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Current Genomics

Author(s): Akansha Sarawad, Spoorti Hosagoudar and Prachi Parvatikar*

DOI: 10.2174/0113892029311541240627111506

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Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges

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Abstract

A pan-genome is a compilation of the common and unique genomes found in a given species. It incorporates the genetic information from all of the genomes sampled, producing a big and diverse set of genetic material. Pan-genomic analysis has various advantages over typical genomics research. It creates a vast and varied spectrum of genetic material by combining the genetic data from all the sampled genomes. Comparing pan-genomics analysis to conventional genomic research, there are a number of benefits. Although the most recent era of pan-genomic studies has used cutting-edge sequencing technology to shed fresh light on biological variety and improvement, the potential uses of pan-genomics in improvement have not yet been fully realized. Pangenome research in various organisms has demonstrated that missing genetic components and the detection of significant Structural Variants (SVs) can be investigated using pan-genomic methods. Many individual-specific sequences have been linked to biological adaptability, phenotypic, and key economic attributes. This study aims to focus on how pangenome analysis uncovers genetic differences in various organisms, including human, and their effects on phenotypes, as well as how this might help us comprehend the diversity of species. The review also concentrated on potential problems and the prospects for future pangenome research.

Keywords: Pan-genomics, telomer genome, human genomics, evolution, OMIM, conventional genomic.

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[1]
(a) Hebert, P.D.N.; Cywinska, A.; Ball, S.L.; deWaard, J.R. Biological identifications through DNA barcodes. Proc. Biol. Sci., 2003, 270(1512), 313-321.
[http://dx.doi.org/10.1098/rspb.2002.2218] [PMID: 12614582];
(b) Bohra, A.; Chand Jha, U.; Godwin, I.D.; Kumar Varshney, R. Genomic interventions for sustainable agriculture. Plant Biotechnol. J., 2020, 18(12), 2388-2405.
[http://dx.doi.org/10.1111/pbi.13472] [PMID: 32875704]
[2]
Heather, J.M.; Chain, B. The sequence of sequencers: The history of sequencing DNA. Genomics, 2016, 107(1), 1-8.
[http://dx.doi.org/10.1016/j.ygeno.2015.11.003] [PMID: 26554401]
[3]
Varshney, R.K.; Nayak, S.N.; May, G.D.; Jackson, S.A. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol., 2009, 27(9), 522-530.
[http://dx.doi.org/10.1016/j.tibtech.2009.05.006] [PMID: 19679362]
[4]
Varshney, R.K.; Bohra, A.; Yu, J.; Graner, A.; Zhang, Q.; Sorrells, M.E. Designing future crops: Genomics-assisted breeding comes of age. Trends Plant Sci., 2021, 26(6), 631-649.
[http://dx.doi.org/10.1016/j.tplants.2021.03.010] [PMID: 33893045]
[5]
Tettelin, H.; Masignani, V.; Cieslewicz, M.J.; Donati, C.; Medini, D.; Ward, N.L.; Angiuoli, S.V.; Crabtree, J.; Jones, A.L.; Durkin, A.S.; DeBoy, R.T.; Davidsen, T.M.; Mora, M.; Scarselli, M.; Margarit y Ros, I.; Peterson, J.D.; Hauser, C.R.; Sundaram, J.P.; Nelson, W.C.; Madupu, R.; Brinkac, L.M.; Dodson, R.J.; Rosovitz, M.J.; Sullivan, S.A.; Daugherty, S.C.; Haft, D.H.; Selengut, J.; Gwinn, M.L.; Zhou, L.; Zafar, N.; Khouri, H.; Radune, D.; Dimitrov, G.; Watkins, K.; O’Connor, K.J.B.; Smith, S.; Utterback, T.R.; White, O.; Rubens, C.E.; Grandi, G.; Madoff, L.C.; Kasper, D.L.; Telford, J.L.; Wessels, M.R.; Rappuoli, R.; Fraser, C.M. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial “pan-genome”. Proc. Natl. Acad. Sci., 2005, 102(39), 13950-13955.
[http://dx.doi.org/10.1073/pnas.0506758102] [PMID: 16172379]
[6]
Golicz, A.A.; Batley, J.; Edwards, D. Towards plant pangenomics. Plant Biotechnol. J., 2016, 14(4), 1099-1105.
[http://dx.doi.org/10.1111/pbi.12499] [PMID: 26593040]
[7]
Vernikos, G.; Medini, D.; Riley, D.R.; Tettelin, H. Ten years of pan-genome analyses. Curr. Opin. Microbiol., 2015, 23, 148-154.
[http://dx.doi.org/10.1016/j.mib.2014.11.016] [PMID: 25483351]
[8]
Medini, D.; Donati, C.; Tettelin, H.; Masignani, V.; Rappuoli, R. The microbial pan-genome. Curr. Opin. Genet. Dev., 2005, 15(6), 589-594.
