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Ezzat M, Zhang W, Amar M, Nishawy E, Zhao L, Belal M, Han Y, Liao L. Origins and Genetic Characteristics of Egyptian Peach. Int J Mol Sci 2024; 25:8497. [PMID: 39126065 PMCID: PMC11313342 DOI: 10.3390/ijms25158497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Peach (Prunus persica), a significant economic fruit tree in the Rosaceae family, is extensively cultivated in temperate and subtropical regions due to its abundant genetic diversity, robust adaptability, and high nutritional value. Originating from China over 4000 years ago, peaches were introduced to Persia through the Silk Road during the Han Dynasty and gradually spread to India, Greece, Rome, Egypt, Europe, and America. Currently grown in more than 80 countries worldwide, the expansion of peach cultivation in Egypt is mainly due to the development and utilization of peach varieties with low chilling requirements. These varieties exhibit unique phenotypic characteristics such as early maturity, reduced need for winter cold temperatures, low water requirements, and high economic value. In this study, a systematic analysis was conducted on the genetic characteristics and kinship relationships of peaches with low chilling requirements in Egypt. We conducted a comprehensive evolutionary and Identity-by-Descent (IBD) analysis on over 300 peach core germplasm resources, including Egyptian cultivars with low chilling requirements, to investigate their origin and genetic characteristics. The evolutionary analysis revealed that 'Bitter almond' is closely related to China's wild relative species Prunus tangutica Batal, while 'Early grand' shares one branch with Chinese ornamental peach cultivars, and 'Nemaguard' clusters with some ancient local varieties from China. The IBD analysis also indicated similar genetic backgrounds, suggesting a plausible origin from China. Similarly, the analysis suggested that 'Swelling' may have originated from the Czech Republic while 'Met ghamr' has connections to South Africa. 'Desert red', 'Early swelling', and 'Florida prince' are likely derived from Brazil. These findings provide valuable insights into the genetic characteristics of Egyptian peach cultivars. They offer a significant foundation for investigating the origin and spread of cultivated peaches worldwide and serve as a valuable genetic resource for breeding low chilling requirement cultivars, which is of considerable significance for the advancement of peach cultivation in Egypt.
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Affiliation(s)
- Mohamed Ezzat
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China; (M.E.); (W.Z.); (M.A.); (E.N.); (L.Z.); (M.B.)
- Plant Genome Laboratory, Department of Genetic Resources, Desert Research Center, El-Matareya, Cairo 11753, Egypt
| | - Weihan Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China; (M.E.); (W.Z.); (M.A.); (E.N.); (L.Z.); (M.B.)
- Sino-African Joint Research Centre, Chinese Academy of Sciences, Beijing 100049, China
| | - Mohamed Amar
- Plant Genome Laboratory, Department of Genetic Resources, Desert Research Center, El-Matareya, Cairo 11753, Egypt
| | - Elsayed Nishawy
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China; (M.E.); (W.Z.); (M.A.); (E.N.); (L.Z.); (M.B.)
- Plant Genome Laboratory, Department of Genetic Resources, Desert Research Center, El-Matareya, Cairo 11753, Egypt
| | - Lei Zhao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China; (M.E.); (W.Z.); (M.A.); (E.N.); (L.Z.); (M.B.)
- Sino-African Joint Research Centre, Chinese Academy of Sciences, Beijing 100049, China
| | - Mohammad Belal
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China; (M.E.); (W.Z.); (M.A.); (E.N.); (L.Z.); (M.B.)
- Plant Genome Laboratory, Department of Genetic Resources, Desert Research Center, El-Matareya, Cairo 11753, Egypt
| | - Yuepeng Han
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China; (M.E.); (W.Z.); (M.A.); (E.N.); (L.Z.); (M.B.)
- Sino-African Joint Research Centre, Chinese Academy of Sciences, Beijing 100049, China
| | - Liao Liao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China; (M.E.); (W.Z.); (M.A.); (E.N.); (L.Z.); (M.B.)
- Sino-African Joint Research Centre, Chinese Academy of Sciences, Beijing 100049, China
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Raja TV, Alex R, Singh U, Kumar S, Das AK, Sengar G, Singh AK. Genome wide mining of SNPs and INDELs through ddRAD sequencing in Sahiwal cattle. Anim Biotechnol 2023; 34:4885-4899. [PMID: 37093232 DOI: 10.1080/10495398.2023.2200517] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The study was conducted in Sahiwal cattle for genome wide identification and annotation of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) in Sahiwal cattle. The double digest restriction-site associated DNA (ddRAD) sequencing, a reduced representation method was used for the identification of variants at nucleotide level. A total of 1,615,211 variants were identified at RD10 and Q30 consisting of 1,480,930 SNPs and 134,281 INDELs with respect to the Bos taurus reference genome. The SNPs were annotated for their location, impact and functional class. The SNPs identified in Sahiwal cattle were found to be associated with a total of 26,229 genes. A total of 1819 SNPs were annotated for 209 candidate genes associated with different production and reproduction traits. The variants identified in the present study may be useful to strengthen the existing bovine SNP chips for reducing the biasness over the taurine cattle breeds. The diversity analysis provides the insight of the genetic architecture of the Sahiwal population Studied. The large genetic variations identified at the nucleotide level provide ample scope for implementing an effective and efficient breed improvement programme for increasing the productivity of Sahiwal cattle.
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Affiliation(s)
- Thiruvothur Venkatesan Raja
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut Cantt, Uttar Pradesh, India
| | - Rani Alex
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Umesh Singh
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut Cantt, Uttar Pradesh, India
| | - Sushil Kumar
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut Cantt, Uttar Pradesh, India
| | - Achintya Kumar Das
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut Cantt, Uttar Pradesh, India
| | - Gyanendra Sengar
- National Research Centre on Pigs, Rani (Near Airport), Guwahati, Assam, India
| | - Amit Kumar Singh
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut Cantt, Uttar Pradesh, India
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Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Sharma N, Chopra A, Kandalkar Y, Choudhary A, Magotra A. Population-wide genetic analysis of Ovar-DQA1 and DQA2 loci across sheep breeds in India revealed their evolutionary importance and fitness of sheep in a tropical climate. Anim Biotechnol 2023; 34:4645-4657. [PMID: 36847639 DOI: 10.1080/10495398.2023.2180010] [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: 03/01/2023]
Abstract
Genetic variability at the major histocompatibility complex (MHC) is important in any species due to significant role played by MHC for antigen presentation. DQA locus has not been studied for its genetic variability across sheep population in India. In the present study, MHC of sheep at DQA1 and DQA2 loci were evaluated across 17 Indian sheep breeds. Results revealed high degree of heterozygosity (10.34% to 100% for DQA1 and 37.39 to 100% for DQA2). 18 DQA1 alleles and 22 DQA2 alleles were isolated in different breeds. Nucleotide content for DQA region revealed richness of AT content (54.85% for DQA1 and 53.89% for DQA2). DQA1 and DQA2 sequences clustered independently. We could see evidence of divergence of DQA as DQA1 and DQA2 across sheep breeds. Wu-Kabat variability index revealed vast genetic variation across DQA1 and DQA2, specifically at peptide binding sites (PBS) that consisted 21 residues for DQA1 and 17 residues for DQA2. Evolutionary analysis revealed the presence of positive and balancing selection for DQA1 locus, however DQA2 was under purifying selection across sheep breeds. Higher heterozygosity and large diversity at both loci especially at PBS indicated the fitness of the sheep population for evading pathogens and adapt to the harsh tropical climate.
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Affiliation(s)
- G R Gowane
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - S S Misra
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - Rani Alex
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Nikita Sharma
- Animal Health Section, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics and Breeding Division, ICAR-Arid Region Campus, Central Sheep and Wool Research Institute, Bikaner, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | | | - Ankit Magotra
- Animal Genetics and Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
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Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Dass G, Chopra A, Kandalkar Y, Vijay V, Choudhary A, Magotra A, Rajendran R. Cross-population genetic analysis revealed genetic variation and selection in the Ovar-DRB1 gene of Indian sheep breeds. Anim Biotechnol 2023; 34:2928-2939. [PMID: 36153754 DOI: 10.1080/10495398.2022.2125404] [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: 11/01/2022]
Abstract
In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of Ovar-DRB diversity across sheep breeds of India. Here, Ovar-DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN > dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.
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Affiliation(s)
- G R Gowane
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - S S Misra
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - Rani Alex
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Gopal Dass
- Animal Genetics & Breeding Division, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics & Breeding Division, ICAR-Arid Region Campus, Central Sheep & Wool Research Institute Bikaner, Avikanagar, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | - V Vijay
- Sonadi Seep Breeding Unit, NWPSI at Navaniya Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | | | - Ankit Magotra
- Animal Genetics & Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - R Rajendran
- Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Theni, India
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Raja TV, Alex R, Singh U, Kumar S, Das AK, Sengar G, Singh AK, Ghosh A, Saha S, Mitra A. Genome-wide identification and annotation of SNPs for economically important traits in Frieswal™, newly evolved crossbred cattle of India. 3 Biotech 2023; 13:310. [PMID: 37621321 PMCID: PMC10444711 DOI: 10.1007/s13205-023-03701-0] [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: 03/03/2023] [Accepted: 06/26/2023] [Indexed: 08/26/2023] Open
Abstract
The Frieswal™ is a crossbred cattle evolved by ICAR-Central Institute for Research on Cattle utilizing more than 15,000 cattle maintained at more than 37 military farms spread all over the agro-climatic regions of the country. The ddRAD sequencing method was used to identify and annotate the SNPs and INDELs. The results of variant calling revealed 1,487,851 SNPs and 128,175 INDELs at a read depth of 10. A total of 3,775,079 effects were identified, and majority (66.41%) of the effects were in the intron region of the genome followed by intergenic (21.87%). Majority (99.18%) of the variants had the modifier effect. The results revealed a higher magnitude of transitions as compared to the transversion. The classification of SNPs by functional class revealed a majority of missense (43%) and silent (56%) effects. Out of 26,278 genes identified, 1841 SNPs were annotated in 207 candidate genes responsible for various milk production and reproduction traits. The observed heterozygosity was 0.2804 against the expected heterozygosity value of 0.2978. The overall average inbreeding coefficient (FIS) was 0.0604. The pathway analysis revealed that the prolactin signaling pathway (GO:0038161) was significant biological process complete for both milk production and reproduction traits. The SNP variations can be effectively used as markers for early and accurate identification of the QTLs and for formulating an efficient and effective breed improvement program in Frieswal™ cattle. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03701-0.
