The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.

Central European Institute of Technology Masaryk University 625 00 Brno Czech Republic

Department of Biology University of Fribourg Chemin du Musée 10 1700 Fribourg Switzerland

Institute of Plant Sciences University of Bern Altenbergrain 21 3013 Bern Switzerland

Royal Botanic Gardens Kew Surrey TW9 3AB UK

See more in PubMed

Alger EI, Edger PP. One subgenome to rule them all: underlying mechanisms of subgenome dominance. Curr Opin Plant Biol. 2020:54:108–113. 10.1016/j.pbi.2020.03.004. PubMed DOI

Bardil A, Tayalé A, Parisod C. Evolutionary dynamics of retrotransposons following autopolyploidy in the buckler mustard species complex. Plant J. 2015:82(4):621–631. 10.1111/tpj.12837. PubMed DOI

Birchler JA, Veitia RA. Gene balance hypothesis. Connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A. 2012:109(37):14746–14753. 10.1073/pnas.1207726109. PubMed DOI PMC

Birchler JA, Yang H. The multiple fates of gene duplications: deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation. Plant Cell. 2022:34(7):2466–2474. 10.1093/plcell/koac076. PubMed DOI PMC

Bird KA, Niederhuth CE, Ou S, Gehan M, Pires JC, Xiong Z, VanBuren R, Edger PP. Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. New Phytol. 2020:230(1):354–371. 10.1111/nph.17137. PubMed DOI PMC

Bird KA, VanBuren R, Puzey JR, Edger PP. The causes and consequences of subgenome dominance in hybrids and recent polyploids. New Phytol. 2018:220(1):87–93. 10.1111/nph.15256. PubMed DOI

Blanc G, Wolfe KH. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 2004:16(7):1679–1691. 10.1105/tpc.021410. PubMed DOI PMC

Blischak PD, Mabry ME, Conant GC, Pires JC. Integrating networks, phylogenomics, and population genomics for the study of polyploidy. Annu Rev Ecol Evol Syst. 2018:49(1):253–278. 10.1146/annurev-ecolsys-121415-032302. DOI

Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, et al. . Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 2014:345(6199):950–953. 10.1126/science.1253435. PubMed DOI

Conant GC, Wolfe KH. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet. 2008:9(12):938–950. 10.1038/nrg2482. PubMed DOI

Dodsworth S, Chase MW, Leitch AR. Is post-polyploidization diploidization the key to the evolutionary success of angiosperms? Bot J Linn Soc. 2016:180(1):1–5. 10.1111/boj.12357. DOI

Douglas GM, Gos G, Steige KA, Salcedo A, Holm K, Josephs EB, Arunkumar R, Ågren JA, Hazzouri KM, Wang W, et al. . Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. Proc Natl Acad Sci U S A. 2015:112(9):2806–2811. 10.1073/pnas.1412277112. PubMed DOI PMC

Dubois M, Claeys H, van den Broeck L, Inzé D. Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought. Plant Cell Environ. 2017:40(2):180–189. 10.1111/pce.12809. PubMed DOI

Edger PP, Smith RD, Mckain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, et al. . Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower. Plant Cell. 2017:29(9):2150–2167. 10.1105/tpc.17.00010. PubMed DOI PMC

Freeling M. Bias in plant gene content following different sorts of duplication. Tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol. 2009:60(1):433–453. 10.1146/annurev.arplant.043008.092122. PubMed DOI

Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr Opin Plant Biol. 2012:15(2):131–139. 10.1016/j.pbi.2012.01.015. PubMed DOI

Freeling M, Xu J, Woodhouse M, Lisch D. A solution to the C-value paradox and the function of junk DNA: the genome balance hypothesis. Mol Plant. 2015:8(6):899–910. 10.1016/j.molp.2015.02.009. PubMed DOI

Garsmeur O, Schnable JC, Almeida A, Jourda C, D’Hont A, Freeling M. Two evolutionarily distinct classes of paleopolyploidy. Mol Biol Evol. 2014:31(2):448–454. 10.1093/molbev/mst230. PubMed DOI

Geiser C, Mandakova T, Arrigo N, Lysak MA, Parisod C. Repeated whole-genome duplication, karyotype reshuffling, and biased retention of stress-responding genes in buckler mustard. Plant Cell. 2016:28(1):17–27. 10.1105/tpc.15.00791. PubMed DOI PMC

Guo X, Mandáková T, Trachtová K, Özüdoğru B, Liu J, Lysak MA. Linked by ancestral bonds: multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe. Mol Biol Evol. 2020:38(5):1695–1714. 10.1093/molbev/msaa327. PubMed DOI PMC