[http://dx.doi.org/10.1016/j.gde.2005.09.006] [PMID: 16185861]
[9]
Khan, A.W.; Garg, V.; Roorkiwal, M.; Golicz, A.A.; Edwards, D.; Varshney, R.K. Super-pangenome by integrating the wild side of a species for accelerated crop improvement. Trends Plant Sci., 2020, 25(2), 148-158.
[http://dx.doi.org/10.1016/j.tplants.2019.10.012] [PMID: 31787539]
[10]
Saxena, R.K.; Edwards, D.; Varshney, R.K. Structural variations in plant genomes. Brief. Funct. Genomics, 2014, 13(4), 296-307.
[http://dx.doi.org/10.1093/bfgp/elu016] [PMID: 24907366]
[11]
Carlos Guimaraes, L.; Benevides de Jesus, L.; Vinicius Canario Viana, M.; Silva, A.; Thiago Juca Ramos, R.; de Castro Soares, S.; Azevedo, V.; Soares, S.C. Inside the pan-genome : Methods and software overview. Curr. Genomics, 2015, 16(4), 245-252.
[http://dx.doi.org/10.2174/1389202916666150423002311] [PMID: 27006628]
[12]
Marschall, T.; Marz, M.; Abeel, T.; Dijkstra, L.; Dutilh, B.E.; Ghaffaari, A.; Kersey, P.; Kloosterman, W.P.; Mäkinen, V.; Novak, A.M. Computational pan-genomics: Status, promises and challenges. Brief. Bioinform., 2018, 19(1), 118-135.
[PMID: 27769991]
[13]
Zhao, Q.; Feng, Q.; Lu, H.; Li, Y.; Wang, A.; Tian, Q.; Zhan, Q.; Lu, Y.; Zhang, L.; Huang, T.; Wang, Y.; Fan, D.; Zhao, Y.; Wang, Z.; Zhou, C.; Chen, J.; Zhu, C.; Li, W.; Weng, Q.; Xu, Q.; Wang, Z.X.; Wei, X.; Han, B.; Huang, X. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat. Genet., 2018, 50(2), 278-284.
[http://dx.doi.org/10.1038/s41588-018-0041-z] [PMID: 29335547]
[14]
Golicz, A.A.; Bayer, P.E.; Barker, G.C.; Edger, P.P.; Kim, H.; Martinez, P.A.; Chan, C.K.K.; Severn-Ellis, A.; McCombie, W.R.; Parkin, I.A.P.; Paterson, A.H.; Pires, J.C.; Sharpe, A.G.; Tang, H.; Teakle, G.R.; Town, C.D.; Batley, J.; Edwards, D. The pangenome of an agronomically important crop plant Brassica oleracea. Nat. Commun., 2016, 7(1), 13390.
[http://dx.doi.org/10.1038/ncomms13390] [PMID: 27834372]
[15]
Hirsch, C.N.; Foerster, J.M.; Johnson, J.M.; Sekhon, R.S.; Muttoni, G.; Vaillancourt, B.; Peñagaricano, F.; Lindquist, E.; Pedraza, M.A.; Barry, K.; de Leon, N.; Kaeppler, S.M.; Buell, C.R. Insights into the maize pan-genome and pan-transcriptome. Plant Cell, 2014, 26(1), 121-135.
[http://dx.doi.org/10.1105/tpc.113.119982] [PMID: 24488960]
[16]
Li, Y.; Zhou, G.; Ma, J.; Jiang, W.; Jin, L.; Zhang, Z.; Guo, Y.; Zhang, J.; Sui, Y.; Zheng, L.; Zhang, S.; Zuo, Q.; Shi, X.; Li, Y.; Zhang, W.; Hu, Y.; Kong, G.; Hong, H.; Tan, B.; Song, J.; Liu, Z.; Wang, Y.; Ruan, H.; Yeung, C.K.L.; Liu, J.; Wang, H.; Zhang, L.; Guan, R.; Wang, K.; Li, W.; Chen, S.; Chang, R.; Jiang, Z.; Jackson, S.A.; Li, R.; Qiu, L. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol., 2014, 32(10), 1045-1052.
[http://dx.doi.org/10.1038/nbt.2979] [PMID: 25218520]
[17]
Vernikos, G.S. A review of pangenome tools and recent studies. In: The Pangenome; Springer: Cham, 2020; pp. 89-112.
[http://dx.doi.org/10.1007/978-3-030-38281-0_4]
[18]
Baker, M. Structural variation: The genome’s hidden architecture. Nat. Methods, 2012, 9(2), 133-137.