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Affiliation(s)
- Thiruvothur Venkatesan Raja
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Rani Alex
- National Dairy Research Institute, Karnal, Haryana India
| | - Umesh Singh
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Sushil Kumar
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Achintya Kumar Das
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Gyanendra Sengar
- National Research Centre on Pigs, Rani (Near Airport), Guwahati, Assam 781 131 India
| | - Amit Kumar Singh
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Unified Campus Salt Lake, College More, EN Block, Sector V, Kolkata, West Bengal 700091 India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Unified Campus Salt Lake, College More, EN Block, Sector V, Kolkata, West Bengal 700091 India
| | - Abhijit Mitra
- Molecular Genetics Laboratory, Cattle Genetics and Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh 650 001 India
- Present Address: Animal Husbandry Commissioner, Department of Animal Husbandry and Dairying, Government of India, New Delhi, India
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Aizenbud Y, Jaffe A, Wang M, Hu A, Amsel N, Nadler B, Chang JT, Kluger Y. Spectral top-down recovery of latent tree models. INFORMATION AND INFERENCE : A JOURNAL OF THE IMA 2023; 12:iaad032. [PMID: 37593361 PMCID: PMC10431953 DOI: 10.1093/imaiai/iaad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/24/2023] [Accepted: 06/24/2023] [Indexed: 08/19/2023]
Abstract
Modeling the distribution of high-dimensional data by a latent tree graphical model is a prevalent approach in multiple scientific domains. A common task is to infer the underlying tree structure, given only observations of its terminal nodes. Many algorithms for tree recovery are computationally intensive, which limits their applicability to trees of moderate size. For large trees, a common approach, termed divide-and-conquer, is to recover the tree structure in two steps. First, separately recover the structure of multiple, possibly random subsets of the terminal nodes. Second, merge the resulting subtrees to form a full tree. Here, we develop spectral top-down recovery (STDR), a deterministic divide-and-conquer approach to infer large latent tree models. Unlike previous methods, STDR partitions the terminal nodes in a non random way, based on the Fiedler vector of a suitable Laplacian matrix related to the observed nodes. We prove that under certain conditions, this partitioning is consistent with the tree structure. This, in turn, leads to a significantly simpler merging procedure of the small subtrees. We prove that STDR is statistically consistent and bound the number of samples required to accurately recover the tree with high probability. Using simulated data from several common tree models in phylogenetics, we demonstrate that STDR has a significant advantage in terms of runtime, with improved or similar accuracy.
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Affiliation(s)
- Yariv Aizenbud
- Program in Applied Mathematics, Yale University, New Haven, CT 06511, USA
| | - Ariel Jaffe
- Program in Applied Mathematics, Yale University, New Haven, CT 06511, USA
| | - Meng Wang
- Department of Pathology, Yale University, New Haven, CT 06511, USA
| | - Amber Hu
- Program in Applied Mathematics, Yale University, New Haven, CT 06511, USA
| | - Noah Amsel
- Program in Applied Mathematics, Yale University, New Haven, CT 06511, USA
| | - Boaz Nadler
- Department of Computer Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph T Chang
- Department of Statistics, Yale University, New Haven, CT 06520, USA
| | - Yuval Kluger
- Program in Applied Mathematics, Yale University, New Haven, CT 06511, USA
- Department of Pathology, Yale University, New Haven, CT 06511, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
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Mantela M, Lambropoulos K, Simserides C. Charge transport properties of ideal and natural DNA segments, as mutation detectors. Phys Chem Chem Phys 2023; 25:7750-7762. [PMID: 36857625 DOI: 10.1039/d3cp00268c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors. Ideal means textbook geometry. Natural means naturally distorted sequences; geometry taken from available databases. A tight-binding (TB) wire model at the base-pair level is recruited, together with a transfer matrix technique. The relevant TB parameters are obtained using a linear combination of all valence orbitals of all atoms, using geometry, either ideal or natural, as the only input. The investigated DNA sequences contain: (i) point substitution mutations - specifically, the transitions guanine (G) ↔ adenine (A) - and (ii) sequences extracted from human chromosomes, modified by expanding the cytosine-adenine-guanine triplet [(CAG)n repeats] to mimic the following diseases: (a) Huntington's disease, (b) Kennedy's disease, (c) Spinocerebellar ataxia 6, (d) Spinocerebellar ataxia 7. Quantities such as eigenspectra, density of states, transmission coefficients, and the - more experimentally relevant - current-voltage (I-V) curves are studied, intending to find adequate features to recognize mutations. To this end, the normalised deviation of the I-V curve from the origin (NDIV) is also defined. The features of the NDIV seem to provide a clearer picture, being sensitive to the number of point mutations and allowing to characterise the degree of danger of developing the aforementioned diseases.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece.
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Mutation Rate and Spectrum of the Silkworm in Normal and Temperature Stress Conditions. Genes (Basel) 2023; 14:genes14030649. [PMID: 36980921 PMCID: PMC10048334 DOI: 10.3390/genes14030649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Mutation rate is a crucial parameter in evolutionary genetics. However, the mutation rate of most species as well as the extent to which the environment can alter the genome of multicellular organisms remain poorly understood. Here, we used parents–progeny sequencing to investigate the mutation rate and spectrum of the domestic silkworm (Bombyx mori) among normal and two temperature stress conditions (32 °C and 0 °C). The rate of single-nucleotide mutations in the normal temperature rearing condition was 0.41 × 10−8 (95% confidence interval, 0.33 × 10−8–0.49 × 10−8) per site per generation, which was up to 1.5-fold higher than in four previously studied insects. Moreover, the mutation rates of the silkworm under the stresses are significantly higher than in normal conditions. Furthermore, the mutation rate varies less in gene regions under normal and temperature stresses. Together, these findings expand the known diversity of the mutation rate among eukaryotes but also have implications for evolutionary analysis that assumes a constant mutation rate among species and environments.
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Suicidal Phenotype of Proofreading-Deficient Herpes Simplex Virus 1 Polymerase Mutants. J Virol 2023; 97:e0135922. [PMID: 36598203 PMCID: PMC9888220 DOI: 10.1128/jvi.01359-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) encodes a family B DNA polymerase (Pol) capable of exonucleolytic proofreading whose functions have been extensively studied in the past. Early studies on the in vitro activity of purified Pol protein found that the enzymatic functions of the holoenzyme are largely separate. Consequently, exonuclease activity can be reduced or abolished by certain point mutations within catalytically important regions, with no or only minor effects on polymerase activity. Despite unimpaired polymerase activity, the recovery of HSV-1 mutants with a catalytically inactive exonuclease has been so far unsuccessful. Hence, mutations such as D368A, which abolish exonuclease activity, are believed to be lethal. Here, we show that HSV-1 can be recovered in the absence of Pol intrinsic exonuclease activity and demonstrate that a lack of proofreading causes the rapid accumulation of likely detrimental mutations. Although mutations that abolish exonuclease activity do not appear to be lethal, the lack of proofreading yields viruses with a suicidal phenotype that cease to replicate within few passages following reconstitution. Hence, we conclude that high replication fidelity conferred by proofreading is essential to maintain HSV-1 genome integrity and that a lack of exonuclease activity produces an initially viable but rapidly suicidal phenotype. However, stably replicating viruses with reduced exonuclease activity and therefore elevated mutation rates can be generated by mutating a catalytically less important site located within a conserved exonuclease domain. IMPORTANCE Recovery of fully exonuclease-deficient herpes simplex virus 1 (HSV-1) DNA polymerase mutants has been so far unsuccessful. However, exonuclease activity is not known to be directly essential for virus replication, and the lethal phenotype of certain HSV-1 polymerase mutants is thus attributed to factors other than exonuclease activity. Here, we showed that the recovery of a variety of exonuclease-deficient HSV-1 polymerase mutants is possible and that these mutants are initially replication competent. We, however, observed a progressive loss of mutant viability upon cell culture passaging, which coincided with the rapid accumulation of mutations in exonuclease-deficient viruses. We thus concluded that a lack of DNA proofreading in exonuclease-deficient viruses causes an initially viable but rapidly suicidal hypermutator phenotype and, consequently, the extinction of mutant viruses within few generations following recovery. This would make the absence of exonuclease activity the primary reason for the long-reported difficulties in culturing exonuclease-deficient HSV-1 mutants.
