing) and indirect effects (altering genotypic richness/diversity and abiotic environment) on ITV. We used exclosures at two successional stages in a Dutch saltmarsh, where grazing pressure at the early successional stage was ca. 1.5 times higher than that of the intermediate successional stage. We measured key functional traits of E. atherica including height, aboveground biomass, flowering (flower or not), specific leaf area, and leaf dry matter content in local communities (1 m × 1 m plots) inside and outside the exclosures. We determined genotypic richness and diversity of each plant using molecular markers. We further measured abiotic variations in topography and clay thickness (a proxy for soil total nitrogen). Structural equation models revealed that small herbivores significantly promoted ITV in height and flowering at the early successional stage, while they marginally promoted ITV in height at the intermediate successional stage. Moreover, the direct effects of herbivores played a major role in promoting ITV. Small herbivores decreased genotypic diversity at the intermediate successional stage, but genotypic richness and diversity did not impact ITV. Small herbivores did not alter topographic variation and variation in clay thickness, but these variations increased ITV in all traits at the early successional stage. Small herbivores may not only impact trait means in plants as studies have shown but also their ITV.
Collapse
Affiliation(s)
- Qingqing Chen
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Christian Smit
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Ido Pen
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Han Olff
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| |
Collapse
|
91
|
Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona). Sci Rep 2022; 12:355. [PMID: 35013469 PMCID: PMC8748427 DOI: 10.1038/s41598-021-04264-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 11/30/2021] [Indexed: 12/25/2022] Open
Abstract
Platostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.
Collapse
|
92
|
Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers. Sci Rep 2022; 12:295. [PMID: 34997147 PMCID: PMC8741888 DOI: 10.1038/s41598-021-04275-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/10/2021] [Indexed: 11/08/2022] Open
Abstract
Analysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species' genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies.
Collapse
|
93
|
Kupper Q, Prospero S. Microsatellite Genotyping in the Chestnut Blight Fungus Cryphonectria parasitica. Methods Mol Biol 2022; 2536:423-433. [PMID: 35819618 DOI: 10.1007/978-1-0716-2517-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This chapter describes the use of polymorphic microsatellite (simple sequence repeats, SSR) markers for genotyping isolates of Cryphonectria parasitica, the causal agent of chestnut blight. The SSR presented are particularly useful to characterize the genetic population structure of this invasive fungal pathogen, including invasion history (e.g., possible source population, introduced genotypes) and reproduction mode (sexual vs. asexual). Microsatellite markers can also be used to track fungal strains in laboratory and field experiments.
Collapse
Affiliation(s)
- Quirin Kupper
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Simone Prospero
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
| |
Collapse
|
94
|
Brooks J, Makunga NP, Hull KL, Brink-Hull M, Malgas R, Roodt-Wilding R. Resprouters Versus Reseeders: Are Wild Rooibos Ecotypes Genetically Distinct? Front Genet 2021; 12:761988. [PMID: 34987548 PMCID: PMC8721207 DOI: 10.3389/fgene.2021.761988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022] Open
Abstract
Aspalathus linearis (Burm. F.) R. Dahlgren (Fabaceae) or rooibos, is a strict endemic species, limited to areas of the Cederberg (Western Cape) and the southern Bokkeveld plateau (Northern Cape) in the greater Cape Floristic Region (CFR) of South Africa. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and genetics, and these ecotypes are broadly distinguished into two main groups, namely, reseeders and resprouters, based on their fire-survival strategy. No previous assessment of genetic diversity or population structure using microsatellite markers has been conducted in A. linearis. This study aimed to test the hypothesis that wild rooibos ecotypes are distinct in genetic variability and that the ecotypes found in the Northern Cape are differentiated from those in the Cederberg that may be linked to a fire-survival strategy as well as distinct morphological and phytochemical differences. A phylogeographical and population genetic analyses of both chloroplast (trnLF intergenic region) and newly developed species-specific nuclear markers (microsatellites) was performed on six geographically representative wild rooibos populations. From the diversity indices, it was evident