A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

Abstract

Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80% of the world’s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48 915 avocado genes of which 39 207 could be ascribed functions. The genome contained 62.6% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.

References

[1] Armenteros JJA et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019; 37: 420-3.

[2] Altenhoff AM, Levy J, Zarowiecki M et al. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Res. 2019; 29: 1152-63.

[3] Bao ZR, Eddy SR . Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002; 12: 1269-76.

[4] Brůna T, Hoff KJ, Lomsadze A et al. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR genomics and bioinformatics. 2021; 3: lqaa108.

[5] Cerritelli SM, Crouch RJ . Ribonuclease H: the enzymes in eukaryotes. FEBS J. 2009; 276: 1494-505.

[6] Chanderbali AS, Albert VA, Ashworth VETM et al. Persea americana (avocado): bringing ancient flowers to fruit in the genomics era. BioEssays. 2008; 30: 386-96.

[7] Chase MW . Relationships between the families of flowering plants. In: R. J. Henry (ed.), Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants. 2005, 7-23. Wallingford: CABI Publishing.

[8] Chaudhary P, Khamar J, Sen DJ . Avocado: the holistic source as a natural doctor. World Journal of Pharmaceutical Research. 2015; 4: 748-61.

[9] Chaw SM, Liu YC, Wu YW et al. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nature Plants. 2019; 5: 63-73.

[10] Chen JH, Hao Z, Guang X et al. Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation. Nature Plants. 2019; 5: 18-25.

[11] Chen Y, Ye W, Zhang Y et al. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res. 2015; 43: 7762-8.

[12] Chen Y, Zhang Y, Wang AY et al. Accurate long-read de novo assembly evaluation with inspector. Genome Biol. 2021; 22: 312.

[13] Chen YC, Li Z, Zhao YX et al. The Litsea genome and the evolution of the laurel family. Nat Commun. 2020; 11: 1-14.

[14] Cheng HY, Concepcion GT, Feng X et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021; 18: 170-5.

[15] Cowan AK. Occurrence, metabolism, transport and function of seven-carbon sugars. Phytochem Rev. 2017; 16: 137-57.

[16] Dainat, Jacques (2021), ’ AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format (Version v0.8.0)’, (Zenodo).

[17] Dong SS, Chen L, Liu Y et al. The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms. PLoS One. 2020; 15: e0231020.

[18] Flynn JM, Hubley R, Goubert C et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A. 2020; 117: 9451-7.

[19] Geering ADW, Maumus F, Copetti D et al. Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nat Commun. 2014; 5: 1-11.

[20] Greiner S, Lehwark P, Bock R . OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019; 47: W59-64.

[21] Gurevich A, Saveliev V, Vyahhi N et al. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29: 1072-5.

[22] Hadi A, Campbell MS, Hassani B et al. The effect of cinnamon supplementation on blood pressure in adults: a systematic review and meta-analysis of randomized controlled trials. Clinical Nutrition ESPEN. 2020; 36: 10-6.

[23] Han GJ, Zhang N, Xu J et al. Characterization of a novel Helitron family in insect genomes: insights into classification, evolution and horizontal transfer. Mob DNA. 2019; 10: 1-15.

[24] Haug-Baltzell A, Stephens SA, Davey S et al. SynMap2 and SynMap3D: web-based whole-genome synteny browsers. Bioinformatics. 2017; 33: 2197-8.

[25] Hiti-Bandaralage J . Micropropagation as an Alternative for Avocado Clonal Propagation. Brisbane: The University of Queensland; 2019.

[26] Humann JL, Lee T, Ficklin S et al. Structural and functional annotation of eukaryotic genomes with GenSAS. Gene Prediction: Methods and Protocols. 2019; 1962: 29-51.

[27] Jedlicka P, Lexa M, Kejnovsky E . What can long terminal repeats tell us about the age of LTR retrotransposons, gene conversion and ectopic recombination? Front Plant Sci. 2020; 11: 644.

[28] Jin JJ, Yu WB, Yang JB et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21: 1-31.

