Abstract
Psidium friedrichsthalianum (O. Berg) Nied. is a tropical tree species in the Myrtaceae family, natively distributed from southern Mexico to eastern Venezuela and Ecuador and commonly known as "Cas'', "Costa Rican guava" or “Sour Guava”. The “Cas” produces a fruit with a rather distinctive acidic flavor and has bioactive compounds with biological potential equal or greater than common Guava; is considered an indigenous crop in Costa Rica with characteristics as a functional food untapped. This species has not been completely domesticated, and can be found in home gardens, paddocks, small groups, and, more recently, in small and medium sized plantations. Also, the plantations of this species do not have technical and scientific support or agronomic promotion from industry, nor are there genetic resources or germplasm readily available to farmers. This limits its commercial development and the implementation of selection or genetic improvement programs. In this study, we present the first draft assembly of the Cas genome using PacBio long reads and the Canu assembly pipeline. Our draft assembly has a total length of 417.64 Mb, with 24 440 contigs and a N50 contig size of 21.3 Kb. Structural annotation resulted in 59 036 gene models. Functional annotation was conducted against the non-redundant set of genes from the KEGG database. Of the 52 422 complete genes models, 15.55% (8 153) presented homology with KEGG orthologs. The genes found in our Cas draft assembly were compared to those found in Eucalyptus grandis W. Hill. in the KEGG repository. According to the KEGG pathway assignments, 33 isoforms were annotated as part of the flavonoid biosynthetic pathway. In addition, 19 isoforms were annotated as part of phenylpropanoid biosynthetic pathway. The results of this study provide an overview of the first draft of the Cas genome assembly using PacBio long reads. This new genomic resource represents the basis for exploring the genetic potential of this crop with characteristics as a functional food.
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Data availability
The whole-genome sequence of Cas has been deposited at the DDBJ/ENA/GenBank databases under BioProject PRJNA725514, under the accession JAGVVM000000000. The version described in this paper is version JAGVVM010000000. Available data includes raw reads, draft assembly sequence, and gene models. https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA725514
References
Argout X, Salse J, Aury JM et al (2011) The genome of Theobroma cacao. Nat Genet 43:101–108. https://doi.org/10.1038/ng.736
Baraona M, Rivera G (1995) Development of jocote (Spondias purpurea L.) and Cas (Psidium friedrichsthalianum Niedz) in the premontano humid forest of Costa Rica. Mesoam Agron 6:23–31
Caballero M, Wegrzyn J (2019) gFACs: gene filtering, analysis, and conversion to unify genome annotations across alignment and gene prediction frameworks. Gen Proteom Bioinform 17(3):305–310. https://doi.org/10.1016/j.gpb.2019.04.002
Chen J, Tang X, Ren C et al (2018) Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower. BMC Gen 19:548. https://doi.org/10.1186/s12864-018-4946-9
Cuadrado-Silva CT, Pozo-Bayón MÁ, Osorio C (2017a) Identification of aroma compounds and precursors of sour guava (Psidium friedrichsthalianum Nied.) following a sensomics approach. Eur Food Res Technol 243:1–10. https://doi.org/10.1007/s00217-016-2716-y
Cuadrado-Silva CT, Pozo-Bayón MÁ, Osorio C (2017) Targeted metabolomic analysis of polyphenols with antioxidant activity in sour Guava (Psidium friedrichsthalianum Ndz.). Fruit Mol 22(1):11. https://doi.org/10.3390/molecules22010011
Feng C, Feng C, Lin X, Liu S, Li Y, Kang M (2021) A chromosome-level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (Psidium guajava). Plant Biotechnol J 19(4):717–730. https://doi.org/10.1111/pbi.13498
Flores G, Dastmalchi K, Wu SB, Whalen K, Dabo AJ, Reynertson K (2013) Phenol-rich extract of the Costa Rican guava pulp (Psidium friedrichsthalianum Ndz) with antioxidant and anti-inflammatory activity. Potential COPD Ther Food Chem 14:889–895. https://doi.org/10.1016/j.foodchem.2013.03.025
