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Computational analysis of the AP2/ERF family in crops genome

BMC Genomics volume 25, Article number: 102 (2024) Cite this article

Abstract

Background

The Apetala 2/ethylene-responsive factor family has diverse functions that enhance development and torment resistance in the plant genome. In variation, the ethylene-responsive factor (ERF) family of TF’s genes is extensive in the crop genome. Generally, the plant-specific ethylene-responsive factor family may divided by the dehydration-responsive element-binding (DREB) subfamily. So, the AP2/ERF super-family demonstrated the repeated AP2 domain during growth. The sole AP2 domain function represents abiotic stress resistance. Also, the AP2 with B3 domain enhances during the replication of brassinosteroid.

Objective

The study objective is to investigate the Apetala 2/ethylene-responsive factor family in a model organism of the Arabidopsis thaliana for comparative analysis towards Solanum lycopersicum (Tomato), Brassica juncea (Indian and Chinese mustard), Zea mays L. (Maize) and Oryza sativa (Indian and Japanese Rice). So, examinations of the large AP2/ERF super-family are mandatory to explore the Apetala 2 (AP2) family, ERF family, DREB subfamily, and RAV family involved during growth and abiotic stress stimuli in crops.

Methods

Therefore, perform bioinformatics and computational methods to the current knowledge of the Apetala 2/ethylene-responsive factor family and their subfamilies in the crop genome. This method may be valuable for functional analysis of particular genes and their families in the plant genome.

Results

Observation data provided evidence of the Apetala 2/ethylene-responsive factor (AP2/ERF) super-family and their sub-family present in Arabidopsis thaliana (Dicots) and compared with Solanum lycopersicum (Dicots), Brassica juncea (Dicots), Zea mays L. (Monocots) and Oryza sativa (Monocots). Also, remarks genes in Oryza sativa. This report upgraded the Apetala 2/ethylene-responsive factor (AP2/ERF) family in the crop genome. So, the analysis documented the conserved domain, motifs, and phylogenetic tree towards Dicots and Monocots species. Those outcomes will be valuable for future studies of the defensive Apetala 2/ethylene-responsive factor family in crops.

Conclusion

Therefore, the study concluded that the several species-specific TF genes in the Apetala 2/ethylene-responsive factor (AP2/ERF) family in Arabidopsis thaliana and compared with crop-species of Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa. Those plant-specific genes regulate during growth and abiotic stress control in plants.

Highlights

• The study is significantly associated with crop development.

• The developmental and abiotic stress-responsible gene families observed in different crops.

• The AP2 family originated during the growing embryo, leaf, and flower.

• The ERF/DREB families initiated abiotic stress such as freezing, drought, salt, low oxygen, oxidative, osmotic, heat, heavy metals, and soil salinity.

• Finally, the RAV family implicated the solution of brassinosteroid.

• So, the analysis data provided valuable information for the Department of Agriculture Biotechnology.

• Also, the documented data are valuable for the plant database and research.

