Unbiased subgenome evolution following a recent whole-genome duplication in pear (Pyrus bretschneideri Rehd.)

Abstract

Genome fractionation (also known as diploidization) frequently occurs following paleopolyploidization events. Biased fractionation between subgenomes has been found in some paleo-allopolyploids, while this phenomenon is absent in paleo-autopolyploids. Pear (Pyrus bretschneideri Rehd.) experienced a recent whole-genome duplication (WGD, ~30 million years ago); however, the evolutionary fate of the two subgenomes derived from this WGD event is not clear. In this study, we identified the two paleo-subgenomes in pear using peach (Prunus persica) as an outgroup and investigated differences in the gene loss rate, evolutionary rate, gene expression level, and DNA methylation level between these two subgenomes. Fractionation bias was not found between the two pear subgenomes, which evolved at similar evolutionary rates. The DNA methylation level of the two subgenomes showed little bias, and we found no expression dominance between the subgenomes. However, we found that singleton genes and homeologous genes within each subgenome showed divergent evolutionary patterns of selective constraints, expression and epigenetic modification. These results provide insights into subgenome evolution following paleopolyploidization in pear.

References

[1] Paterson, A. H., Freeling, M., Tang, H. & Wang, X. Insights from the comparison of plant genome sequences. Annu Rev Plant Biol 61, 349-372 (2010).

[2] Jiao, Y. & Paterson, A. H. Polyploidy-associated genome modifications during land plant evolution. Philos. Trans. R. Soc. Lond. 369, 5042-5050 (2014).

[3] Bowers, J. E., Chapman, B. A., Rong, J. & Paterson, A. H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433-438 (2003).

[4] Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of key innovations in angiosperms. Curr. Opin. Plant. Biol. 30, 159-165 (2016).

[5] Fawcett, J. A., Maere, S. & Van de Peer, Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc. Natl Acad. Sci. USA 106, 5737-5742 (2009).

[6] Wendel, J. F. The wondrous cycles of polyploidy in plants. Am. J. Bot. 102, 1753-1756 (2015).

[7] Barker, M. S., Arrigo, N., Baniaga, A. E., Li, Z. & Levin, D. A. On the relative abundance of autopolyploids and allopolyploids. New Phytol. 210, 391-398 (2016).

[8] Dodsworth, S., Chase, M. W. & Leitch, A. R. Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?. Bot. J. Linn. Soc. 180, 1-5 (2016).

[9] Soltis, D. E., Visger, C. J., Marchant, D. B. & Soltis, P. S. Polyploidy: pitfalls and paths to a paradigm. Am. J. Bot. 103, 1146-1166 (2016).

[10] Wang, X. et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43, 1035-1039 (2011).

[11] Liu, S. et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat. Commun. 5, 3930 (2014).

[12] Schnable, J. C., Springer, N. M. & Freeling, M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl Acad. Sci. USA 108, 4069-4074 (2011).

[13] Cheng, F. et al. Gene retention, fractionation and subgenome differences in polyploid plants. Nat. Plants 4, 258-268 (2018).

[14] Liu, Y. et al. Two highly similar poplar paleo-subgenomes suggest an autotetraploid ancestor of Salicaceae plants. Front. Plant Sci. 8, 571 (2017).

[15] Zhao, M., Zhang, B., Lisch, D. & Ma, J. Patterns and consequences of subgenome differentiation provide insights into the nature of paleopolyploidy in plants. Plant Cell 29, 2974-2994 (2017).

[16] Sun, H. et al. Karyotype stability and unbiased fractionation in the Paleo-Allotetraploid Cucurbita Genomes. Mol. Plant 10, 1293-1306 (2017).

[17] Brohammer, A. B., Kono, T. J. Y., Springer, N. M., McGaugh, S. E. & Hirsch, C. N. The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. Plant J. 93, 131-141 (2018).

[18] Freeling, M. et al. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr. Opin. Plant. Biol. 15, 131-139 (2012).

[19] Renny-Byfield, S., Rodgers-Melnick, E. & Ross-Ibarra, J. Gene fractionation and function in the ancient subgenomes of maize. Mol. Biol. Evol. 34, 1825-1832 (2017).