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Gelova SP, Doherty KN, Alasmar S, Chan K. Intrinsic base substitution patterns in diverse species reveal links to cancer and metabolism. Genetics 2022; 222:iyac144. [PMID: 36149294 PMCID: PMC9630983 DOI: 10.1093/genetics/iyac144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/07/2022] [Indexed: 11/12/2022] Open
Abstract
Analyses of large-scale cancer sequencing data have revealed that mutagenic processes can create distinctive patterns of base substitutions, called mutational signatures. Interestingly, mutational patterns resembling some of these signatures can also be observed in normal cells. To determine whether similar patterns exist more generally, we analyzed large data sets of genetic variation, including mutations from 7 model species and single nucleotide polymorphisms in 42 species, totaling >1.9 billion variants. We found that base substitution patterns for most species closely match single base substitution (SBS) mutational signature 5 in the Catalog of Somatic Mutations in Cancer (COSMIC) database. SBS5 is ubiquitous in cancers and also present in normal human cells, suggesting that similar patterns of genetic variation across so many species are likely due to conserved biochemistry. We investigated the mechanistic origins of the SBS5-like mutational pattern in Saccharomyces cerevisiae, and show that translesion DNA synthesis and sugar metabolism are directly linked to this form of mutagenesis. We propose that conserved metabolic processes in cells are coupled to continuous generation of genetic variants, which can be acted upon by selection to drive the evolution of biological entities.
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Affiliation(s)
- Suzana P Gelova
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Kassidy N Doherty
- Biopharmaceutical Sciences Undergraduate Program, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Salma Alasmar
- Biopharmaceutical Sciences Undergraduate Program, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kin Chan
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Selection signatures in melanocortin-1 receptor gene of turkeys (Meleagris gallopavo) raised in hot humid tropics. Trop Anim Health Prod 2022; 54:183. [PMID: 35525911 DOI: 10.1007/s11250-022-03185-9] [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: 08/22/2021] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
Feather colours are used by avian species for defense, adaptation and signaling. Melanocortin-1 receptor (MC1R) gene is one of the genes responsible for feather colour. This study identified selection signatures in MC1R gene of Nigerian indigenous turkeys (NIT) using British United turkeys (BUT) as control breed to investigate the evolutionary processes that have shaped NIT with various feather colours. Complete MC1R gene of 146 NIT (76 males and 70 females) and 32 BUT (18 males and 14 females) were sequenced. Transition/transversion and codon usage biases were predicted using MEGA v6 software. The selective force acting on the gene was predicted using HyPhy software. The FST values were estimated using Arlequin v3.5. The highest transition/transversion bias was predicted for white BUT (1.00) while the lowest was predicted for black NIT (0.50). Negative dN-dS values, indicative of purifying selection, were observed in MC1R gene of all the turkeys. The highest pairwise FST was observed between the MC1R gene of white BUT and black NIT while the least was observed between lavender NIT and white NIT. No recombination event was observed in black NIT and white BUT. The relative synonymous codon usage was the same among different colours for some codons. Presence of purifying selection in MC1R gene of all the turkeys with different feather colours confirms that the gene plays role in many biological processes such as feather colouration, behaviour, pain perception, immunity, growth and adaptation. The results also suggested that the genetic mechanisms generating different feather colours in turkeys are conserved.
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12
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Sen P, Aziz R, Deka RC, Feil EJ, Ray SK, Satapathy SS. Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria. J Mol Evol 2022; 90:114-123. [PMID: 35084523 DOI: 10.1007/s00239-021-10045-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022]
Abstract
Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition in the secondary structure regions of RNA genes. Here, we performed an analysis of transition and transversion frequencies in tRNA genes defined well with secondary structure and compared with the intergenic regions in five bacterial species namely Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae using a large genome sequence data set. In general, the transversion frequency was observed to be lower than that of transition in both tRNA genes and intergenic regions. The transition to transversion ratio was observed to be greater in tRNA genes than that in the intergenic regions in all the five bacteria that we studied. Interestingly, the intraspecies base substitution analysis in tRNA genes revealed that non-compensatory substitutions were more frequent than compensatory substitutions in the stem region. Further, transition to transversion ratio in the loop region was observed to be significantly lesser than that among the non-compensatory substitutions in the stem region. This indicated that the transversion is more deleterious than transition in the stem regions. In addition, substitutions from amino bases (A/C) to keto bases (G/T) were also observed to be more than the reverse substitutions in the stem region. Substitution from amino bases to keto bases are likely to facilitate the stable G:U pairing unlike the reverse substitution that facilitates the unstable A:C pairing in the stem region of tRNA. This work provides additional support that the secondary structure of tRNA molecule is what drives the different substitutions in its gene sequence.
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Affiliation(s)
- Piyali Sen
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Ruksana Aziz
- Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Ramesh C Deka
- Chemical Sciences, Tezpur University, Napaam, Tezpur, Assam, 784028, India
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK.
| | - Suvendra Kumar Ray
- Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
| | - Siddhartha Sankar Satapathy
- Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
- Center for Multidisciplinary Research, Tezpur University, Napaam, Tezpur, Assam, 784028, India.
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13
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The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life (Basel) 2021; 11:life11080773. [PMID: 34440517 PMCID: PMC8398314 DOI: 10.3390/life11080773] [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: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
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14
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Riddiford N, Siudeja K, van den Beek M, Boumard B, Bardin AJ. Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells. Genome Res 2021; 31:1419-1432. [PMID: 34168010 PMCID: PMC8327918 DOI: 10.1101/gr.268441.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 06/15/2021] [Indexed: 12/15/2022]
Abstract
Spontaneous mutations can alter tissue dynamics and lead to cancer initiation. Although large-scale sequencing projects have illuminated processes that influence somatic mutation and subsequent tumor evolution, the mutational dynamics operating in the very early stages of cancer development are currently not well understood. To explore mutational processes in the early stages of cancer evolution, we exploited neoplasia arising spontaneously in the Drosophila intestine. Analysing whole-genome sequencing data with a dedicated bioinformatic pipeline, we found neoplasia formation to be driven largely through the inactivation of Notch by structural variants, many of which involve highly complex genomic rearrangements. The genome-wide mutational burden in neoplasia was found to be similar to that of several human cancers. Finally, we identified genomic features associated with spontaneous mutation, and defined the evolutionary dynamics and mutational landscape operating within intestinal neoplasia over the short lifespan of the adult fly. Our findings provide unique insight into mutational dynamics operating over a short timescale in the genetic model system, Drosophila melanogaster.
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Affiliation(s)
- Nick Riddiford
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Katarzyna Siudeja
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Marius van den Beek
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Benjamin Boumard
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Allison J Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
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15
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Silliman K, Indorf JL, Knowlton N, Browne WE, Hurt C. Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama. BMC Ecol Evol 2021; 21:104. [PMID: 34049492 PMCID: PMC8164322 DOI: 10.1186/s12862-021-01836-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Background The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. Results To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow. Conclusions Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01836-3.
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Affiliation(s)
- Katherine Silliman
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA. .,Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA.
| | - Jane L Indorf
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Carla Hurt
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.,Department of Biology, Tennessee Tech University, Cookeville, TN, 38505, USA
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16
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Derilus D, Rahman MZ, Serrano AE, Massey SE. Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. INFECTION GENETICS AND EVOLUTION 2020; 87:104642. [PMID: 33296723 DOI: 10.1016/j.meegid.2020.104642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 11/29/2022]
Abstract
Apicomplexans are alveolate parasites which include Plasmodium falciparum, the main cause of malaria, one of the world's biggest killers from infectious disease. Apicomplexans are characterized by a reduction in proteome size, which appears to result from metabolic and functional simplification, commensurate with their parasitic lifestyle. However, other factors may also help to explain gene loss such as population bottlenecks experienced during transmission, and the effect of reducing the overall genomic information content. The latter constitutes an 'informational constraint', which is proposed to exert a selective pressure to evolve and maintain genes involved in informational fidelity and error correction, proportional to the quantity of information in the genome (which approximates to proteome size). The dynamics of gene loss was examined in 41 Apicomplexan genomes using orthogroup analysis. We show that loss of genes involved in amino acid metabolism and steroid biosynthesis can be explained by metabolic redundancy with the host. We also show that there is a marked tendency to lose DNA repair genes as proteome size is reduced. This may be explained by a reduction in size of the informational constraint and can help to explain elevated mutation rates in pathogens with reduced genome size. Multiple Sequentially Markovian Coalescent (MSMC) analysis indicates a recent bottleneck, consistent with predictions generated using allele-based population genetics approaches, implying that relaxed selection pressure due to reduced population size might have contributed to gene loss. However, the non-randomness of pathways that are lost challenges this scenario. Lastly, we identify unique orthogroups in malaria-causing Plasmodium species that infect humans, with a high proportion of membrane associated proteins. Thus, orthogroup analysis appears useful for identifying novel candidate pathogenic factors in parasites, when there is a wide sample of genomes available.
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Affiliation(s)
- D Derilus
- Environmental Sciences Department, University of Puerto Rico-Rio Piedras, United States of America
| | - M Z Rahman
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America
| | - A E Serrano
- Department of Microbiology, University of Puerto Rico-School of Medicine, Medical Sciences, United States of America
| | - S E Massey
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America.