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Introduction

The plant-specific Apetala 2/ethylene-responsive factor family genes are predominant in the dicotyledonous and monocotyledonous plant genomes. Also, the AP2/ERF (Apetala 2/ethylene-responsive factor) family is typically divided into subfamilies: (1) The primary AP2 family, (2) the ERF/DREB family, and the last (3) RAV family. The AP2 family illustrated the duplex AP2 domain associated with developmental processes like growing embryos, leaves, and flowers in plants. The classical ERF family proposed the sole AP2 domain plays a core function in the Apetala 2/ethylene-responsive factor (AP2/ERF) family. So, the defensive ERF family and stress-responsive DREB subfamily functioned as abiotic stress controls such as freezing, drought, salt, low oxygen, oxidative, osmotic, heat, ABA ethylene, jasmonic acid, and abscisic acids have major upshot on the growth and production of plants. The third RAV family proposed a combined function of the AP2 with the B3 domain involved during the reaction of brassinosteroid in the plant genome. Those identified twice Apetala 2 domain, sole Apetala 2 domain, and combined between Apetala 2 with B3 domain consist of amino acid residues involved in DNA binding [1]. The first AP2 (Apetala 2) domain is reports in a model organism of Arabidopsis thaliana. Recent empirical data illustrated the repeated AP2 domain regulates during the developmental processes in crop variety (i.e. flower, meristem, leaf, and embryo development) [2,3,4,5,6]. On the other hand, the ethylene-responsive factor (ERF) family divides into two main subfamilies: C-repeat/dehydration-responsive element binding factors family (CBF/DREB family) [7,8,9]. The plant-specific AP2 domain observed as a conserved DNA-binding domain called ethylene-responsive element binding factors or ERFs (i.e. ERF1, ERF2, ERF3, and ERF4) generally binds to the GCC box motifs [10,11,12]. However, the major Apetala 2/ethylene-responsive factor (AP2/ERF) family implicates diverse functions like hormonal signal transduction, cellular processes, regulation of metabolism, and growth processes in plants [6, 8, 13,14,15,16,17,18,19,20,21,22,23]. In December, 2000, the Arabidopsis Genome Initiative (AGI) sequenced the genome of a model plant called Arabidopsis thaliana and identified 145 genes in the broad AP2/ERF family [8]. Also, particular genes in the supreme AP2/ERF family require to determine again. So, we can observe the likelihood of AP2 domain-mediated genes play a role and physiological aspect in plant species. Also, a transgenic experiment will be necessary to govern the biological phenomenon of a particular gene in the defensive AP2/ERF family in plant genomes. The previous evolutionary study shows that the large Apetala 2/ethylene-responsive factor families classified into subfamilies are closely related [24,25,26]. A comparative and functional study of the particular gene from the AP2/ERF (Apetala 2/ethylene-responsive factor) family in crop-specific Arabidopsis thaliana (Dicots), Solanum lycopersicum (Dicots), Brassica juncea (Dicots), Zea mays L. (Monocots) and Oryza sativa (Monocots) is necessary for functional abundance. This process and evaluation of the link between gene families would provide a significant direction for predicting and upgrading the species-specific transcription factor genes in the particular genome. The current availability of the draft genome sequences of Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L., and Oryza sativa allowed comparative and functional analysis between plant genomes, which is valuable for the practical and evolutionary diversity of gene families in the genome. In this work, an establishment and comprehensive investigation of the Apetala 2/ethylene-responsive factor family in Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa attempts. Also, the genes in the Apetala 2/ethylene-responsive factor family in the Arabidopsis thaliana genome was survey again and also compared with crops of Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa. A comparative and functional study between Dicots (Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea) and Monocots (Zea mays L. and Oryza sativa) perform. So, the study reviewed the comparative and functional genomics of the Apetala 2/ethylene-responsive factor family response to growth and abiotic stress response in plants.

Results

The primary sequence demonstrated the formation of nucleotides and peptides in the ERF109 (RRTF1) gene in Arabidopsis thaliana. The sequence composed of 1386 nucleotides and 268 peptides among 64 peptides bind to the DNA sequence called AP2 domain (Table 1).

Table 1 Query sequence
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So, take a closer look at the plant-specific AP2/ERF family and analyze genes known so far; those have different composition and functional domains. Also, the observation summarized the total number of Apetala 2 domains in a model organism of Arabidopsis thaliana and compared it with crops of Solanum lycopersicum, Brassica juncea, Zea mays L., and Oryza sativa (Table 2).