[20] Pophaly, S. D. & Tellier, A. Population level purifying selection and gene expression shape subgenome evolution in maize. Mol. Biol. Evol. 32, 3226-3235 (2015).

[21] Woodhouse, M. R. et al. Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc. Natl Acad. Sci. USA 111, 5283-5288 (2014).

[22] Cheng, F. et al. Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa. New Phytol. 211, 288-299 (2016).

[23] Kagale, S. et al. The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure. Nat. Commun. 5, 3706 (2014).

[24] Chalhoub, B. et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345, 950-953 (2014).

[25] Zhang, T. et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat. Biotechnol. 33, 531-U252 (2015).

[26] Li, J. T. et al. The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). Sci. Rep. 5, 8199 (2015).

[27] Wu, J. et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 23, 396-408 (2013).

[28] Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178-D1186 (2012).

[29] Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49- e49 (2012).

[30] Wang, L. et al. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol. 15, R39 (2014).

[31] Irfan, M. et al. Modification of CTAB protocol for maize genomic DNA extraction. Res. J. Biotechnol. 8, 41-45 (2013).

[32] Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).

[33] Kagale, S. et al. The developmental transcriptome atlas of the biofuel crop Camelina sativa. Plant J. 88, 879-894 (2016).

[34] Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525-527 (2016).

[35] Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572 (2011).

[36] Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160-W165 (2016).

[37] Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 25, 402-408 (2001).

[38] Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).

[39] Verde, I. et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat. Genet. 45, 487-U447 (2013).

[40] Shulaev, V. et al. The genome of woodland strawberry (Fragaria vesca). Nat. Genet. 43, 109-116 (2011).

[41] Tang., H., Krishnakumar., V. & Li., J. jcvi: JCVI utility libraries. Zenodo (2015). (Available at https://doi.org/10.5281/zenodo.11020)

[42] Li, Z. et al. Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms. Plant Cell 28, 326-344 (2016).

[43] Vanneste, K., Baele, G., Maere, S. & Van de Peer, Y. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res. 24, 1334-1347 (2014).

[44] Murat, F. et al. Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. Genome Biol. Evol. 7, 735-749 (2015).

[45] Garsmeur, O. et al. Two evolutionarily distinct classes of paleopolyploidy. Mol. Biol. Evol. 31, 448-454 (2014).

[46] Schnable, J. C., Pedersen, B. S., Subramaniam, S. & Freeling, M. Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses. Front. Plant Sci. 2, 2 (2011).

[47] Thomas, B. C., Pedersen, B. & Freeling, M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16, 934-946 (2006).

[48] Woodhouse, M. R. et al. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol. 8, e1000409 (2010).

[49] Zemach, A. et al. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl Acad. Sci. USA 107, 18729-18734 (2010).

[50] Wang, H. et al. CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proc. Natl Acad. Sci. USA 112, 13729-13734 (2015).

[51] De Smet, R. et al. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc. Natl Acad. Sci. USA 110, 2898-2903 (2013).

[52] Huminiecki, L. & Wolfe, K. H. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res. 14, 1870-1879 (2004).

[53] Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545 (1999).

[54] Lynch, M. & Force, A. The probability of duplicate gene preservation by subfunctionalization. Genetics 154, 459-473 (2000).

[55] Arsovski, A. A., Pradinuk, J., Guo, X. Q., Wang, S. & Adams, K. L. Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis. Plant Physiol. 169, 2982-2991 (2015).

[56] He, X. & Zhang, J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169, 1157-1164 (2005).

[57] Ohno, S. Evolution by Gene Duplication. (New York: Springer-Verlag, 1970).

[58] Qian, W. F., Liao, B. Y., Chang, A. Y. F. & Zhang, J. Z. Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet. 26, 425-430 (2010).

[59] Gout, J. F. & Lynch, M. Maintenance and loss of duplicated genes by dosage subfunctionalization. Mol. Biol. Evol. 32, 2141-2148 (2015).

[60] Wang, L. et al. Comparative epigenomics reveals evolution of duplicated genes in potato and tomato. Plant J 93, 460-471 (2018).