Hendriks KP, Kiefer C, Al-Shehbaz IA, Bailey CD, Hooft van Huysduynen A, Nikolov LA, Nauheimer L, Zuntini AR, German DA, Franzke A, et al. . Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol. 2023:33(19):4052–4068.e6. 10.1016/j.cub.2023.08.026. PubMed DOI

Hohmann N, Wolf EM, Lysak MA, Koch MA. A time-calibrated road map of Brassicaceae species radiation and evolutionary history. Plant Cell. 2015:27(10):2770–2784. 10.1105/tpc.15.00482. PubMed DOI PMC

Hollister JD, Smith LM, Guo Y-L, Ott F, Weigel D, Gaut BS. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A. 2011:108(6):2322–2327. 10.1073/pnas.1018222108. PubMed DOI PMC

Innan H, Kondrashov F. The evolution of gene duplications. Classifying and distinguishing between models. Nat Rev Genet. 2010:11(2):97–108. 10.1038/nrg2689. PubMed DOI

Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, et al. . Ancestral polyploidy in seed plants and angiosperms. Nature. 2011:473(7345):97–100. 10.1038/nature09916. PubMed DOI

Kagale S, Robinson SJ, Nixon J, Xiao R, Huebert T, Condie J, Kessler D, Clarke WE, Edger PP, Links MG, et al. . Polyploid evolution of the Brassicaceae during the Cenozoic era. Plant Cell. 2014:26(7):2777–2791. 10.1105/tpc.114.126391. PubMed DOI PMC

Kajitani R, Yoshimura D, Okuno M, Minakuchi Y, Kagoshima H, Fujiyama A, Kubokawa K, Kohara Y, Toyoda A, Itoh T. Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions. Nat Commun. 2019:10(1):1702. 10.1038/s41467-019-09575-2. PubMed DOI PMC

Kang M, Wu H, Liu H, Liu W, Zhu M, Han Y, Liu W, Chen C, Song Y, Tan L, et al. . The pan-genome and local adaptation of Arabidopsis thaliana. Nat Commun. 2023:14(1):6259. 10.1038/s41467-023-42029-4. PubMed DOI PMC

Kellogg EA. Has the connection between polyploidy and diversification actually been tested? Curr Opin Plant Biol. 2016:30:25–32. 10.1016/j.pbi.2016.01.002. PubMed DOI

Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, Muetzel B, Wirkner U, Ansorge W, Pääbo S. A neutral model of transcriptome evolution. PLoS Biol. 2004:2(5):E132. 10.1371/journal.pbio.0020132. PubMed DOI PMC

Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J. 2016:88(6):1058–1070. 10.1111/tpj.13312. PubMed DOI

Knauer AC, Bakhtiari M, Schiestl FP. Crab spiders impact floral-signal evolution indirectly through removal of florivores. Nat Commun. 2018:9(1):1367. 10.1038/s41467-018-03792-x. PubMed DOI PMC

Koonin EV, Wolf YI. Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet. 2010:11(7):487–498. 10.1038/nrg2810. PubMed DOI PMC

Lee JS, Adams KL. Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress. Plant Genome. 2020:13(3):e20057. 10.1002/tpg2.20057. PubMed DOI

Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics. 2011:12(1):323. 10.1186/1471-2105-12-323. PubMed DOI PMC

Li X, Wang Y, Cai C, Ji J, Han F, Zhang L, Chen S, Zhang L, Yang Y, Tang Q, et al. . Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea. Nat Genet. 2024:56(3):517–529. 10.1038/s41588-024-01655-4. PubMed DOI PMC

Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. 2000:290(5494):1151–1155. 10.1126/science.290.5494.1151. PubMed DOI

Lysak MA, Mandakova T, Schranz ME. Comparative paleogenomics of crucifers. Ancestral genomic blocks revisited. Curr Opin Plant Biol. 2016:30:108–115. 10.1016/j.pbi.2016.02.001. PubMed DOI

Mandáková T, Li Z, Barker MS, Lysak MA. Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention. Plant J. 2017:91(1):3–21. 10.1111/tpj.13553. PubMed DOI

Mandáková T, Lysak MA. Post-polyploid diploidization and diversification through dysploid changes. Curr Opin Plant Biol. 2018:42:55–65. 10.1016/j.pbi.2018.03.001. PubMed DOI

Maumus F, Quesneville H. Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat Commun. 2014:5(1):4104. 10.1038/ncomms5104. PubMed DOI PMC