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17
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Dasari CM, Bhukya R. Comparative analysis of protein synthesis rate in COVID-19 with other human coronaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104432. [PMID: 32592845 PMCID: PMC7314694 DOI: 10.1016/j.meegid.2020.104432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 12/24/2022]
Abstract
The genetic code contains information that impacts the efficiency and rate of translation. Translation elongation plays a crucial role in determining the composition of the proteome, errors within a protein contributes towards disease processes. It is important to analyze the novel coronavirus (2019-nCoV) at the codon level to find similarities and variations in hosts to compare with other human coronavirus (CoVs). This requires a comparative and comprehensive study of various human and zoonotic nature CoVs relating to codon usage bias, relative synonymous codon usage (RSCU), proportions of slow codons, and slow di-codons, the effective number of codons (ENC), mutation bias, codon adaptation index (CAI), and codon frequencies. In this work, seven different CoVs were analyzed to determine the protein synthesis rate and the adaptation of these viruses to the host cell. The result reveals that the proportions of slow codons and slow di-codons in human host of 2019-nCoV and SARS-CoV found to be similar and very less compared to the other five coronavirus types, which suggest that the 2019-nCoV and SARS-CoV have faster protein synthesis rate. Zoonotic CoVs have high RSCU and codon adaptation index than human CoVs which implies the high translation rate in zoonotic viruses. All CoVs have more AT% than GC% in genetic codon compositions. The average ENC values of seven CoVs ranged between 38.36 and 49.55, which implies the CoVs are highly conserved and are easily adapted to host cells. The mutation rate of 2019-nCoV is comparatively less than MERS-CoV and NL63 that shows an evidence for genetic diversity. Host-specific codon composition analysis portrays the relation between viral host sequences and the capability of novel virus replication in host cells. Moreover, the analysis provides useful measures for evaluating a virus-host adaptation, transmission potential of novel viruses, and thus contributes to the strategies of anti-viral drug design.
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Affiliation(s)
- Chandra Mohan Dasari
- Department of Computer Science and Engineering, National Institute of Technology, Warangal, Telangana-506004, India.
| | - Raju Bhukya
- Department of Computer Science and Engineering, National Institute of Technology, Warangal, Telangana-506004, India.
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18
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Matyášek R, Kovařík A. Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts. Genes (Basel) 2020; 11:E761. [PMID: 32646049 PMCID: PMC7397057 DOI: 10.3390/genes11070761] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022] Open
Abstract
The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide.
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Affiliation(s)
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic;
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19
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Devadasan MJ, Kumar DR, Vineeth MR, Choudhary A, Surya T, Niranjan SK, Verma A, Sivalingam J. Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle. 3 Biotech 2020; 10:309. [PMID: 32582506 DOI: 10.1007/s13205-020-02297-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
The present study was carried out in Tharparkar cattle for identification of genome-wide SNPs and microsatellites, and then annotate the identified high-quality SNPs to milk production, fertility, carcass, adaptability and immune response of economically important traits. A total of 146,011 SNPs were identified with respect to Bos taurus reference genome which are indicus specific, out of which 10,519 SNPs were found to be novel. Similarly, a total of 87,047 SNPs were identified with respect to Bos indicus reference genome. After final annotation of SNPs identified with respect to Bos indicus reference genome, 2871 SNPs were found to be associated in 383 candidate genes having to do with milk production, fertility, carcass, immune response and adaptability traits. Following that, 2571 microsatellites were identified. The information mined from the data might be of importance for the future breed improvement programs, conservation efforts and for enhancing the SNPs density of the existing bovine SNP chips.
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Affiliation(s)
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | - M R Vineeth
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - T Surya
- ICAR-National Dairy Research Institute, Karnal, India
| | - S K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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20
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Bücking R, Cox MP, Hudjashov G, Saag L, Sudoyo H, Stoneking M. Archaic mitochondrial DNA inserts in modern day nuclear genomes. BMC Genomics 2019; 20:1017. [PMID: 31878873 PMCID: PMC6933719 DOI: 10.1186/s12864-019-6392-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.
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Affiliation(s)
- Robert Bücking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D04103, Germany.
| | - Murray P Cox
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Georgi Hudjashov
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, 10430, Indonesia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D04103, Germany
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21
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Wylde Z, Spagopoulou F, Hooper AK, Maklakov AA, Bonduriansky R. Parental breeding age effects on descendants' longevity interact over 2 generations in matrilines and patrilines. PLoS Biol 2019; 17:e3000556. [PMID: 31765371 PMCID: PMC6901263 DOI: 10.1371/journal.pbio.3000556] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/09/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023] Open
Abstract
Individuals within populations vary enormously in mortality risk and longevity, but the causes of this variation remain poorly understood. A potentially important and phylogenetically widespread source of such variation is maternal age at breeding, which typically has negative effects on offspring longevity. Here, we show that paternal age can affect offspring longevity as strongly as maternal age does and that breeding age effects can interact over 2 generations in both matrilines and patrilines. We manipulated maternal and paternal ages at breeding over 2 generations in the neriid fly Telostylinus angusticollis. To determine whether breeding age effects can be modulated by the environment, we also manipulated larval diet and male competitive environment in the first generation. We found separate and interactive effects of parental and grand-parental ages at breeding on descendants' mortality rate and life span in both matrilines and patrilines. These breeding age effects were not modulated by grand-parental larval diet quality or competitive environment. Our findings suggest that variation in maternal and paternal ages at breeding could contribute substantially to intrapopulation variation in mortality and longevity.
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Affiliation(s)
- Zachariah Wylde
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Foteini Spagopoulou
- Uppsala Centre for Evolution and Genomics, Uppsala University, Uppsala, Sweden
| | - Amy K. Hooper
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Alexei A. Maklakov
- Uppsala Centre for Evolution and Genomics, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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22
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Růžička M, Souček P, Kulhánek P, Radová L, Fajkusová L, Réblová K. Bending of DNA duplexes with mutation motifs. DNA Res 2019; 26:341-352. [PMID: 31230075 PMCID: PMC6704406 DOI: 10.1093/dnares/dsz013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/27/2019] [Indexed: 01/30/2023] Open
Abstract
Mutations can be induced by environmental factors but also arise spontaneously during DNA replication or due to deamination of methylated cytosines at CpG dinucleotides. Sites where mutations occur with higher frequency than would be expected by chance are termed hotspots while sites that contain mutations rarely are termed coldspots. Mutations are permanently scanned and repaired by repair systems. Among them, the mismatch repair targets base pair mismatches, which are discriminated from canonical base pairs by probing altered elasticity of DNA. Using biased molecular dynamics simulations, we investigated the elasticity of coldspots and hotspots motifs detected in human genes associated with inherited disorders, and also of motifs with Czech population hotspots and de novo mutations. Main attention was paid to mutations leading to G/T and A+/C pairs. We observed that hotspots without CpG/CpHpG sequences are less flexible than coldspots, which indicates that flexible sequences are more effectively repaired. In contrary, hotspots with CpG/CpHpG sequences exhibited increased flexibility as coldspots. Their mutability is more likely related to spontaneous deamination of methylated cytosines leading to C > T mutations, which are primarily targeted by base excision repair. We corroborated conclusions based on computer simulations by measuring melting curves of hotspots and coldspots containing G/T mismatch.
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Affiliation(s)
- Michal Růžička
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Přemysl Souček
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Radová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno, Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species. G3-GENES GENOMES GENETICS 2019; 9:2325-2336. [PMID: 31097479 PMCID: PMC6643897 DOI: 10.1534/g3.119.400220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have estimated the average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity. The other perennials, except for G. tomentella, had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except for G. cyrtoloba and G. stenophita which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Most genic sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced a very similar evolution as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.
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Thomas BT, Ogunkanmi LA, Iwalokun BA, Popoola OD. Transition-transversion mutations in the polyketide synthase gene of Aspergillus section Nigri. Heliyon 2019; 5:e01881. [PMID: 31338447 PMCID: PMC6579908 DOI: 10.1016/j.heliyon.2019.e01881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/25/2019] [Accepted: 05/30/2019] [Indexed: 11/21/2022] Open
Abstract
This study determined the transition-transversion mutation in the pks gene of Aspergillus section Nigri in order to gain insight into the patterns of nucleotide base substitution and the process of molecular evolution using standard recommended techniques. Results obtained depict frequent occurrence of transition (23 ± 0.96) than transversion (11.37 ± 1.38) (p < 0.05) with C/T being the most frequently observed transitional base substitution and C/A the most frequently occurring transversional base change. The number of single base insertions (56 ± 1.00) were significantly higher than the observed single base deletions (38 ± 2.00) (p < 0.05) while varying degrees of two or more base deletions and insertions were also observed both inside and outside the open reading frame. The maximum likelihood value estimated for the pks gene was calculated to be -9458.80 in 423 positions of the final dataset while the transition-transversion ratio was estimated to be 0.50. The Tajima's neutrality test approaches seven (7) with the nucleotide diversity estimated to be approximately 65%. Evolutionary test depicts positive selection as ratio of non synonymous to synonymous divergence was found to be greater than ratio of the number of non synonymous to synonymous polymorphisms. The proportion of substitution driven by positive selection was calculated to be approximately 96.2%. This research therefore provides an insight into the understanding of pks gene mutation patterns as some of the observed indels resulted in frame shift mutations.