[http://dx.doi.org/10.1038/nmeth.1858] [PMID: 22290183]
[19]
Springer, N.M.; Ying, K.; Fu, Y.; Ji, T.; Yeh, C.T.; Jia, Y.; Wu, W.; Richmond, T.; Kitzman, J.; Rosenbaum, H.; Iniguez, A.L.; Barbazuk, W.B.; Jeddeloh, J.A.; Nettleton, D.; Schnable, P.S. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet., 2009, 5(11), e1000734.
[http://dx.doi.org/10.1371/journal.pgen.1000734] [PMID: 19956538]
[20]
Ellis, J.; Dodds, P.; Pryor, T. Structure, function and evolution of plant disease resistance genes. Curr. Opin. Plant Biol., 2000, 3(4), 278-284.
[http://dx.doi.org/10.1016/S1369-5266(00)00080-7] [PMID: 10873844]
[21]
Tao, Y.; Zhao, X.; Mace, E.; Henry, R.; Jordan, D. Exploring and exploiting pan-genomics for crop improvement. Mol. Plant, 2019, 12(2), 156-169.
[http://dx.doi.org/10.1016/j.molp.2018.12.016] [PMID: 30594655]
[22]
Ashikawa, I.; Hayashi, N.; Yamane, H.; Kanamori, H.; Wu, J.; Matsumoto, T.; Ono, K.; Yano, M. Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance. Genetics, 2008, 180(4), 2267-2276.
[http://dx.doi.org/10.1534/genetics.108.095034] [PMID: 18940787]
[23]
Lin, Z.; Li, X.; Shannon, L.M.; Yeh, C.T.; Wang, M.L.; Bai, G.; Peng, Z.; Li, J.; Trick, H.N.; Clemente, T.E.; Doebley, J.; Schnable, P.S.; Tuinstra, M.R.; Tesso, T.T.; White, F.; Yu, J. Parallel domestication of the Shattering1 genes in cereals. Nat. Genet., 2012, 44(6), 720-724.
[http://dx.doi.org/10.1038/ng.2281] [PMID: 22581231]
[24]
Yang, Q.; Li, Z.; Li, W.; Ku, L.; Wang, C.; Ye, J.; Li, K.; Yang, N.; Li, Y.; Zhong, T.; Li, J.; Chen, Y.; Yan, J.; Yang, X.; Xu, M. CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. Proc. Natl. Acad. Sci., 2013, 110(42), 16969-16974.
[http://dx.doi.org/10.1073/pnas.1310949110] [PMID: 24089449]
[25]
Fu, H.; Dooner, H.K. Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci., 2002, 99(14), 9573-9578.
[http://dx.doi.org/10.1073/pnas.132259199] [PMID: 12060715]
[26]
Badet, T.; Oggenfuss, U.; Abraham, L.; McDonald, B.A.; Croll, D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. BMC Biol., 2020, 18(1), 12.
[http://dx.doi.org/10.1186/s12915-020-0744-3] [PMID: 32046716]
[27]
Plissonneau, C.; Hartmann, F.E.; Croll, D. Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome. BMC Biol., 2018, 16(1), 5.
[http://dx.doi.org/10.1186/s12915-017-0457-4] [PMID: 29325559]
[28]
Agarwal, G.; Gitaitis, R.D.; Dutta, B. Pan-genome of novel Pantoea stewartii subsp. indologenes reveals genes involved in onion pathogenicity and evidence of lateral gene transfer. Microorganisms, 2021, 9(8), 1761.
[http://dx.doi.org/10.3390/microorganisms9081761] [PMID: 34442840]
[29]
González, V.M.; Aventín, N.; Centeno, E.; Puigdomènech, P. High presence/absence gene variability in defense-related gene clusters of Cucumis melo. BMC Genomics, 2013, 14(1), 782.
[http://dx.doi.org/10.1186/1471-2164-14-782] [PMID: 24219589]
[30]
Shen, J.; Araki, H.; Chen, L.; Chen, J.Q.; Tian, D. Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics, 2006, 172(2), 1243-1250.
[http://dx.doi.org/10.1534/genetics.105.047290] [PMID: 16452149]
[31]
Winzer, T.; Gazda, V.; He, Z.; Kaminski, F.; Kern, M.; Larson, T.R.; Li, Y.; Meade, F.; Teodor, R.; Vaistij, F.E.; Walker, C.; Bowser, T.A.; Graham, I.A. A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine. Science, 2012, 336(6089), 1704-1708.
[http://dx.doi.org/10.1126/science.1220757] [PMID: 22653730]
[32]
Swanson-Wagner, R.A.; Eichten, S.R.; Kumari, S.; Tiffin, P.; Stein, J.C.; Ware, D.; Springer, N.M. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res., 2010, 20(12), 1689-1699.
[http://dx.doi.org/10.1101/gr.109165.110] [PMID: 21036921]
[33]
Rouli, L.; Merhej, V.; Fournier, P.E.; Raoult, D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect., 2015, 7, 72-85.