that the wild rooibos populations have low-to-moderate genetic diversity (He: 0.618-0.723; Ho: 0.528-0.704). The Jamaka population (Cederberg, Western Cape) had the lowest haplotype diversity (H = 0.286), and the lowest nucleotide diversity (π = 0.006) even though the data revealed large variations in haplotype diversity (h = 0.286-0.900) and nucleotide diversity (π = 0.006-0.025) between populations and amongst regions where wild rooibos populations are found. Our data suggests that populations of rooibos become less diverse from the Melkkraal population (Suid Bokkeveld, Northern Cape) down towards the Cederberg (Western Cape) populations, possibly indicative of clinal variation. The largest genetic differentiation was between Heuningvlei (Cederberg, Western Cape) and Jamaka (FST = 0.101) localities within the Cederberg mountainous region, and, Blomfontein (Northern Cape) and Jamaka (Cederberg) (FST = 0.101). There was also a significant isolation by distance (R2 = 0.296, p = 0.044). The presence of three main clusters is also clearly reflected in the discriminant analysis of principal components (DAPC) based on the microsatellite marker analyses. The correct and appropriate management of wild genetic resources of the species is urgently needed, considering that the wild Cederberg populations are genetically distinct from the wild Northern Cape plants and are delineated in accordance with ecological functional traits of reseeding or resprouting, respectively. The haplotype divergence of the ecotypes has also provided insights into the genetic history of these populations and highlighted the need for the establishment of appropriate conservation strategies for the protection of wild ecotypes.
Collapse
Affiliation(s)
- J. Brooks
- Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - N. P. Makunga
- Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - K. L. Hull
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - M. Brink-Hull
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - R. Malgas
- Department of Conservation Ecology and Entomology, Stellenbosch University, Matieland, South Africa
| | - R. Roodt-Wilding
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| |
Collapse
|
95
|
Liu H, Zhang Y, Wang Z, Su Y, Wang T. Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences. Front Genet 2021; 12:759557. [PMID: 34868238 PMCID: PMC8635753 DOI: 10.3389/fgene.2021.759557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.
Collapse
Affiliation(s)
- Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuli Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| |
Collapse
|
96
|
Wang Y, Xie S, Li J, Tang J, Ju T, Mao K. Building a reference transcriptome for Juniperus squamata (Cupressaceae) based on single-molecule real-time sequencing. BMC Genom Data 2021; 22:55. [PMID: 34865616 PMCID: PMC8647495 DOI: 10.1186/s12863-021-01013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Cupressaceae is the second largest family of coniferous trees (Coniferopsida) with important economic and ecological values. However, like other conifers, the members of Cupressaceae have extremely large genome (> 8 gigabytes), which limited the researches of these taxa. A high-quality transcriptome is an important resource for gene discovery and annotation for non-model organisms. DATA DESCRIPTION Juniperus squamata, a tetraploid species which is widely distributed in Asian mountains, represents the largest genus, Juniperus, in Cupressaceae. Single-molecule real-time sequencing was used to obtain full-length transcriptome of Juniperus squamata. The full-length transcriptome was corrected with Illumina RNA-seq data from the same individual. A total of 47,860 non-redundant full-length transcripts, N50 of which was 2839, were obtained. A total of 57,393 simple sequence repeats were identified and 268,854 open reading frames were predicted for Juniperus squamata. A BLAST alignment against non-redundant protein database was conducted and 10,818 sequences were annotated in Gene Ontology database. InterPro analysis shows that 30,403 sequences have been functionally characterized against its member database. This data presents the first comprehensive transcriptome characterization of Juniperus species, and provides an important reference for researches on the genomics and evolutionary history of Cupressaceae plants and conifers in the future.
Collapse
Affiliation(s)
- Yufei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Siyu Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Jieshi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Tsam Ju
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
| |
Collapse
|
97
|
Admas S, Tesfaye K, Haileselassie T, Shiferaw E, Flynn KC. Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm. PLoS One 2021; 16:e0260651. [PMID: 34843606 PMCID: PMC8629288 DOI: 10.1371/journal.pone.0260651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.