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Affiliation(s)
- Benjamin Thoha Thomas
- Department of Microbiology, Olabisi Onabanjo University, Ago Iwoye, Ogun State, Nigeria
| | | | - Bamidele Abiodun Iwalokun
- Division of Molecular Biology and Biotechnology, Nigeria Institute of Medical Research, Yaba, Lagos, Nigeria
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Xu Y, Zeng A, Song L, Li J, Yan J. Comparative transcriptomics analysis uncovers alternative splicing events and molecular markers in cabbage (Brassica oleracea L.). PLANTA 2019; 249:1599-1615. [PMID: 30771045 DOI: 10.1007/s00425-019-03108-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/07/2019] [Indexed: 05/20/2023]
Abstract
Alternative splicing (AS) events were identified and verified in cabbage by comparative transcriptome analysis. The corresponding markers were developed and the germplasm resources were identified. Alternative splicing (AS) is a central regulatory mechanism that greatly contributes to plant gene expression and transcriptome diversity. A large body of evidence has shown that AS complexity is relevant for plant development, evolution, complexity, and adaptation. Both insertion/deletion (InDel) and single nucleotide polymorphism (SNP) are typically co-dominant inheritance markers and have abundant polymorphisms. These have been widely used for marker-assisted selection, genetic mapping, and germplasm identification in plants. However, little is known about the molecular mechanisms underlying AS events and the development of markers including SNP and InDel from the cabbage transcriptome. In this study, three cabbage transcriptome datasets were collected and aligned to the cabbage reference genome to analyze AS events and marker development. 31,524 AS events were identified from three cabbage genotypes, accounting for 20.8% of the total cabbage genes. Alternative 3' splice site donor (A3SS) was the most frequent type of the four main AS events in cabbage. 70,475 InDels and 706,269 SNPs were identified with average frequencies of 1 InDel/6.9 kb and 1 SNP/0.7 kb, respectively. 71,942 potential SSRs were identified in 53,129 assembled unigenes with a density of 1 SSR/6.8 kb. The ratio of SNPs with synonymous/non-synonymous mutations was 1:0.65. 142 InDels and 36 SNPs were randomly selected and validated via Sanger sequencing and polymorphism was found among 66.2% of the InDels and 78.6% of the SNPs. Furthermore, 35 informative InDel markers were successfully used for genetic diversity analysis on 36 cabbage accessions. These results facilitate understanding of the molecular regulation mechanism underlying AS events in cabbage. They also provide molecular marker resource data for genetic mapping construction and germplasm identification, and facilitate the genetic improvement of cabbage via breeding.
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Affiliation(s)
- Yuanyuan Xu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Aisong Zeng
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
| | - Lixiao Song
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Jiaqing Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Jiyong Yan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
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Biswas R, Panja AS, Bandopadhyay R. In Silico Analyses of Burial Codon Bias Among the Species of Dipterocarpaceae Through Molecular and Phylogenetic Data. Evol Bioinform Online 2019; 15:1176934319834888. [PMID: 31223230 PMCID: PMC6563522 DOI: 10.1177/1176934319834888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/07/2019] [Indexed: 11/15/2022] Open
Abstract
Introduction: DNA barcode, a molecular marker, is used to distinguish among the closely
related species, and it can be applied across a broad range of taxa to
understand ecology and evolution. MaturaseK gene (matK) and
rubisco bisphosphate carboxylase/oxygenase form I gene
(rbcL) of the chloroplast are highly conserved in a
plant system, which are used as core barcode. This present endeavor entails
the comprehensive examination of the under threat plant species based on
success of discrimination on DNA barcode under selection pressure. Result: The family Dipterocarpaceae comprising of 15 genera is under threat due to
some factors, namely, deforestation, habitat alteration, poor seed, pollen
dispersal, etc. Species of this family was grouped into 6 clusters for
matK and 5 clusters and 2 sub-clusters for
rbcL in the phylogenetic tree by using neighbor-joining
method. Cluster I to cluster VI of matK and cluster I to
cluster V of rbcL genes were analyzed by various codon and
substitution bias tools. Mutational pressure guided the codon bias which was
favored by the avoidance of higher GC content and significant negative
correlation between GC12 and GC3 (in sub-cluster I of cluster I
[0.03 < P], cluster I
[0.00001 < P], and cluster II
[0.01 < P] of rbcL, and cluster IV
[0.013 < P] of matK). After
refining the results, it could be speculated that the lower null expectation
values (R = 0.5 or <0.5) were less divergent from the
evolutionary perspective. Apart from that, the higher null expectation
values (R = >0.85) also showed the same result, which
possibly could be due to the negative impact of very high and low transition
rate than transversion. Conclusion: Through the analysis of inter-generic, inter/intra-specific variation and
phylogenetic data, it was found that both selection and mutation played an
important role in synonymous codon choice in these genes, but they acted
inconsistently on the genes, both matK and
rbcL. In vitro stable proteins of both
matK and rbcL were selected through
natural selection rather than mutational selection. matK
gene had higher individual discrimination and barcode success compared with
rbcL. These discriminatory approaches may describe the
problem related to the extinction of plant species. Hence, it becomes very
imperative to identify and detect the under threat plant species in
advance.
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Affiliation(s)
- Raju Biswas
- UGC-Center of Advanced Study, Department of Botany, The University of Burdwan, Bardhaman, India
| | - Anindya Sundar Panja
- Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, India
| | - Rajib Bandopadhyay
- UGC-Center of Advanced Study, Department of Botany, The University of Burdwan, Bardhaman, India
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27
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Rajkumar MS, Garg R, Jain M. Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance. Sci Rep 2018; 8:16795. [PMID: 30429540 PMCID: PMC6235875 DOI: 10.1038/s41598-018-35140-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 10/31/2018] [Indexed: 12/16/2022] Open
Abstract
Seed size/weight is a major agronomic trait which determine crop productivity in legumes. To understand the genetic basis of seed size determination, we sought to identify DNA polymorphisms between two small (Himchana 1 and Pusa 362) and two large-seeded (JGK 3 and PG 0515) chickpea cultivars via whole genome resequencing. We identified a total of 75535 single nucleotide polymorphisms (SNPs), 6486 insertions and deletions (InDels), 1938 multi-nucleotide polymorphisms (MNPs) and 5025 complex variants between the two small and two large-seeded chickpea cultivars. Our analysis revealed 814, 244 and 72 seed-specific genes harboring DNA polymorphisms in promoter or non-synonymous and large-effect DNA polymorphisms, respectively. Gene ontology analysis revealed enrichment of cell growth and division related terms in these genes. Among them, at least 22 genes associated with quantitative trait loci, and those involved in cell growth and division and encoding transcription factors harbored promoter and/or large-effect/non-synonymous DNA polymorphisms. These also showed higher expression at late-embryogenesis and/or mid-maturation stages of seed development in the large-seeded cultivar, suggesting their role in seed size/weight determination in chickpea. Altogether, this study provided a valuable resource for large-scale genotyping applications and a few putative candidate genes that might play crucial role in governing seed size/weight in chickpea.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India. .,National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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28
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Lalitha R, Chandavar VR. Analysis of genetic diversity in CYTB and control region sequences of Melanochelys trijuga (Schweigger, 1812) from Karnataka. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2018. [DOI: 10.1016/j.japb.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Delord C, Lassalle G, Oger A, Barloy D, Coutellec M, Delcamp A, Evanno G, Genthon C, Guichoux E, Le Bail P, Le Quilliec P, Longin G, Lorvelec O, Massot M, Reveillac E, Rinaldo R, Roussel J, Vigouroux R, Launey S, Petit EJ. A cost‐and‐time effective procedure to develop
SNP
markers for multiple species: A support for community genetics. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Chrystelle Delord
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
- HYDRECO Guyane SARLLaboratoire‐Environnement de Petit Saut Kourou France
| | - Gilles Lassalle
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Adrien Oger
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | - Guillaume Evanno
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | | | | | | | - Olivier Lorvelec
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | - Elodie Reveillac
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | | | | | - Regis Vigouroux
- HYDRECO Guyane SARLLaboratoire‐Environnement de Petit Saut Kourou France
| | - Sophie Launey
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
| | - Eric J. Petit
- ESE, Ecology and Ecosystem HealthAgrocampus OuestINRA Rennes France
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30
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Identification of novel single nucleotide polymorphism at thyroid hormone responsive (THRSP) gene of native goat breeds of India. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2017.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Shea DJ, Shimizu M, Itabashi E, Miyaji N, Miyazaki J, Osabe K, Kaji M, Okazaki K, Fujimoto R. Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F 1 hybrid cultivar of Chinese cabbage. BREEDING SCIENCE 2018; 68:375-380. [PMID: 30100805 PMCID: PMC6081294 DOI: 10.1270/jsbbs.17124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
The genome-wide characterization of single nucleotide polymorphism (SNP) between cultivars or between inbred lines contributes to the creation of genetic markers that are important for plant breeding. Functional markers derived from polymorphisms within genes that affect phenotypic variation are especially valuable in plant breeding. Here, we report on the genome re-sequencing and analysis of the two parental inbred lines of the commercial F1 hybrid Chinese cabbage cultivar "W77". Through the genome-wide identification and classification of the SNPs and indels present in each parental line, we identified about 1,500 putative non-functional genes in each parent. We designed cleaved amplified polymorphic sequence (CAPS) markers using specific mutations found at Eco RI restriction sites in the parental lines and confirmed their Mendelian segregation by constructing a linkage map using 96 F2 plants derived from the F1 hybrid cultivar, "W77". Our results and data will be a useful genomic resource for future studies of gene function and metagenomic studies in Chinese cabbage.