[http://dx.doi.org/10.1016/j.nmni.2015.06.005] [PMID: 26442149]
[34]
Abudahab, K.; Prada, J.M.; Yang, Z.; Bentley, S.D.; Croucher, N.J.; Corander, J.; Aanensen, D.M. PANINI: Pangenome neighbour identification for bacterial populations. Microb. Genom., 2019, 5(4), 4.
[http://dx.doi.org/10.1099/mgen.0.000220] [PMID: 30465642]
[35]
Santos, A.R.; Barbosa, E.; Fiaux, K.; Zurita-Turk, M.; Chaitankar, V.; Kamapantula, B.; Abdelzaher, A.; Ghosh, P.; Tiwari, S.; Barve, N.; Jain, N.; Barh, D.; Silva, A.; Miyoshi, A.; Azevedo, V. PANNOTATOR: An automated tool for annotation of pan-genomes. Genet. Mol. Res., 2013, 12(3), 2982-2989.
[http://dx.doi.org/10.4238/2013.August.16.2] [PMID: 24065654]
[36]
Fouts, D.E.; Brinkac, L.; Beck, E.; Inman, J.; Sutton, G. PanOCT: Automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species. Nucleic Acids Res., 2012, 40(22), e172.
[http://dx.doi.org/10.1093/nar/gks757] [PMID: 22904089]
[37]
Hennig, A.; Bernhardt, J.; Nieselt, K. Pan-Tetris: An interactive visualisation for pan-genomes. BMC Bioinformatics, 2015, 16(S11)(11), S3.
[http://dx.doi.org/10.1186/1471-2105-16-S11-S3] [PMID: 26328606]
[38]
Sheikhizadeh, S.; Schranz, M.E.; Akdel, M.; de Ridder, D.; Smit, S. PanTools: Representation, storage and exploration of pan-genomic data. Bioinformatics, 2016, 32(17), i487-i493.
[http://dx.doi.org/10.1093/bioinformatics/btw455] [PMID: 27587666]
[39]
Pedersen, T.L.; Nookaew, I.; Wayne Ussery, D.; Månsson, M. PanViz: Interactive visualization of the structure of functionally annotated pangenomes. Bioinformatics, 2017, 33(7), 1081-1082.
[http://dx.doi.org/10.1093/bioinformatics/btw761] [PMID: 28057677]
[40]
Pantoja, Y.; Pinheiro, K.; Veras, A.; Araújo, F.; Lopes de Sousa, A.; Guimarães, L.C.; Silva, A.; Ramos, R.T.J. PanWeb: A web interface for pan-genomic analysis. PLoS One, 2017, 12(5), e0178154.
[http://dx.doi.org/10.1371/journal.pone.0178154] [PMID: 28542514]
[41]
Ding, W.; Baumdicker, F.; Neher, R.A.; Pan, X. panX: pan-genome analysis and exploration. Nucleic Acids Res., 2018, 46(1), e5.
[http://dx.doi.org/10.1093/nar/gkx977] [PMID: 29077859]
[42]
Liu, Y.Y.; Chiou, C.S.; Chen, C.C. PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing. Sci. Rep., 2016, 6(1), 36213.
[http://dx.doi.org/10.1038/srep36213] [PMID: 27824078]
[43]
Thorpe, H.A.; Bayliss, S.C.; Sheppard, S.K.; Feil, E.J. Piggy: A rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria. Gigascience, 2018, 7(4), 1-11.
[http://dx.doi.org/10.1093/gigascience/giy015] [PMID: 29635296]
[44]
Lees, J.A.; Galardini, M.; Bentley, S.D.; Weiser, J.N.; Corander, J. pyseer: A comprehensive tool for microbial pangenome-wide association studies. Bioinformatics, 2018, 34(24), 4310-4312.
[http://dx.doi.org/10.1093/bioinformatics/bty539] [PMID: 30535304]
[45]
Jandrasits, C.; Dabrowski, P.W.; Fuchs, S.; Renard, B.Y. seq-seq- pan: Building a computational pan-genome data structure on whole genome alignment. BMC Genomics, 2018, 19(1), 47.
[http://dx.doi.org/10.1186/s12864-017-4401-3] [PMID: 29334898]
[46]
Ozer, E.A.; Allen, J.P.; Hauser, A.R. Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. BMC Genomics, 2014, 15(1), 737.
[http://dx.doi.org/10.1186/1471-2164-15-737] [PMID: 25168460]
[47]
Chaudhari, N.M.; Gupta, V.K.; Dutta, C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci. Rep., 2016, 6(1), 24373.
[http://dx.doi.org/10.1038/srep24373] [PMID: 27071527]
[48]
Mawla, A.M.; van der Meulen, T.; Huising, M.O. Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers. BMC Genomics, 2023, 24(1), 202.