[29] Jones TM, Anderson ANNEJ, Albersheim P . Host-pathogen interactions IV. Studies on the polysaccharide-degrading enzymes secreted by fusarium oxysporum f. sp. lycopersici. Physiol Plant Pathol. 1972; 2: 153-66.

[30] Kim D, Paggi JM, Park C et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37: 907-15.

[31] Li Z, Defoort J, Tasdighian S et al. Gene duplicability of Core genes is highly consistent across all angiosperms. Plant Cell. 2016; 28: 326-44.

[32] Luo XZ, Chen SY, Zhang Y . PlantRep: a database of plant repetitive elements. Plant Cell Rep. 2022; 41: 1163-6.

[33] Lyons E, Freeling M . How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 2008; 53: 661-73.

[34] Maitera ON, Osemeahon SA, Barnabas HL . Proximate and elemental analysis of avocado fruit obtained from Taraba state, Nigeria. Indian J Sci Technol. 2014; 2: 67-73.

[35] Manni M, Berkeley MR, Seppey M et al. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021; 38: 4647-54.

[36] Mikheenko A, Prjibelski A, Saveliev V et al. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics. 2018; 34: i142-50.

[37] Moelling K, Broecker F, Russo G et al. RNase H as gene modifier, driver of evolution and antiviral defense. Front Microbiol. 2017; 8: 1745.

[38] Naamati G, Fromer M, Linial M . Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: a source for gene novelty? BMC Genomics. 2009; 10: 1-17.

[39] Nath O, Fletcher SJ, Hayward A et al. A comprehensive high-quality DNA and RNA extraction protocol for a range of cultivars and tissue types of the Woody crop avocado. Plan Theory. 2022; 11: 242.

[40] Nielsen H, Engelbrecht J, Brunak S et al. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997; 10: 1-6.

[41] Pertea M, Kim D, Pertea GM et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11: 1650-67.

[42] Raines CA, Lloyd JC, Dyer TA . New insights into the structure and function of sedoheptulose-1,7-bisphosphatase; an important but neglected Calvin cycle enzyme. J Exp Bot. 1999; 50: 1-8.

[43] Rendon-Anaya M et al. The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proc Natl Acad Sci U S A. 2019; 116: 17081-9.

[44] Rhie A, Walenz BP, Koren S et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020; 21: 245.

[45] Sandhya S, Srivastava H, Kaila T et al. Methods and tools for plant organelle genome sequencing, assembly, and downstream analysis. Legume Genomics: Methods Mol Biol. 2020; 2107: 49-98.

[46] Schaffer B, Wolstenholme BN, Whiley AW . The Avocado Botany, Production and Uses 2nd Edition Introduction. In: B. Schaffer, B. Nigel Wolstenholme, A. W. Whiley (eds.), Avocado: Botany, Production and Uses.2nd ed. 2013, 1-9. Wallingford: CABI Publishing.

[47] Seppey M, Manni M, Zdobnov EM . BUSCO: assessing genome assembly and annotation completeness. Gene Prediction: Methods in Molecular Biology. 2019; 1962: 227-45.

[48] Simon L, Rabanal FA, Dubos T et al. Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana. Nucleic Acids Res. 2018; 46: 3019-33.

[49] Smit, AFA, Hubley, R, and Green, P (2019), ’ 2013-2015. RepeatMasker Open-4.0’.

[50] Song Y, Yao X, Tan Y et al. Complete chloroplast genome sequence of the avocado: gene organization, comparative analysis, and phylogenetic relationships with other Lauraceae. Can J For Res. 2016; 46: 1293-301.

[51] Tillich M, Lehwark P, Pellizzer T et al. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45: W6-11.

[52] Wakabayashi K. Changes in cell wall polysaccharides during fruit ripening. J Plant Res. 2000; 113: 231-7.

[53] Wang WW, Lanfear R . Long-reads reveal that the chloroplast genome exists in two distinct versions in Most plants. Genome Biology and Evolution. 2019; 11: 3372-81.

[54] Xu L, Dong Z, Fang L et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 2019; 47: W52-8.