Collapse
Affiliation(s)
- Sintayehu Admas
- Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail:
| | - Kassahun Tesfaye
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | | | | | - K. Colton Flynn
- Grassland Soil and Water Research Laboratory, USDA-ARS, Temple, Texas, United States of America
| |
Collapse
|
98
|
Setzke C, Wong C, Russello MA. Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon. Sci Rep 2021; 11:22798. [PMID: 34815428 PMCID: PMC8611073 DOI: 10.1038/s41598-021-01958-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population history and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism genotypic data from archival scale samples, and applied this approach to a study of kokanee salmon (Oncorhynchus nerka) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (> 90% average genotyping across all individuals) and low genotyping error (< 0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrated GT-seq as a valuable tool for collecting genome-wide data from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.
Collapse
Affiliation(s)
- Christopher Setzke
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Carmen Wong
- Parks Canada Yukon Field Unit, Suite 205 - 300 Main St, Whitehorse, YT, Y1A 2B5, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
| |
Collapse
|
99
|
Wu F, Zhang S, Gao Q, Liu F, Wang J, Wang X. Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers. BMC PLANT BIOLOGY 2021; 21:544. [PMID: 34800974 PMCID: PMC8605504 DOI: 10.1186/s12870-021-03330-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/10/2021] [Indexed: 05/08/2023]
Abstract
Vicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total of 8799 SSRs were identified in the V. amoena genomic-enriched sequences, and the most abundant repeat number was four. A total of 569 sampled individuals were assayed to evaluate the genetic diversity of the V. amoena populations based on 21 polymorphic SSR primers. The polymorphism information content (PIC) ranged from 0.896 to 0.968, with an average of 0.931, which indicated that the markers were highly informative. Based on analysis of molecular variance, 88% of the variance occurred within populations, and the remaining 12% of the variance occurred among populations. The high degree of gene flow (Nm= 4.958) also showed slight differentiation among the V. amoena populations. The V. amoena populations were mainly clustered by steppe and mountain habitats based on principal coordinate analysis (PCoA) and STRUCTURE analysis. This indicated that the elevation and special habitat of geographical origins may be important factors affecting the clustered pattern of V. amoena populations. Neighbour-joining (NJ) analysis did not separate the populations well by geographical origin, which indicated that the genetic structure of V. amoena was complex and needs further study. Overall, our results showed that the newly developed SSR markers could benefit the V. amoena research community by providing genetic background information to help establish a foundation for breeding improvement and germplasm resource conservation.
Collapse
Affiliation(s)
- Feifei Wu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shangxiong Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiu Gao
- National Herbage Germplasm Conservation center of China, Beijing, 10025, China
| | - Fang Liu
- National Herbage Germplasm Conservation center of China, Beijing, 10025, China
| | - Jianli Wang
- Grass and Science Institute, Heilongjiang Academy of Agricultural Science, Harbin, 150086, China
| | - Xianguo Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
100
|
An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants? Funct Integr Genomics 2021; 22:35-53. [PMID: 34751851 DOI: 10.1007/s10142-021-00815-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 10/19/2022]
Abstract
Microsatellites (SSRs) are tandem repeat sequences in eukaryote genomes, including plant cytoplasmic genomes. The mitochondrial genome (mtDNA) has been shown to vary in size, number, and distribution of SSRs among different plant groups. Thus, SSRs contribute with genomic diversity in mtDNAs. However, the abundance, distribution, and evolutionary significance of SSRs in mtDNA from a wide range of algae and plants have not been explored. In this study, the mtDNAs of 204 plant and algal species were investigated related to the presence of SSRs. The number of SSRs was positively correlated with genome size. Its distribution is dependent on plant and algal groups analyzed, although the cluster analysis indicates the conservation of some common motifs in algal and terrestrial plants that reflect common ancestry of groups. Many SSRs in coding and non-coding regions can be useful for molecular markers. Moreover, mitochondrial SSRs are highly abundant, representing an important source for natural or induced genetic variation, i.e., for biotechnological approaches that can modulate mtDNA gene regulation. Thus, this comparative study increases the understanding of the plant and algal SSR evolution and brings perspectives for further studies.
Collapse
|