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Affiliation(s)
- Daniel J. Shea
- Graduate School of Science and Technology, Niigata University,
Ikarashi-ninocho, Niigata 950-2181,
Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center,
Narita, Kitakami, Iwate 024-0003,
Japan
| | - Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, NARO,
Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Junji Miyazaki
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, La Trobe University,
Melbourne VICAustralia
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University,
Onna-son, Okinawa 904-0495,
Japan
| | - Makoto Kaji
- Watanabe Seed Co., Ltd.,
Machiyashiki, Misato-cho, Miyagi 987-0003,
Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University,
Ikarashi-ninocho, Niigata 950-2181,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
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32
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Dasgupta D, Jasmine J, Mukherji S. Characterization, phylogenetic distribution and evolutionary trajectories of diverse hydrocarbon degrading microorganisms isolated from refinery sludge. 3 Biotech 2018; 8:273. [PMID: 29868311 DOI: 10.1007/s13205-018-1297-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/20/2018] [Indexed: 12/01/2022] Open
Abstract
Phylogenic association between bacteria living under harsh conditions can provide important information on adaptive mechanism, survival strategy and their potential application. Indigenous microorganisms isolated from toxic refinery oily sludge with ability to degrade a diverse range of hydrocarbons were identified and characterized. The strains including Pseudomonas aeruginosa RS1, Microbacterium sp. RS2, Bacillus sp. RS3, Acinetobacter baumannii RS4 and Stenotrophomonas sp. RS5 could utilize n-alkanes, cycloalkanes, polynuclear aromatic hydrocarbons (PAHs) with 2-4 rings and also substituted PAHs as sole substrate. The phylogenetic position of Bacillus sp. RS3 and Pseudomonas sp. RS1 was tested by applying the maximum likelihood (ML) method to the aligned 16S rRNA nucleotide sequences of PAH and aliphatic hydrocarbon degrading strains belonging to the corresponding genus. The base substitution matrix created with each set of organisms capable of degrading aromatic and aliphatic hydrocarbons showed significant transitional event with high values of transition: transversion ratio (R) under all conditions. The guanine-cytosine (GC) content of the hydrocarbon degrading test strains was also found to be highest for the clade which harbored them. The test strains consistently occupied a distinct terminal end within the phylogenetic tree constructed by ML analysis. This study reveals that the refinery sludge imposed environmental stress on the bacterial strains which possibly caused significant genetic alteration and phenotypic adaptation. Due to the divergent evolution of the Pseudomonas and Bacillus strains in the sludge, they appeared distinctly different from other hydrocarbon degrading strains of the same genus.
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Affiliation(s)
- Debdeep Dasgupta
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
- 2Present Address: Amity Institute of Biotechnology, Amity University Mumbai, Bhatan, Post-Somathne, Panvel, Mumbai, Maharashtra 410206 India
| | - Jublee Jasmine
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
| | - Suparna Mukherji
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
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Lalitha R, Chandavar VR. Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka. J Adv Res 2017; 9:87-95. [PMID: 30046490 PMCID: PMC6057446 DOI: 10.1016/j.jare.2017.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022] Open
Abstract
The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop) conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A complete region spanning 1.14 kb and ∼1 kb was amplified by HotStart PCR and sequenced by Sanger sequencing. The Cyt b sequence revealed 85 substitution sites, no indels and 17 parsimony informative sites, whereas D-loop showed 189 variable sites, 51 parsimony informative sites with 5′ functional domains TAS, CSB-F, CSBs (1, 2, 3) preceding tandem repeat at 3′ end. Current data highlights the intraspecific variations in these target regions and variations validated using suitable evolutionary models points out that the overall point mutations observed in the region are transitions leading to no structural and functional alterations. The mitochondrial data generated uncover the genetic diversity within species and conservationist can utilize the data to estimate the effective population size or for forensic identification of animal or its seizures during unlawful trade activities.
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Affiliation(s)
- R Lalitha
- Molecular Endocrinology Laboratory, Department of Biotechnology, Yuvaraja's College, A Constituent Autonomous College of University of Mysore, Mysore 570005, India
| | - V R Chandavar
- Molecular Endocrinology Laboratory, Department of Biotechnology, Yuvaraja's College, A Constituent Autonomous College of University of Mysore, Mysore 570005, India
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Abstract
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be overrepresented among documented adaptive substitutions. To test this hypothesis, we assembled two sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory. We find that the frequency of transitions in these data sets is much higher than would be predicted under a null model where mutation has no effect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.
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Affiliation(s)
- Arlin Stoltzfus
- Genome-scale Measurements Group, Material Measurement Laboratory, NIST, and Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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35
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Koosha M, Oshaghi MA, Sedaghat MM, Vatandoost H, Azari-Hamidian S, Abai MR, Hanafi-Bojd AA, Mohtarami F. Sequence analysis of mtDNA COI barcode region revealed three haplotypes within Culex pipiens assemblage. Exp Parasitol 2017; 181:102-110. [PMID: 28818649 DOI: 10.1016/j.exppara.2017.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
Members of the Culex (Culex) pipiens assemblage are known vectors of deadly encephalitides, periodic filariasis, and West Nile virus throughout the world. However, members of this assemblage are morphologically indistinguishable or hard to distinguish and play distinct roles in transmission of the diseases. The current study aimed to provide further evidence on utility of the two most popular nuclear (ITS2-rDNA) and mitochondrial (COI barcode region) genetic markers to identify members of the assemblage. Culex pipiens assemblage specimens from different climate zones of Iran were collected and identified to species level based on morphological characteristics. Nucleotide sequences of the loci for the specimens plus available data in the GenBank were analyzed to find species specific genetic structures useful for diagnosis purposes. ITS2 region was highly divergent within species or populations suggesting lack of consistency as a reliable molecular marker. In contrast, sequence analysis of 710 bp of COI gene revealed three fixed haplotypes named here "C, T, H" within the assemblage which can be distinguished by HaeIII and AluI enzymes. There were a correlation between the haplotypes and the world climate regions, where the haplotypes H/T and C are present mainly in temperate and tropical regions of the world, respectively. In the New world, Australia, and Japan only haplotype H is found. In conjunction between tropical and temperate regions such Iran, China, and Turkey, a mix of C/H or C/H/T are present. Although, the haplotypes are not strictly species-specific, however, Cx. quinquefasciatus was mainly of haplotype C. Due to the lack of mating barrier and questionable taxonomic situation of the complex members, the mentioned haplotypes in combination with other morphological and molecular characters might be used to address the genetic structure of the studied populations.
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Affiliation(s)
- Mona Koosha
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, P.O.Box 14155-6446, Tehran, Iran
| | - Mohammad Ali Oshaghi
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, P.O.Box 14155-6446, Tehran, Iran.
| | - Mohammad Mehdi Sedaghat
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, P.O.Box 14155-6446, Tehran, Iran
| | - Hassan Vatandoost
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, P.O.Box 14155-6446, Tehran, Iran
| | - Shahyad Azari-Hamidian
- School of Health, Guilan University of Medical Sciences, P.O. Box: 3391, Rasht, Iran; Research Center of Health and Environment, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Reza Abai
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, P.O.Box 14155-6446, Tehran, Iran
| | - Ahmad Ali Hanafi-Bojd
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, P.O.Box 14155-6446, Tehran, Iran
| | - Fatemeh Mohtarami
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, P.O.Box 14155-6446, Tehran, Iran
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36
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Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species. Sci Rep 2017; 7:5966. [PMID: 28729554 PMCID: PMC5519738 DOI: 10.1038/s41598-017-06084-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023] Open
Abstract
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
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Luo X, Xu L, Liang D, Wang Y, Zhang W, Zhu X, Zhu Y, Jiang H, Tang M, Liu L. Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.). BMC Genomics 2017; 18:505. [PMID: 28673249 PMCID: PMC5496183 DOI: 10.1186/s12864-017-3874-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/20/2017] [Indexed: 11/17/2022] Open
Abstract
Background Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inheritance markers, which have been widely used in germplasm identification, genetic mapping and marker-assisted selection in plants. So far, however, little information is available on utilization of AS events and development of SNP and InDel markers from transcriptome in radish. Results In this study, three radish transcriptome datasets were collected and aligned to the reference radish genome. A total of 56,530 AS events were identified from three radish genotypes with intron retention (IR) being the most frequent AS type, which accounted for 59.4% of the total expressed genes in radish. In all, 22,412 SNPs and 9436 InDels were identified with an average frequency of 1 SNP/17.9 kb and 1 InDel/42.5 kb, respectively. A total of 43,680 potential SSRs were identified in 31,604 assembled unigenes with a density of 1 SSR/2.5 kb. The ratio of SNPs with nonsynonymous/synonymous mutations was 1.05:1. Moreover, 35 SNPs and 200 InDels were randomly selected and validated by Sanger sequencing, 83.9% of the SNPs and 70% of the InDels exhibited polymorphism among these three genotypes. In addition, the 15 SNPs and 125 InDels were found to be unevenly distributed on 9 linkage groups. Furthermore, 40 informative InDel markers were successfully used for the genetic diversity analysis on 32 radish accessions. Conclusions These results would not only provide new insights into transcriptome complexity and AS regulation, but also furnish large amount of molecular marker resources for germplasm identification, genetic mapping and further genetic improvement of radish in breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3874-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongyi Liang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Yuelin Zhu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Haiyan Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Shagin DA, Shagina IA, Zaretsky AR, Barsova EV, Kelmanson IV, Lukyanov S, Chudakov DM, Shugay M. A high-throughput assay for quantitative measurement of PCR errors. Sci Rep 2017; 7:2718. [PMID: 28578414 PMCID: PMC5457411 DOI: 10.1038/s41598-017-02727-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/18/2017] [Indexed: 01/01/2023] Open
Abstract
The accuracy with which DNA polymerase can replicate a template DNA sequence is an extremely important property that can vary by an order of magnitude from one enzyme to another. The rate of nucleotide misincorporation is shaped by multiple factors, including PCR conditions and proofreading capabilities, and proper assessment of polymerase error rate is essential for a wide range of sensitive PCR-based assays. In this paper, we describe a method for studying polymerase errors with exceptional resolution, which combines unique molecular identifier tagging and high-throughput sequencing. Our protocol is less laborious than commonly-used methods, and is also scalable, robust and accurate. In a series of nine PCR assays, we have measured a range of polymerase accuracies that is in line with previous observations. However, we were also able to comprehensively describe individual errors introduced by each polymerase after either 20 PCR cycles or a linear amplification, revealing specific substitution preferences and the diversity of PCR error frequency profiles. We also demonstrate that the detected high-frequency PCR errors are highly recurrent and that the position in the template sequence and polymerase-specific substitution preferences are among the major factors influencing the observed PCR error rate.