Table 2 Summary of the AP2 domain and RRTF1
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Also, the gene ontology (GO) annotation demonstrated the sequence accuracy of the RRTF1 (ERF109) gene in the defensive AP2/ERF family in all species (Table 3). Further, the GO annotation of the RRTF1 gene demonstrated the molecular function, cellular component, and biological process in particular organisms. Also, remark genes in Oryza sativa (Indian Rice): Os02g42580, Os02g52880, Os03g02650, Os04g36640, Os04g48330, Os06g42910 and Os12g07030. The observed gene in the crop of Oryza sativa: LOC_Os06g09717.1 was completely identical with OsERF#139 (Os06g09730) and OsERF#010 (Os06g09690), afterward proposed a new gene Id: Os06g09717. So, the crop-specific transcription factor data analysis documented the total AP2 domain-mediated isoforms in the AP2 family, ERF family, DREB subfamily, and RAV family between Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa accordingly. Also, the multiple hits of repeated AP2 domain, single AP2 domain, and B3 domain are listed from all species for sequence alignment. The MSA demonstrated the high censuses (90%) sequence is conserved in the AP2 family, ERF family, DREB subfamily, and RAV family between the plant-specific Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa (Figs. 1, 2, 3, and 4). In contrast, the RRTF1 gene was conserved among all species with their sequence-specific motifs (Figs. 5 and 6). The phylogenetic tree demonstrated the molecular evolutionary link between the RRTF1 genes in the Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa (Fig. 7). Also, the phylogeny analysis demonstrated the particular clade represented the AP2 family, ERF family, DREB sub-family and RAV family (Fig. 8). Further, the RRTF1 (Redox responsive transcription factor 1) expression is highly revealed in the flowering stage and minimal in the germinating period of the plants and observed abundant in flower, blade, hypocotyl, lateral root, and cotyledon.

Table 3 Summary of the GO annotation
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Fig. 1
figure 1

Conserved repeated AP2 domain in the AP2 family

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Fig. 2
figure 2

Conserved single AP2 domain in the ERF family

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Fig. 3
figure 3

Conserved single AP2 domain in the DREB subfamily

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Fig. 4
figure 4

Conserved AP2 with B3 domain in the RAV family

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Fig. 5
figure 5

Conserved AP2 domain in RRTF1

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Fig. 6
figure 6

Sequence motifs in RRTF1 (a, b, and c)

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Fig. 7
figure 7

The molecular evolutionary link of the RRTF1 among all species

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Fig. 8
figure 8

Evolutionary link between genes in the AP2/ERF family

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Discussion

The study demonstrated the Apetala 2/ethylene-responsive factor family between Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L., and Oryza sativa. The earlier empirical data suggested that Sakuma et al. (2002) reported 17, 121, and 6 genes in the Apetala 2 family, ethylene-responsive factor family, and Related to ABI3 and VPI family in a superior model plant of Arabidopsis thaliana respectively. Also, the collaboration of Nakano et al. (2006) suggested 18, 122, and 6 AP2 domain-associated isoforms in the Apetala 2 family, ethylene-responsive factor family, and Related to the ABI3 family in universal Arabidopsis thaliana and also compared with 139 specimens in the ethylene-responsive factor family of Oryza sativa. This study upgraded the total number of plant-specific genes in the Apetala 2 (AP2) family, ethylene-responsive factor (ERF) family, DREB subfamily, and RAV (Related to the ABI3) family of the crop-specific Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L. and Oryza sativa (Table 4). The Brassica juncea exhibited the highest number of specific hits, whereas Oryza sativa showed the lowest. So, the study forwarded the developmental genes in the AP2 family (i.e. flower, meristem, leaf, and embryo development). In contrast, the abiotic stress-responsive genes in the ERF (ethylene-responsive factor) family and DREB subfamily (i.e. low oxygen, freezing, drought, salt, oxidative, osmotic, heat, ABA ethylene, jasmonic acid, and abscisic acids) (Table 5). At last, the involvement of the RAV family in a brassinosteroid response were observed.

Table 4 Summary of the AP2/ERF super-family
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Table 5 Biological Function of genes in the AP2/ERF family
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So, the AP2/ERF super-family is necessary to explore the sub-families involved during the growth and survival of crops. A comparative analysis of crops' genomes is mandatory for agriculture science and development. Also, the crops are manageable through agriculture biotechnology for research and development. In contrast, approximately 80% of crops produce in India. Those crops are economically beneficial around the globe.