Flores G, Wu SB, Negrin A, Kennelly EJ (2015) Chemical composition and antioxidant activity of seven cultivars of guava (Psidium guajava) fruits. Food Chem 170:327–335. https://doi.org/10.1016/j.foodchem.2014.08.076
Foo L, Lu Y, Howell AB, Vorsa N (2000) A-Type proanthocyanidin trimers from cranberry that inhibit adherence of uropathogenic P-fimbriated Escherichia coli. J Nat Prod Chem 63(9):1225–1228. https://doi.org/10.1021/np000128u
González E, Vaillant F, Pérez AG, Rojas T (2012) Antioxidant protection mediated by in vitro cells of human erythrocytes by some common tropical fruits. J Nutr Food Sci 2:139. https://doi.org/10.4172/2155-9600.1000139
Govaerts R, Sobral N, Ashton P, Barrie F, Holst BK, Landrum LL, Matsumoto K, Fernanda Mazine F, Nic Lughadha, Proença C (2008) World checklist of myrtaceae: Kew Publishing, Royal botanic gardens. pp. 1–455
Granados-Chinchilla F, Villegas E, Molina A, Arias C (2016) Composition, chemical fingerprinting and antimicrobial assessment of costa rican cultivated guavas (Psidium friedrichsthalianum (O. Berg) Ndz and Psidium guajava L.) essential oils from leaves and fruits. Nat Prod Chem Res 4:5. https://doi.org/10.4172/2329-6836.1000236
Grattapaglia D, Vaillancourt RE, Shepherd M, Thumma BR, Foley W, Külheim C, Potts BM (2012) Progress in Myrtaceae genetics and genomics: eucalyptus as the pivotal genus. Tree Genet Gen 8:463–508. https://doi.org/10.1007/s11295-012-0491-x
Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8):1072–1075. https://doi.org/10.1093/bioinformatics/btt086
Hollman PCH, Katan MB (1997) Absorption, metabolism and health effects of dietary flavonoids in man. Biomed Pharmacother 51:305–310. https://doi.org/10.1016/S0753-3322(97)88045-6
Howell AB (2002) Cranberry proanthocyanidins and the maintenance of urinary tract health. Crit Rev Food Sci Nutr 42(S3):273–278. https://doi.org/10.1080/10408390209351915
Kanehisa M (2019) Toward understanding the origin and evolution of cellular organisms. Protein Sci 28(11):1947–1951. https://doi.org/10.1002/pro.371
Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M (2021) KEGG: integrating viruses and cellular organisms. Nucl Acids Res 49(1):545–551. https://doi.org/10.1093/nar/gkaa970
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nuc Acids Res 28(1):27–30. https://doi.org/10.1093/nar/28.1.27
Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. https://doi.org/10.1016/j.jmb.2015.11.006
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Gen Res 27(5):722–736. https://doi.org/10.1101/gr.215087.116
León J (2000) Botany of tropical crops. San José, Costa Rica: Ed. Ilca. pp. 445
Lucas EJ, Holst B, Sobral M, Mazine FF, Barnes-Proença CE, Ribeiro da Costa I, Vasconcelos TNC (2019) A new subtribal classification of tribe Myrteae (Myrtaceae). Syst Bot 44(3):560–569. https://doi.org/10.1600/036364419X15620113920608
Martens S, Preuss A, Matern U (2010) Multifunctional flavonoid dioxygenases: flavonols and anthocyanin biosynthesis in Arabidopsis thaliana L. Phytochemistry 71:1040–1049. https://doi.org/10.1016/j.phytochem.2010.04.016
Mochida K et al (2016) Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. Plant J 89(2):181–194. https://doi.org/10.1111/tpj.13385
Myburg A, Grattapaglia D, Tuskan G (2014) El genoma de Eucalyptus grandis. Nature 510:356–362. https://doi.org/10.1038/nature13308
Ren W, Qiao Z, Wang H, Zhu L, Zhang L (2003) Flavonoids: promising anticancer agents. Med Res Rev 23:519–534. https://doi.org/10.1002/med.10033
Rojas-Garbanzo C, Rodríguez L, Pérez AM, Mayorga-Gross AL, Vásquez-Chaves V, Fuentes E, Palomo I (2021) Anti-platelet activity and chemical characterization by UPLC-DAD-ESI-QTOF-MS of the main polyphenols in extracts from Psidium leaves and fruits. Food Res Int 141(1):45. https://doi.org/10.1016/j.foodres.2020.110070
Rojas-Garbanzo C, Wintera J, Montero ML, Zimmermanna BF, Schiebera A (2019) Characterization of phytochemicals in Costa Rican guava (Psidium friedrichsthalianum Ndz) fruit and stability of main compounds during juice processing: (U) HPLC-DAD- ESI-TQD-MS. J Food Compos Anal 75:26–42. https://doi.org/10.1016/j.foodres.2020.110070