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Affiliation(s)
- Dmitriy A Shagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Andrew R Zaretsky
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ekaterina V Barsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ilya V Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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39
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Minaya MA, Korom M, Wang H, Belshe RB, Morrison LA. The herpevac trial for women: Sequence analysis of glycoproteins from viruses obtained from infected subjects. PLoS One 2017; 12:e0176687. [PMID: 28448558 PMCID: PMC5407825 DOI: 10.1371/journal.pone.0176687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/16/2017] [Indexed: 12/03/2022] Open
Abstract
The Herpevac Trial for Women revealed that three dose HSV-2 gD vaccine was 58% protective against culture-positive HSV-1 genital disease, but it was not protective against HSV-2 infection or disease. To determine whether vaccine-induced immune responses had selected for a particular gD sequence in strains infecting vaccine recipients compared with viruses infecting control subjects, genetic sequencing studies were carried out on viruses isolated from subjects infected with HSV-1 or HSV-2. We identified naturally occurring variants among the gD sequences obtained from 83 infected subjects. Unique or low frequency amino acid substitutions in the ectodomain of gD were found in 6 of 39 HSV-1-infected subjects and in 7 of 44 HSV-2-infected subjects. However, no consistent amino acid change was identified in isolates from gD-2 vaccine recipients compared with infected placebo recipients. gC and gE surround and partially shield gD from neutralizing antibody, and gB also participates closely in the viral entry process. Therefore, these genes were sequenced from a number of isolates to assess whether sequence variation may alter protein conformation and influence the virus strain’s capacity to be neutralized by vaccine-induced antibody. gC and gE genes sequenced from HSV-1-infected subjects showed more variability than their HSV-2 counterparts. The gB sequences of HSV-1 oral isolates resembled each other more than they did gB sequences rom genital isolates. Overall, however, comparison of glycoprotein sequences of viral isolates obtained from infected subjects did not reveal any singular selective pressure on the viral cell attachment protein or surrounding glycoproteins due to administration of gD-2 vaccine.
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Affiliation(s)
- Miguel A. Minaya
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Maria Korom
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Hong Wang
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Robert B. Belshe
- Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Lynda A. Morrison
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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40
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Martín-Navarro A, Gaudioso-Simón A, Álvarez-Jarreta J, Montoya J, Mayordomo E, Ruiz-Pesini E. Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides. BMC Bioinformatics 2017; 18:158. [PMID: 28270093 PMCID: PMC5341421 DOI: 10.1186/s12859-017-1562-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several methods have been developed to predict the pathogenicity of missense mutations but none has been specifically designed for classification of variants in mtDNA-encoded polypeptides. Moreover, there is not available curated dataset of neutral and damaging mtDNA missense variants to test the accuracy of predictors. Because mtDNA sequencing of patients suffering mitochondrial diseases is revealing many missense mutations, it is needed to prioritize candidate substitutions for further confirmation. Predictors can be useful as screening tools but their performance must be improved. RESULTS We have developed a SVM classifier (Mitoclass.1) specific for mtDNA missense variants. Training and validation of the model was executed with 2,835 mtDNA damaging and neutral amino acid substitutions, previously curated by a set of rigorous pathogenicity criteria with high specificity. Each instance is described by a set of three attributes based on evolutionary conservation in Eukaryota of wildtype and mutant amino acids as well as coevolution and a novel evolutionary analysis of specific substitutions belonging to the same domain of mitochondrial polypeptides. Our classifier has performed better than other web-available tested predictors. We checked performance of three broadly used predictors with the total mutations of our curated dataset. PolyPhen-2 showed the best results for a screening proposal with a good sensitivity. Nevertheless, the number of false positive predictions was too high. Our method has an improved sensitivity and better specificity in relation to PolyPhen-2. We also publish predictions for the complete set of 24,201 possible missense variants in the 13 human mtDNA-encoded polypeptides. CONCLUSIONS Mitoclass.1 allows a better selection of candidate damaging missense variants from mtDNA. A careful search of discriminatory attributes and a training step based on a curated dataset of amino acid substitutions belonging exclusively to human mtDNA genes allows an improved performance. Mitoclass.1 accuracy could be improved in the future when more mtDNA missense substitutions will be available for updating the attributes and retraining the model.
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Affiliation(s)
- Antonio Martín-Navarro
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain.,Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain
| | - Andrés Gaudioso-Simón
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain
| | - Jorge Álvarez-Jarreta
- Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain.,Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, Zaragoza, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain.,Instituto de Investigación Sanitaria de Aragón (IISA), Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Universidad de Zaragoza, Zaragoza, Spain
| | - Elvira Mayordomo
- Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain. .,Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, Zaragoza, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain. .,Instituto de Investigación Sanitaria de Aragón (IISA), Universidad de Zaragoza, Zaragoza, Spain. .,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Universidad de Zaragoza, Zaragoza, Spain. .,Fundación ARAID, Universidad de Zaragoza, Zaragoza, Spain.
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41
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Raimondi D, Orlando G, Messens J, Vranken WF. Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State. Hum Mutat 2016; 38:86-94. [PMID: 27667481 DOI: 10.1002/humu.23129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 09/13/2016] [Accepted: 09/20/2016] [Indexed: 01/08/2023]
Abstract
Cysteines are among the rarest amino acids in nature, and are both functionally and structurally very important for proteins. The ability of cysteines to form disulfide bonds is especially relevant, both for constraining the folded state of the protein and for performing enzymatic duties. But how does the variation record of human proteins reflect their functional importance and structural role, especially with regard to deleterious mutations? We created HUMCYS, a manually curated dataset of single amino acid variants that (1) have a known disease/neutral phenotypic outcome and (2) cause the loss of a cysteine, in order to investigate how mutated cysteines relate to structural aspects such as surface accessibility and cysteine oxidation state. We also have developed a sequence-based in silico cysteine oxidation predictor to overcome the scarcity of experimentally derived oxidation annotations, and applied it to extend our analysis to classes of proteins for which the experimental determination of their structure is technically challenging, such as transmembrane proteins. Our investigation shows that we can gain insights into the reason behind the outcome of cysteine losses in otherwise uncharacterized proteins, and we discuss the possible molecular mechanisms leading to deleterious phenotypes, such as the involvement of the mutated cysteine in a structurally or enzymatically relevant disulfide bond.
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Affiliation(s)
- Daniele Raimondi
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium.,Machine Learning Group, ULB, Brussels, Belgium
| | - Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium.,Machine Learning Group, ULB, Brussels, Belgium
| | - Joris Messens
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium
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Transition and Transversion Mutations Are Biased towards GC in Transposons of Chilo suppressalis (Lepidoptera: Pyralidae). Genes (Basel) 2016; 7:genes7100072. [PMID: 27669309 PMCID: PMC5083911 DOI: 10.3390/genes7100072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/13/2016] [Accepted: 09/18/2016] [Indexed: 12/04/2022] Open
Abstract
Transposons are often regulated by their hosts, and as a result, there are transposons with several mutations within their host organisms. To gain insight into the patterns of the variations, nucleotide substitutions and indels of transposons were analysed in Chilo suppressalis Walker. The CsuPLE1.1 is a member of the piggyBac-like element (PLE) family, which belongs to the DNA transposons, and the Csu-Ty3 is a member of the Ty3/gypsy family, which belongs to the RNA transposons. Copies of CsuPLE1.1 and Csu-Ty3 were cloned separately from different C. suppressalis individuals, and then multiple sequence alignments were performed. There were numerous single-base substitutions in CsuPLE1.1 and Csu-Ty3, but only a few insertion and deletion mutations. Similarly, in both transposons, the occurring frequencies of transitions were significantly higher than transversions (p ≤ 0.01). In the single-base substitutions, the most frequently occurring base changes were A→G and T→C in both types of transposons. Additionally, single-base substitution frequencies occurring at positions 1, 2 or 3 (pos1, pos2 or pos3) of a given codon in the element transposase were not significantly different. Both in CsuPLE1.1 and Csu-Ty3, the patterns of nucleotide substitution had the same characteristics and nucleotide mutations were biased toward GC. This research provides a perspective on the understanding of transposon mutation patterns.
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Lu M, Krutovsky KV, Nelson CD, Koralewski TE, Byram TD, Loopstra CA. Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics 2016; 17:730. [PMID: 27624183 PMCID: PMC5022155 DOI: 10.1186/s12864-016-3081-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/09/2016] [Indexed: 01/06/2023] Open
Abstract
Background Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. Results The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r2) between pairs of SNPs linked within single scaffolds decaying to half maximum (r2 = 0.22) within 55 bp, to r2 = 0.1 within 192 bp, and to r2 = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. Conclusions The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3081-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mengmeng Lu
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA. .,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, 37077, Germany. .,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str, Moscow, 119333, Russia. .,Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, 660036, Russia.