Conclusion

The ecosystem depends on a balance among flora and fauna. The living organisms build on the food cycle to manage the Eco-system. Ecologically, plants are the subject of survival organisms. In addition, the crops are vital for a healthy life span. The cultivation of crops proposes the knowledge of agriculture biotechnology. So, the perusal of crop genomes is necessary to observe stress and developmental-responsive genes in particular species. This study summarized genes in the AP2/ERF super-family in different crops-genomes. Those species-specific genes are necessary for the growth and survival of crops. Crops are economically valuable worldwide. Therefore, the study provided extensive knowledge of the agronomic, economic, and ecological traits and possibly other benefits of crops. Also, the documented data provide valuable information in plant databases for agriculture research and development.

Methods

Sequences and database

The current draft genome sequences of Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L., and Oryza sativa was download from the TAIR (https://www.arabidopsis.org/) and Ensemble (https://asia.ensembl.org/index.html) genome database. The Arabidopsis Information Resource (TAIR) database provides the option to attain the target sequence of model organisms of Arabidopsis thaliana. Also, SMART (http://smart.embl-heidelberg.de/) and Pfam (http://pfam.xfam.org/) retrieves to identify the particular domains in the AP2/ERF family.

Standalone tools and gene ontology (GO) annotation

The HMMER algorithm executes by the MSA of the specific domain as a profile search. HMMER is a statistical algorithm that allows MSA (making multiple sequence alignment) of the particular domain as a profile search. It is an implemented practice of the probabilistic norm called the profile hidden Markov pattern. Standalone BLAST2 performs for homolog genes in both organisms. Also, BLAST2GO performs for the sequence accuracy of a specific transcription factor in the genome. BLAST2GO (BioBam) is a bioinformatics and statistical tool for high-throughput GO annotation of the novel sequence.

Sequence domain, motif, and phylogeny

Multiple sequence alignment (MSA) systems was used to calculate the average match of the homologous sequences for the identities, similarities, and differences that appear. MSA of multiple hits sequences analysis done by a web-based application MultAlin (http://multalin.toulouse.inra.fr/multalin/) for identification and upgradation of the conserved domain. Also, the MEME suite is commonly known as a computational web-based tool for analysis and even discovery of sequence-specific motifs, so retrieve specific motifs via MEME suite (https://meme-suite.org/meme/). Finally, the perusal of the molecular evolutionary link between genes and their particular families in between Arabidopsis thaliana, Solanum lycopersicum, Brassica juncea, Zea mays L., and Oryza sativa, performed MEGA7 for constructing a phylogenetic tree by Neighbor-Joining Methods.

Availability of data and materials

The data and material may be available on request through the corresponding author of Shouhartha Choudhury (Email Id: shouharthac@gmail.com).

Gene Id 829591

TF Id: AT4G344110.1

https://www.arabidopsis.org/

https://www.arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&show_obsolete=F&name=ERF109&sub_type=gene&SEARCH_EXACT=4&SEARCH_CONTAINS=1

https://www.arabidopsis.org/servlets/TairObject?id=126772&type=locus

http://plants.ensembl.org/index.html

References

  1. Lang-Mladek C, et al. Transgenerational inheritance and resetting of stress-induced loss of epigenetic gene silencing in Arabidopsis. Mol Plant. 2010;3(3):594–602.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Elliott RC, et al. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. Plant Cell. 1996;8(2):155–68.

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Chuck G, Meeley RB, Hake S. The control of maize spikelet meristem fate by theAPETALA2 like gene indeterminate spikelet1. Genes Dev. 1998;12(8):1145–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Moose SP, Sisco PH. Glossy15, an APETALA2-like gene from maize that regulates leaf epidermal cell identity. Genes Dev. 1996;10(23):3018–27.

    Article  CAS  PubMed  Google Scholar 

  5. Boutilier K, et al. Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell. 2002;14(8):1737–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Sakuma Y, et al. DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration-and cold-inducible gene expression. Biochem Biophys Res Commun. 2002;290(3):998–1009.