Nallu S, Hill JA, Don K, Sahagun C, Zhang W, Meslin C, Snell-Rood E, Clark NL, Morehouse NI, Bergelson J, et al. . The molecular genetic basis of herbivory between butterflies and their host plants. Nat Ecol Evol. 2018:2(9):1418–1427. 10.1038/s41559-018-0629-9. PubMed DOI PMC

One Thousand Plant Transcriptomes Initiative . One thousand plant transcriptomes and the phylogenomics of green plants. Nature. 2019:574(7780):679–685. 10.1038/s41586-019-1693-2. PubMed DOI PMC

Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, et al. . Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 2019:20(1):275. 10.1186/s13059-019-1905-y. PubMed DOI PMC

Parisod C. Duplicated gene networks promote ‘hopeful’ phenotypic variation. Trends Genet. 2024:40(2):109–111. 10.1016/j.tig.2023.12.004. PubMed DOI

Parisod C, Alix K, Just J, Petit M, Sarilar V, Mhiri C, Ainouche M, Chalhoub B, Grandbastien MA. Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol. 2010:186(1):37–45. 10.1111/j.1469-8137.2009.03096.x. PubMed DOI

Ranallo-Benavidez TR, Jaron KS, Schatz MC. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun. 2020:11(1):1432. 10.1038/s41467-020-14998-3. PubMed DOI PMC

Renny-Byfield S, Gong L, Gallagher JP, Wendel JF. Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution. Mol Biol Evol. 2015:32(4):1063–1071. 10.1093/molbev/msv001. PubMed DOI

Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020:21(1):245. 10.1186/s13059-020-02134-9. PubMed DOI PMC

Robinson MD, McCarthy DJ, Smyth GK. Edger: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010:26(1):139–140. 10.1093/bioinformatics/btp616. PubMed DOI PMC

Ross-Ibarra J, Wright SI, Foxe JP, Kawabe A, DeRose-Wilson L, Gos G, Charlesworth D, Gaut BS. Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS One. 2008:3(6):e2411. 10.1371/journal.pone.0002411. PubMed DOI PMC

Schranz ME, Mohammadin S, Edger PP. Ancient whole genome duplications, novelty and diversification. The WGD radiation lag-time model. Curr Opin Plant Biol. 2012:15(2):147–153. 10.1016/j.pbi.2012.03.011. PubMed DOI

Shimizu-Inatsugi R, Terada A, Hirose K, Kudoh H, Sese J, Shimizu KK. Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Mol Ecol. 2017:26(1):193–207. 10.1111/mec.13738. PubMed DOI

Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy. Pitfalls and paths to a paradigm. Am J Bot. 2016:103(7):1146–1166. 10.3732/ajb.1500501. PubMed DOI

Tank DC, Eastman JM, Pennell MW, Soltis PS, Soltis DE, Hinchliff CE, Brown JW, Sessa EB, Harmon LJ. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. New Phytol. 2015:207(2):454–467. 10.1111/nph.13491. PubMed DOI

van de Peer Y, Ashman T-L, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. Plant Cell. 2021:33(1):11–26. 10.1093/plcell/koaa015. PubMed DOI PMC

van de Peer Y, Mizrachi E, Marchal K. The evolutionary significance of polyploidy. Nat Rev Genet. 2017:18(7):411–424. 10.1038/nrg.2017.26. PubMed DOI

Visendi P. De novo assembly of linked reads using supernova 2.0. In: Plant bioinformatics: methods and protocols. New York (NY): Springer US; 2022. p. 233–243. PubMed

Wendel JF. The wondrous cycles of polyploidy in plants. Am J Bot. 2015:102(11):1753–1756. 10.3732/ajb.1500320. PubMed DOI

Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X. Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc Natl Acad Sci U S A. 2014:111(14):5283–5288. 10.1073/pnas.1402475111. PubMed DOI PMC

Woodhouse MR, Tang H, Freeling M. Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell. 2011:23(12):4241–4253. 10.1105/tpc.111.093567. PubMed DOI PMC

Zhang K, Zhang L, Cui Y, Yang Y, Wu J, Liang J, Li X, Zhang X, Zhang Y, Guo Z, et al. . The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids. Proc Natl Acad Sci U S A. 2023:120(42):e2305208120. 10.1073/pnas.2305208120. PubMed DOI PMC

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. 2017:29(12):2974–2994. 10.1105/tpc.17.00595. PubMed DOI PMC

Zhou S-S, Yan X-M, Zhang K-F, Liu H, Xu J, Nie S, Jia K-H, Jiao S-Q, Zhao W, Zhao Y-J, et al. . A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes. Sci Data. 2021:8(1):174. doi:10.1038/s41597-021-00968-x. PubMed DOI PMC