[http://dx.doi.org/10.1186/s12864-023-09293-6] [PMID: 37069576]
[49]
Schaeffer, M.; Nollmann, M. Contributions of 3D chromatin structure to cell-type-specific gene regulation. Curr. Opin. Genet. Dev., 2023, 79, 102032.
[http://dx.doi.org/10.1016/j.gde.2023.102032] [PMID: 36893484]
[50]
Yaschenko, A.E.; Fenech, M.; Mazzoni-Putman, S.; Alonso, J.M.; Stepanova, A.N. Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help? Curr. Opin. Plant Biol., 2022, 68, 102241.
[http://dx.doi.org/10.1016/j.pbi.2022.102241] [PMID: 35700675]
[51]
El-Zein, M.; Cheishvili, D.; Gotlieb, W.; Gilbert, L.; Hemmings, R.; Behr, M.A.; Szyf, M.; Franco, E.L. Genome-wide DNA methylation profiling identifies two novel genes in cervical neoplasia. Int. J. Cancer, 2020, 147(5), 1264-1274.
[http://dx.doi.org/10.1002/ijc.32880] [PMID: 31983058]
[52]
Chen, P.; Bandoy, D.J.D.; Weimer, B.C. Bacterial Epigenomics: epigenetics in the age of population genomics.The Pangenome: Diversity, Dynamics and Evolution of Genomes; Tettelin, H.; Medini, D., Eds.; Springer: Cham, Switzerland, 2020.
[http://dx.doi.org/10.1007/978-3-030-38281-0_11]
[53]
Cui, W.J.; Zhang, B.; Zhao, R.; Liu, L.X.; Jiao, J.; Zhang, Z.; Tian, C.F. Lineage-specific rewiring of core pathways predating innovation of legume nodules shapes symbiotic efficiency. mSystems, 2021, 6(2), e01299-20.
[http://dx.doi.org/10.1128/mSystems.01299-20] [PMID: 33850043]
[54]
Broadbent, J.A.; Broszczak, D.A.; Tennakoon, I.U.K.; Huygens, F. Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains. Expert Rev. Proteomics, 2016, 13(4), 355-365.
[http://dx.doi.org/10.1586/14789450.2016.1155986] [PMID: 26889693]
[55]
Ma, B.; France, M.; Ravel, J. Meta-Pangenome: At the crossroad of pangenomics and metagenomics.The Pangenome: Diversity, Dynamics and Evolution of Genomes; Tettelin, H.; Medini, D., Eds.; Springer: Cham, Switzerland, 2020.
[http://dx.doi.org/10.1007/978-3-030-38281-0_9]
[56]
Zhong, C.; Chen, C.; Wang, L.; Ning, K. Integrating pan-genome with metagenome for microbial community profiling. Comput. Struct. Biotechnol. J., 2021, 19, 1458-1466.
[http://dx.doi.org/10.1016/j.csbj.2021.02.021] [PMID: 33841754]
[57]
Li, T.; Yin, Y. Critical assessment of pan-genomic analysis of metagenome-assembled genomes. Brief. Bioinform., 2022, 23(6), bbac413.
[http://dx.doi.org/10.1093/bib/bbac413] [PMID: 36124775]
[58]
Zhai, Y.; Wei, C. Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes. Front. Microbiol., 2022, 13, 948138.
[http://dx.doi.org/10.3389/fmicb.2022.948138] [PMID: 36081802]
[59]
Romero Picazo, D.; Werner, A.; Dagan, T.; Kupczok, A. Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance. Genome Biol. Evol., 2022, 14(7), evac098.
[http://dx.doi.org/10.1093/gbe/evac098] [PMID: 35731940]
[60]
Jaiswal, A.K.; Tiwari, S.; Tavares, G.C.; Da Silva, W.M.; De Castro Oliveira, L.; Ibraim, I.C.; Guimarães, L.C.; Gomide, A.C.P.; Jamal, S.B.; Pantoja, Y. Pan-genomics: Applications, challenges, and future prospects. In: Pan-omics focused to Crick’s central dogma; Elsevier: Amsterdam, The Netherlands, 2020; pp. 1-41.
[61]
Innamorati, K.A.; Earl, J.P.; Aggarwal, S.D.; Ehrlich, G.D.; Hiller, N.L. The bacterial guide to designing a diversified gene portfolio.The Pangenome: Diversity, Dynamics and Evolution of Genomes; Tettelin, H.; Medini, D., Eds.; Springer: Cham, Switzerland, 2020.
[http://dx.doi.org/10.1007/978-3-030-38281-0_3]
[62]
Tiwary, B.K. Pan-genomics: Applications, challenges, and future prospects. In: Evolutionary pan-genomics and applications; Elsevier: Amsterdam, The Netherlands, 2020; pp. 65-80.