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, 23332 Success Road, Saucier, MS, 39574, USA.,University of Kentucky, Forest Health Research and Education Center, 730 Rose Street, Lexington, KY, 40546, USA
| | - Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA
| | - Thomas D Byram
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Texas A&M Forest Service, 2585 TAMU, College Station, TX, 77843-2585, USA
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
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Bhalla AD, Khodadadi-Jamayran A, Li Y, Lynch DR, Napierala M. Deep sequencing of mitochondrial genomes reveals increased mutation load in Friedreich's ataxia. Ann Clin Transl Neurol 2016; 3:523-36. [PMID: 27386501 PMCID: PMC4931717 DOI: 10.1002/acn3.322] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 12/02/2022] Open
Abstract
Objective Friedreich's ataxia (FRDA) is an autosomal recessive trinucleotide repeat expansion disorder caused by epigenetic silencing of the frataxin gene (FXN). Current research suggests that damage and variation of mitochondrial DNA (mtDNA) contribute to the molecular pathogenesis of FRDA. We sought to establish the extent of the mutation burden across the mitochondrial genome in FRDA cells and investigate the molecular mechanisms connecting FXN downregulation and the acquisition of mtDNA damage. Methods Damage and mutation load in mtDNA of a panel of FRDA and control fibroblasts were determined using qPCR and next‐generation MiSeq sequencing, respectively. The capacity of FRDA and control cells to repair oxidative lesions in their mtDNA was measured using a quantitative DNA damage assay. Comprehensive RNA sequencing gene expression analyses were conducted to assess the status of DNA repair and metabolism genes in FRDA cells. Results Acute or prolonged downregulation of FXN expression resulted in a significant increase in mtDNA damage that translated to a significant elevation of mutation load in mtDNA. The predominant mutations identified throughout the mtDNA were C>T, G>A transitions (P = 0.007). Low FXN expression reduced capacity to repair oxidative damage in mtDNA. Downregulation of FXN expression strongly correlated (r = 0.73) with decreased levels of base excision repair (BER) DNA glycosylase NTHL1. Interpretation Downregulation of FXN expression in FRDA cells elevates mtDNA damage, increases mutation load of the mitochondrial genome, and diminishes DNA repair capacity. Progressive accumulation of mtDNA mutations in vulnerable FRDA patient cells reduces mitochondrial fitness ultimately leading to cell death.
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Affiliation(s)
- Angela D Bhalla
- Department of Biochemistry and Molecular Genetics University of Alabama at Birmingham UAB Stem Cell Institute 1825 University Blvd. Birmingham Alabama 35294
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics University of Alabama at Birmingham UAB Stem Cell Institute 1825 University Blvd. Birmingham Alabama 35294
| | - Yanjie Li
- Department of Biochemistry and Molecular Genetics University of Alabama at Birmingham UAB Stem Cell Institute 1825 University Blvd. Birmingham Alabama 35294
| | - David R Lynch
- Division of Neurology and Pediatrics Children's Hospital of Philadelphia Abramson Research Center Room 502 Philadelphia Pennsylvania 19104
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics University of Alabama at Birmingham UAB Stem Cell Institute 1825 University Blvd. Birmingham Alabama 35294; Department of Molecular Biomedicine Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan 61-704 Poland
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Geller R, Estada Ú, Peris JB, Andreu I, Bou JV, Garijo R, Cuevas JM, Sabariegos R, Mas A, Sanjuán R. Highly heterogeneous mutation rates in the hepatitis C virus genome. Nat Microbiol 2016; 1:16045. [PMID: 27572964 DOI: 10.1038/nmicrobiol.2016.45] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/09/2016] [Indexed: 01/10/2023]
Abstract
Spontaneous mutations are the ultimate source of genetic variation and have a prominent role in evolution. RNA viruses such as hepatitis C virus (HCV) have extremely high mutation rates, but these rates have been inferred from a minute fraction of genome sites, limiting our view of how RNA viruses create diversity. Here, by applying high-fidelity ultradeep sequencing to a modified replicon system, we scored >15,000 spontaneous mutations, encompassing more than 90% of the HCV genome. This revealed >1,000-fold differences in mutability across genome sites, with extreme variations even between adjacent nucleotides. We identify base composition, the presence of high- and low-mutation clusters and transition/transversion biases as the main factors driving this heterogeneity. Furthermore, we find that mutability correlates with the ability of HCV to diversify in patients. These data provide a site-wise baseline for interrogating natural selection, genetic load and evolvability in HCV, as well as for evaluating drug resistance and immune evasion risks.
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Affiliation(s)
- Ron Geller
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Úrsula Estada
- Unitat de Genómica, Servei Central de Suport a la Investigació Experimental, Universitat de València, 46100 Burjassot, València, Spain
| | - Joan B Peris
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Iván Andreu
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Juan-Vicente Bou
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Rosario Sabariegos
- Regional Center for Biomedical Research, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - Antonio Mas
- Regional Center for Biomedical Research, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain.,Departament de Genètica, Universitat de València, 46100 Burjassot, València, Spain
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Crowgey EL, Stabley DL, Chen C, Huang H, Robbins KM, Polson SW, Sol-Church K, Wu CH. An integrated approach for analyzing clinical genomic variant data from next-generation sequencing. J Biomol Tech 2015; 26:19-28. [PMID: 25649353 DOI: 10.7171/jbt.15-2601-002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Next-generation sequencing (NGS) technologies provide the potential for developing high-throughput and low-cost platforms for clinical diagnostics. A limiting factor to clinical applications of genomic NGS is downstream bioinformatics analysis for data interpretation. We have developed an integrated approach for end-to-end clinical NGS data analysis from variant detection to functional profiling. Robust bioinformatics pipelines were implemented for genome alignment, single nucleotide polymorphism (SNP), small insertion/deletion (InDel), and copy number variation (CNV) detection of whole exome sequencing (WES) data from the Illumina platform. Quality-control metrics were analyzed at each step of the pipeline by use of a validated training dataset to ensure data integrity for clinical applications. We annotate the variants with data regarding the disease population and variant impact. Custom algorithms were developed to filter variants based on criteria, such as quality of variant, inheritance pattern, and impact of variant on protein function. The developed clinical variant pipeline links the identified rare variants to Integrated Genome Viewer for visualization in a genomic context and to the Protein Information Resource's iProXpress for rich protein and disease information. With the application of our system of annotations, prioritizations, inheritance filters, and functional profiling and analysis, we have created a unique methodology for downstream variant filtering that empowers clinicians and researchers to interpret more effectively the relevance of genomic alterations within a rare genetic disease.
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Affiliation(s)
- Erin L Crowgey
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
| | - Deborah L Stabley
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
| | - Chuming Chen
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
| | - Hongzhan Huang
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
| | - Katherine M Robbins
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
| | - Shawn W Polson
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
| | - Katia Sol-Church
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
| | - Cathy H Wu
- 1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA
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Hu Z, Mbacké B, Perumal R, Guèye MC, Sy O, Bouchet S, Prasad PVV, Morris GP. Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. BMC Genomics 2015; 16:1048. [PMID: 26654432 PMCID: PMC4674952 DOI: 10.1186/s12864-015-2255-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/30/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal. RESULTS We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage. CONCLUSIONS We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.
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Affiliation(s)
- Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
| | - Bassirou Mbacké
- Ecole Nationale Supérieure d'Agriculture, Université de Thiès, Thiès, BP 296, Senegal.
| | - Ramasamy Perumal
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- Agricultural Research Center-Hays, Kansas State University, Hays, KS, 67601, USA.
| | - Mame Codou Guèye
- Institut Sénégalais de Recherches Agricoles, Thiès, BP 3320, Senegal.
| | - Ousmane Sy
- Institut Sénégalais de Recherches Agricoles, Thiès, BP 3320, Senegal.
| | - Sophie Bouchet
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
| | - P V Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
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Wang W, Ma L, Becher H, Garcia S, Kovarikova A, Leitch IJ, Leitch AR, Kovarik A. Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. Chromosoma 2015; 125:683-99. [PMID: 26637996 PMCID: PMC5023732 DOI: 10.1007/s00412-015-0556-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/05/2015] [Indexed: 11/28/2022]
Abstract
In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.
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Affiliation(s)
- Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Sònia Garcia
- Laboratori de Botànica-Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Alena Kovarikova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
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Abstract
A pattern in which nucleotide transitions are favored several fold over transversions is common in molecular evolution. When this pattern occurs among amino acid replacements, explanations often invoke an effect of selection, on the grounds that transitions are more conservative in their effects on proteins. However, the underlying hypothesis of conservative transitions has never been tested directly. Here we assess support for this hypothesis using direct evidence: the fitness effects of mutations in actual proteins measured via individual or paired growth experiments. We assembled data from 8 published studies, ranging in size from 24 to 757 single-nucleotide mutations that change an amino acid. Every study has the statistical power to reveal significant effects of amino acid exchangeability, and most studies have the power to discern a binary conservative-vs-radical distinction. However, only one study suggests that transitions are significantly more conservative than transversions. In the combined set of 1,239 replacements (544 transitions, 695 transversions), the chance that a transition is more conservative than a transversion is 53 % (95 % confidence interval 50 to 56) compared with the null expectation of 50 %. We show that this effect is not large compared with that of most biochemical factors, and is not large enough to explain the several-fold bias observed in evolution. In short, the available data have the power to verify the “conservative transitions” hypothesis if true, but suggest instead that selection on proteins plays at best a minor role in the observed bias.
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Affiliation(s)
- Arlin Stoltzfus
- Institute for Bioscience and Biotechnology Research, Rockville, MD Genome-scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD
| | - Ryan W Norris
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University
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50
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Guo Y, Wiegert-Rininger KE, Vallejo VA, Barry CS, Warner RM. Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp. BMC Genomics 2015; 16:726. [PMID: 26400485 PMCID: PMC4581106 DOI: 10.1186/s12864-015-1931-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/16/2015] [Indexed: 12/20/2022] Open
Abstract
Background Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper. Results Here we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts from P. axillaris were mapped in an interspecific Petunia population and evaluated for co-localization with QTL for development rate. Conclusions The high quality of the three Petunia spp. transcriptomes coupled with the utility of the SNP data will serve as a resource for further exploration of genetic diversity within the genus and will facilitate efforts to develop genetic and physical maps to aid the identification of QTL associated with traits of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1931-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yufang Guo
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Veronica A Vallejo
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Ryan M Warner
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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