Rojas-Gómez M, García-Piñeres A, Bolaños-Villegas P, Arrieta-Espinoza G, Fuchs EJ (2021) Genome size and chromosome number of Psidium friedrichsthalianum (O. Berg) Nied (“Cas”) in six populations of Costa Rica Caryologia. Int J Cytol, Cytosystematics Cytogenet 73(3):55–63. https://doi.org/10.13128/caryologia-646
Satué-Gracia MT, Heinonen M, Frankel EN (1997) Anthocyanins as antioxidants on human low-density lipoprotein and lecithin-liposome systems. J Agric Food Chem 45(9):3362–3367. https://doi.org/10.1021/jf970234a
Seppey M, Manni M, Zdobnov EM (2019) BUSCO: Assessing genome assembly and annotation completeness. In: Kollmar M (ed) Gene prediction methods in molecular biology, vol 1962. Humana, New York. https://doi.org/10.1007/978-1-4939-9173-0_14
Srivastava HC (1977) Cytological studies in Psidium friedrichsthalianum Niedenzu. Cytologia 42:395–400. https://doi.org/10.1508/cytologia.42.395
Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24(5):637–644. https://doi.org/10.1093/bioinformatics/btn013
Sun J, Chu YF, Wu X, Liu RH (2002) Antioxidant and antiproliferative activities of common fruits. J Agric Food Chem 50(25):7449–7454. https://doi.org/10.1021/jf0207530
Thaptimthong T, Kasemsuk T, Sibmooh N, Unchern S (2016) Platelet inhibitory effects of juices from Pachyrhizus erosus L. root and Psidium guajava L. fruit: a randomized controlled trial in healthy volunteers. BMC Complement Altern Med 16(1):269. https://doi.org/10.1186/s12906-016-1255-1
Thrimawithana AH, Jones D, Hilario E, Grierson E, Liachko I, Sullivan S et al (2019) A whole genome assembly of Leptospermum scoparium (Myrtaceae) for Mānuka research. N Z J Crop Hortic Sci. https://doi.org/10.1080/01140671.2019.1657911
Wang H, Cao G, Prior RL (1997) Oxygen radical absorbing capacity of anthocyanins. J Agric Food Chem 45:304–309. https://doi.org/10.1021/jf960421t
Wang K, Huang G, Zhu Y (2016) Transposable elements play an important role during cotton genome evolution and fibre cell development. Sci ChinaLifeSci. 59: 112–121
Wendel J, Jackson S, Blake CM, Wing RA (2016) Evolution of plant genome architecture. Gen Biol 17:37. https://doi.org/10.1186/s13059-016-0908-1
Wilson PG, O’Brien M, Heslewood MM, Quinn C (2004) Relationships within Myrtaceae sensu lato based on a matK phylogeny. Plant Syst Evol 251:3–19. https://doi.org/10.1007/s00606-004-0162-y
Winkel-Shirley B (2001) Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol 126:485–493. https://doi.org/10.1104/pp.126.2.485
Yan X, Murphy BT, Hammond GB, Vinson JA, Neto CC (2002) Antioxidant activities and antitumor screening of extracts from cranberry fruit (Vaccinium macrocarpon). J Agric Food Chem 50:5844–5849. https://doi.org/10.1021/jf0202234
Acknowledgements
We thank local Cas farmer, Mr. Alfonso Ruíz, who provided free samples from his farm.
Funding
This work was supported by the Centro Nacional de Alta Tecnología (CeNAT-CONARE), Foundation of Costa Rica (3-006-213777).
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MR-G: Conceptualization, methodology, investigation, formal analysis, writing—original draft, project administration. JPJ-M: Methodology, formal analysis, writing—review and editing, data curation. MM-V: Methodology, formal analysis, data curation, writing—review and editing. RL-Mo: Review and editing, funding acquisition, project administration. MC: Review and editing, supervision. EM: Review and editing, supervision, funding acquisition. EF: Conceptualization, investigation, writing—review and editing.
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Rojas-Gómez, M., Jiménez-Madrigal, J.P., Montero-Vargas, M. et al. A draft genome assembly of “Cas” (Psidium friedrichsthalianum (O. Berg) Nied.): an indigenous crop of Costa Rica untapped. Genet Resour Crop Evol 69, 39–47 (2022). https://doi.org/10.1007/s10722-021-01291-5
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DOI: https://doi.org/10.1007/s10722-021-01291-5