[63]
Douglas, G.M.; Shapiro, B.J. Genic selection within prokaryotic pangenomes. Genome Biol. Evol., 2021, 13(11), evab234.
[http://dx.doi.org/10.1093/gbe/evab234] [PMID: 34665261]
[64]
Hyun, J.C.; Monk, J.M.; Palsson, B.O. Comparative pangenomics: Analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity. BMC Genomics, 2022, 23(1), 7.
[http://dx.doi.org/10.1186/s12864-021-08223-8] [PMID: 34983386]
[65]
Anderson, B.D.; Bisanz, J.E. Challenges and opportunities of strain diversity in gut microbiome research. Front. Microbiol., 2023, 14, 1117122.
[http://dx.doi.org/10.3389/fmicb.2023.1117122] [PMID: 36876113]
[66]
Maistrenko, O.M.; Mende, D.R.; Luetge, M.; Hildebrand, F.; Schmidt, T.S.B.; Li, S.S.; Rodrigues, J.F.M.; von Mering, C.; Pedro Coelho, L.; Huerta-Cepas, J.; Sunagawa, S.; Bork, P. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. ISME J., 2020, 14(5), 1247-1259.
[http://dx.doi.org/10.1038/s41396-020-0600-z] [PMID: 32047279]
[67]
Köstlbacher, S.; Collingro, A.; Halter, T.; Schulz, F.; Jungbluth, S.P.; Horn, M. Pangenomics reveals alternative environmental lifestyles among chlamydiae. Nat. Commun., 2021, 12(1), 4021.
[http://dx.doi.org/10.1038/s41467-021-24294-3] [PMID: 34188040]
[68]
de Korne-Elenbaas, J.; Bruisten, S.M.; van Dam, A.P.; Maiden, M.C.J.; Harrison, O.B. The Neisseria gonorrhoeae accessory genome and its association with the core genome and antimicrobial resistance. Microbiol. Spectr., 2022, 10(3), e02654-21.
[http://dx.doi.org/10.1128/spectrum.02654-21] [PMID: 35604129]
[69]
Mesa, V.; Monot, M.; Ferraris, L.; Popoff, M.; Mazuet, C.; Barbut, F.; Delannoy, J.; Dupuy, B.; Butel, M.J.; Aires, J. Core-, pan- and accessory genome analyses of Clostridium neonatale: Insights into genetic diversity. Microb. Genom., 2022, 8(5), mgen000813.
[http://dx.doi.org/10.1099/mgen.0.000813] [PMID: 35550024]
[70]
Zakham, F.; Sironen, T.; Vapalahti, O.; Kant, R. Pan and core genome analysis of 183 Mycobacterium tuberculosis strains revealed a high inter-species diversity among the human adapted strains. Antibiotics, 2021, 10(5), 500.
[http://dx.doi.org/10.3390/antibiotics10050500] [PMID: 33924811]
[71]
Golchha, N.C.; Nighojkar, A.; Nighojkar, S. Redefining genomic view of Clostridioides difficile through pangenome analysis and identification of drug targets from its core genome. Drug Target Insights, 2022, 16, 17-24.
[PMID: 36415217]
[72]
Whelan, F.J.; Hall, R.J.; McInerney, J.O. Evidence for selection in the abundant accessory gene content of a prokaryote pangenome. Mol. Biol. Evol., 2021, 38(9), 3697-3708.
[http://dx.doi.org/10.1093/molbev/msab139] [PMID: 33963386]
[73]
Zarebski, A.E.; du Plessis, L.; Parag, K.V.; Pybus, O.G. A computationally tractable birth-death model that combines phylogenetic and epidemiological data. PLOS Comput. Biol., 2022, 18(2), e1009805.
[http://dx.doi.org/10.1371/journal.pcbi.1009805] [PMID: 35148311]
[74]
Tranchant-Dubreuil, C.; Rouard, M.; Sabot, F. Plant Pangenome: Impacts on phenotypes and evolution. In: Annual Plant Reviews Online; Roberts, J.A., Ed.; Wiley: Hoboken, NJ, USA, 2019; pp. 453-478.
[http://dx.doi.org/10.1002/9781119312994.apr0664]
[75]
Miga, K.H.; Wang, T. The need for a human pangenome reference sequence. Annu. Rev. Genomics Hum. Genet., 2021, 22(1), 81-102.