    Article  CAS  PubMed  Google Scholar 

  7. Dubouzet JG, et al. OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt-and cold-responsive gene expression. Plant J. 2003;33(4):751–63.

    Article  CAS  PubMed  Google Scholar 

  8. Sakuma Y, et al. Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell. 2006;18(5):1292–309.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Fujimoto SY, et al. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box–mediated gene expression. Plant Cell. 2000;12(3):393–404.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Alonso JM, et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 2004;301(5633):653–7.

    Article  Google Scholar 

  11. Hu YX, et al. Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res. 2004;14(1):8–15.

    Article  CAS  PubMed  Google Scholar 

  12. Ohme-Takagi M, Shinshi H. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell. 1995;7(2):173–82.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Shinshi H, Usami S, Ohme-Takagi M. Identification of an ethylene-responsive region in the promoter of a tobacco class I chitinase gene. Plant Mol Biol. 1995;27(5):923–32.

    Article  CAS  PubMed  Google Scholar 

  14. Ohme-Takagi M, Suzuki K, Shinshi H. Regulation of ethylene-induced transcription of defense genes. Plant Cell Physiol. 2000;41(11):1187–92.

    Article  CAS  PubMed  Google Scholar 

  15. Stockinger EJ, Gilmour SJ, Thomashow MF. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci. 1997;94(3):1035–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Liu Q, et al. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought-and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell. 1998;10(8):1391–406.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Van Der Fits L, Memelink J. The jasmonate-inducible AP2/ERF-domain transcription factor ORCA3 activates gene expression via interaction with a jasmonate-responsive promoter element. Plant J. 2001;25(1):43–53.

    PubMed  Google Scholar 

  18. Aharoni A, et al. The SHINE clade of AP2 domain transcription factors activates wax biosynthesis, alters cuticle properties, and confers drought tolerance when overexpressed in Arabidopsis. Plant Cell. 2004;16(9):2463–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Broun P. Transcription factors as tools for metabolic engineering in plants. Curr Opin Plant Biol. 2004;7(2):202–9.

    Article  CAS  PubMed  Google Scholar 

  20. Gong H, et al. Silicon alleviates oxidative damage of wheat plants in pots under drought. Plant Sci. 2005;169(2):313–21.

    Article  CAS  Google Scholar 

  21. Van der Graaff E, et al. Activation tagging of the LEAFY PETIOLE gene affects leaf petiole development in Arabidopsis thaliana. Development. 2000;127(22):4971–80.

    Article  PubMed  Google Scholar 

  22. Banno H, et al. Overexpression of Arabidopsis ESR1 induces initiation of shoot regeneration. Plant Cell. 2001;13(12):2609–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kranz HD, et al. Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana. Plant J. 1998;16(2):263–76.

    Article  CAS  PubMed  Google Scholar 

  24. Bailey PC, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell. 2003;15(11):2497–502.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Reyes JC, Muro-Pastor MI, Florencio FJ. The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol. 2004;134(4):1718–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Nakano T, et al. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 2006;140(2):411–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The author was grateful to Assam University, Silchar, Assam, India, for providing the requisite lab facilities during research work.

Dedication

This research paper is a gift to my beloved friend Catherine Tresa Alexander.

Funding

The author did not avail of financial assistance from any source in undertaking the present study.

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Authors and Affiliations

  1. Har Gobind Khorana School of Life Sciences, Assam University, Silchar-788011, Assam, India

    Shouhartha Choudhury

  2. Department of Biotechnology, Assam University, Silchar-788011, Assam, India

    Shouhartha Choudhury

  3. Department of Life Science and Bioinformatics, Assam University, Silchar-788011, Assam, India

    Shouhartha Choudhury

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This research paper contains the sole author. The author proposed the idea, experimented, analyzed the data and prepared the manuscript.

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Choudhury, S. Computational analysis of the AP2/ERF family in crops genome. BMC Genomics 25, 102 (2024). https://doi.org/10.1186/s12864-024-09970-0

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Keywords

BMC Genomics

ISSN: 1471-2164

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