[http://dx.doi.org/10.1146/annurev-genom-120120-081921] [PMID: 33929893]
[76]
Wang, T.; Antonacci-Fulton, L.; Howe, K.; Lawson, H.A.; Lucas, J.K.; Phillippy, A.M.; Popejoy, A.B.; Asri, M.; Carson, C.; Chaisson, M.J.P.; Chang, X.; Cook-Deegan, R.; Felsenfeld, A.L.; Fulton, R.S.; Garrison, E.P.; Garrison, N.A.; Graves-Lindsay, T.A.; Ji, H.; Kenny, E.E.; Koenig, B.A.; Li, D.; Marschall, T.; McMichael, J.F.; Novak, A.M.; Purushotham, D.; Schneider, V.A.; Schultz, B.I.; Smith, M.W.; Sofia, H.J.; Weissman, T.; Flicek, P.; Li, H.; Miga, K.H.; Paten, B.; Jarvis, E.D.; Hall, I.M.; Eichler, E.E.; Haussler, D. The Human Pangenome Project: A global resource to map genomic diversity. Nature, 2022, 604(7906), 437-446.
[http://dx.doi.org/10.1038/s41586-022-04601-8] [PMID: 35444317]
[77]
Singh, V.; Pandey, S.; Bhardwaj, A. From the reference human genome to human pangenome: Premise, promise and challenge. Front. Genet., 2022, 13, 1042550.
[http://dx.doi.org/10.3389/fgene.2022.1042550] [PMID: 36437921]
[78]
Liao, W.W.; Asri, M.; Ebler, J.; Doerr, D.; Haukness, M.; Hickey, G.; Lu, S.; Lucas, J.K.; Monlong, J.; Abel, H.J.; Buonaiuto, S.; Chang, X.H.; Cheng, H.; Chu, J.; Colonna, V.; Eizenga, J.M.; Feng, X.; Fischer, C.; Fulton, R.S.; Garg, S.; Groza, C.; Guarracino, A.; Harvey, W.T.; Heumos, S.; Howe, K.; Jain, M.; Lu, T.Y.; Markello, C.; Martin, F.J.; Mitchell, M.W.; Munson, K.M.; Mwaniki, M.N.; Novak, A.M.; Olsen, H.E.; Pesout, T.; Porubsky, D.; Prins, P.; Sibbesen, J.A.; Sirén, J.; Tomlinson, C.; Villani, F.; Vollger, M.R.; Antonacci-Fulton, L.L.; Baid, G.; Baker, C.A.; Belyaeva, A.; Billis, K.; Carroll, A.; Chang, P.C.; Cody, S.; Cook, D.E.; Cook-Deegan, R.M.; Cornejo, O.E.; Diekhans, M.; Ebert, P.; Fairley, S.; Fedrigo, O.; Felsenfeld, A.L.; Formenti, G.; Frankish, A.; Gao, Y.; Garrison, N.A.; Giron, C.G.; Green, R.E.; Haggerty, L.; Hoekzema, K.; Hourlier, T.; Ji, H.P.; Kenny, E.E.; Koenig, B.A.; Kolesnikov, A.; Korbel, J.O.; Kordosky, J.; Koren, S.; Lee, H.; Lewis, A.P.; Magalhães, H.; Marco-Sola, S.; Marijon, P.; McCartney, A.; McDaniel, J.; Mountcastle, J.; Nattestad, M.; Nurk, S.; Olson, N.D.; Popejoy, A.B.; Puiu, D.; Rautiainen, M.; Regier, A.A.; Rhie, A.; Sacco, S.; Sanders, A.D.; Schneider, V.A.; Schultz, B.I.; Shafin, K.; Smith, M.W.; Sofia, H.J.; Abou Tayoun, A.N.; Thibaud-Nissen, F.; Tricomi, F.F.; Wagner, J.; Walenz, B.; Wood, J.M.D.; Zimin, A.V.; Bourque, G.; Chaisson, M.J.P.; Flicek, P.; Phillippy, A.M.; Zook, J.M.; Eichler, E.E.; Haussler, D.; Wang, T.; Jarvis, E.D.; Miga, K.H.; Garrison, E.; Marschall, T.; Hall, I.M.; Li, H.; Paten, B. A draft human pangenome reference. Nature, 2023, 617(7960), 312-324.
[http://dx.doi.org/10.1038/s41586-023-05896-x] [PMID: 37165242]
[79]
Neou, M.; Villa, C.; Armignacco, R.; Jouinot, A.; Raffin-Sanson, M.L.; Septier, A.; Letourneur, F.; Diry, S.; Diedisheim, M.; Izac, B.; Gaspar, C.; Perlemoine, K.; Verjus, V.; Bernier, M.; Boulin, A.; Emile, J.F.; Bertagna, X.; Jaffrezic, F.; Laloe, D.; Baussart, B.; Bertherat, J.; Gaillard, S.; Assié, G. Pangenomic classification of pituitary neuroendocrine tumors. Cancer Cell, 2020, 37(1), 123-134.e5.
[http://dx.doi.org/10.1016/j.ccell.2019.11.002] [PMID: 31883967]
[80]
Treangen, T.J.; Ondov, B.D.; Koren, S.; Phillippy, A.M. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol., 2014, 15(11), 524.
[http://dx.doi.org/10.1186/s13059-014-0524-x] [PMID: 25410596]
[81]
Land, M.; Hauser, L.; Jun, S.R.; Nookaew, I.; Leuze, M.R.; Ahn, T.H.; Karpinets, T.; Lund, O.; Kora, G.; Wassenaar, T.; Poudel, S.; Ussery, D.W. Insights from 20 years of bacterial genome sequencing. Funct. Integr. Genomics, 2015, 15(2), 141-161.
[http://dx.doi.org/10.1007/s10142-015-0433-4] [PMID: 25722247]
[82]
Islam, M.S.; Coronejo, S.; Subudhi, P.K. Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes. Theor. Appl. Genet., 2020, 133(8), 2461-2475.
[http://dx.doi.org/10.1007/s00122-020-03611-2] [PMID: 32488303]
[83]
Khan, S.Y.; Ali, M.; Lee, M.C.W.; Ma, Z.; Biswas, P.; Khan, A.A.; Naeem, M.A.; Riazuddin, S.; Riazuddin, S.; Ayyagari, R.; Hejtmancik, J.F.; Riazuddin, S.A. Whole genome sequencing data of multiple individuals of Pakistani descent. Sci. Data, 2020, 7(1), 350.
[http://dx.doi.org/10.1038/s41597-020-00664-2] [PMID: 33051442]
[84]
Mao, X.; Zhang, H.; Qiao, S.; Liu, Y.; Chang, F.; Xie, P.; Zhang, M.; Wang, T.; Li, M.; Cao, P.; Yang, R.; Liu, F.; Dai, Q.; Feng, X.; Ping, W.; Lei, C.; Olsen, J.W.; Bennett, E.A.; Fu, Q. The deep population history of northern East Asia from the Late Pleistocene to the Holocene. Cell, 2021, 184(12), 3256-3266.e13.
[http://dx.doi.org/10.1016/j.cell.2021.04.040] [PMID: 34048699]
[85]
Lappalainen, T.; Scott, A.J.; Brandt, M.; Hall, I.M. Genomic analysis in the age of human genome sequencing. Cell, 2019, 177(1), 70-84.
[http://dx.doi.org/10.1016/j.cell.2019.02.032] [PMID: 30901550]
[86]
Alkan, C.; Coe, B.P.; Eichler, E.E. Genome structural variation discovery and genotyping. Nat. Rev. Genet., 2011, 12(5), 363-376.
[http://dx.doi.org/10.1038/nrg2958] [PMID: 21358748]
[87]
Mancini-DiNardo, D.; Judkins, T.; Kidd, J.; Bernhisel, R.; Daniels, C.; Brown, K.; Meek, K.; Craft, J.; Holladay, J.; Morris, B.; Roa, B.B. Detection of large rearrangements in a hereditary pan-cancer panel using next-generation sequencing. BMC Med. Genomics, 2019, 12(1), 138.
[http://dx.doi.org/10.1186/s12920-019-0587-3] [PMID: 31623605]
[88]
Rhoads, A.; Au, K.F. PacBio sequencing and its applications. Genom. Proteom. Bioinform., 2015, 13(5), 278-289.
[http://dx.doi.org/10.1016/j.gpb.2015.08.002] [PMID: 26542840]
[89]
van Dijk, E.L.; Jaszczyszyn, Y.; Naquin, D.; Thermes, C. The third revolution in sequencing technology. Trends Genet., 2018, 34(9), 666-681.
[http://dx.doi.org/10.1016/j.tig.2018.05.008] [PMID: 29941292]
[90]
Senol Cali, D.; Kim, J.S.; Ghose, S.; Alkan, C.; Mutlu, O. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Brief. Bioinform., 2019, 20(4), 1542-1559.
[http://dx.doi.org/10.1093/bib/bby017] [PMID: 29617724]
[91]
Rosen, B.D.; Bickhart, D.M.; Schnabel, R.D.; Koren, S.; Elsik, C.G.; Tseng, E.; Rowan, T.N.; Low, W.Y.; Zimin, A.; Couldrey, C.; Hall, R.; Li, W.; Rhie, A.; Ghurye, J.; McKay, S.D.; Thibaud-Nissen, F.; Hoffman, J.; Murdoch, B.M.; Snelling, W.M.; McDaneld, T.G.; Hammond, J.A.; Schwartz, J.C.; Nandolo, W.; Hagen, D.E.; Dreischer, C.; Schultheiss, S.J.; Schroeder, S.G.; Phillippy, A.M.; Cole, J.B.; Van Tassell, C.P.; Liu, G.; Smith, T.P.L.; Medrano, J.F. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience, 2020, 9(3), giaa021.
[http://dx.doi.org/10.1093/gigascience/giaa021] [PMID: 32191811]