Domestication history and genetic changes for the newly evolved flower color in the ornamental plant Lobularia maritima (Brassicaceae)

Abstract

Lobularia maritima (sweet alyssum) is a popular ornamental plant that displays a range of flower colors, particularly white and purple. However, the genetic underpinning and evolutionary history of flower colors have remained unknown. To address this, we performed a de novo assembly of a chromosome-level genome for this species and conducted comparative population genomic analyses of both domestic and wild representatives. These analyses revealed distinct genetic clusters corresponding to wild and domestic groups, with further subdivisions based on geographic and phenotypic differences. Importantly, all cultivars originated from a single domestication event within the Tunisia group. One wild group did not contribute genetically to the current cultivars. The new mutations in key gene of the anthocyanin biosynthetic pathway, PAP1, that arose following domestication led to the origin of purple flower coloration in the cultivars. Moreover, the contrasting PAP1 haplotypes in white and purple varieties lead to differential expression of CHS and DFR, which in turn contributes to the observed flower color differences. These findings provide key insights into the domestication history and genetic regulation of flower color in L. maritima, laying the groundwork for future genetic breeding efforts focused on this plant, especially introducing genetic sources from other wild groups.

Acknowledgements

This research was supported by the National Natural Science Foundation of China (32171606). We wish to express our profound gratitude to the late Professor Zhenxiang Xi, whose guidance and wisdom have left an indelible mark on our work. His teachings continue to inspire us and have been instrumental in shaping this research.

Author Contributions

Q.H., J.L.-P., and J.L. designed the research, W.Y., M.L., L.H., and J. L.-P. collected the materials and performed the genome sequencing, W.Y., M.L., J.J., L.H., L.F., and P.J. performed the analyses and experiments, and W.Y., J.L., J.L.-P., and Q.H. wrote the manuscript. All authors contributed to the manuscript and approved the final version.

Data availability

All raw sequence data and genome assembly data have been deposited in National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, under accession number PRJCA027303.

Conflict of interest statement:

No conflict of interest declared.

Supplementary data

Supplementary data is available at Horticulture Research online.

References

[1] Koes RE, Quattrocchio F, Mol JNM. The flavonoid biosynthetic pathway in plants: function and evolution. BioEssays. 1994; 16: 123-32

[2] Chalker-Scott L. Environmental significance of anthocyanins in plant stress responses. Photochem Photobiol. 1999; 70:1-9

[3] Gould KS. Nature’s Swiss Army knife: the diverse protective roles of anthocyanins in leaves. Biomed Res Int. 2004; 2004: 314-20

[4] Holton T, Cornish E. Genetics and biochemistry of anthocyanin biosynthesis. Plant Cell. 1995; 7:1071-83

[5] Sun W, Liang L, Meng X. et al. Biochemical and molecular char-acterization of a flavonoid 3-O-glycosyltransferase responsible for anthocyanins and flavonols biosynthesis in Freesia hybrida. Front Plant Sci. 2016; 7:410

[6] Qi F, Liu Y, Luo Y. et al. Functional analysis of the ScAG and ScAGL 11 MADS-box transcription factors for anthocyanin biosynthesis and bicolour pattern formation in Senecio cruentus ray florets. Hortic Res. 2022; 9:uhac071

[7] Zhao D, Tao J. Recent advances on the development and reg-ulation of flower color in ornamental plants. Front Plant Sci. 2015; 6:261

[8] Liu Y, Qian J, Li J. et al. Hydroxylation decoration patterns of flavonoids in horticultural crops: chemistry, bioactivity, and biosynthesis. Hortic Res. 2022; 9:uhab068

[9] Tanaka Y, Sasaki N, Ohmiya A. Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant J. 2008; 54: 733-49

[10] Sharma H, Sharma P, Kumar A. et al. Multifaceted regulation of anthocyanin biosynthesis in plants: a comprehensive review. J Plant Growth Regul. 2024; 43:3048-62

[11] Ramsay NA, Glover BJ. MYB-bHLH-WD40 protein complex and the evolution of cellular diversity. Trends Plant Sci. 2005; 10: 63-70

[12] Xie S, Lei Y, Chen H. et al. R2R3-MYB transcription factors regu-late anthocyanin biosynthesis in grapevine vegetative tissues. Front Plant Sci. 2020; 11:527

[13] Borevitz JO, Xia Y, Blount J. et al. Activation tagging identifies a conserved MYB regulator of Phenylpropanoid biosynthesis. Plant Cell. 2000; 12:2383-93

[14] Tohge T, Nishiyama Y, Hirai MY. et al. Functional genomics by integrated analysis of metabolome and transcriptome of Ara-bidopsis plants over-expressing an MYB transcription factor. Plant J. 2005; 42:218-35

[15] Bhargava A, Mansfield SD, Hall HC. et al. MYB75 functions in regulation of secondary cell wall formation in the Arabidopsis inflorescence stem. Plant Physiol. 2010; 154:1428-38

[16] Tao H, Gao F, Li L. et al. WRKY33 negatively regulates antho-cyanin biosynthesis and cooperates with PHR1 to medi-ate acclimation to phosphate starvation. Plant Commun. 2024; 5:100821

[17] Borgen L. Lobularia (Cruciferae): A Biosystematic Study with Special Reference to the Macaronesian Region. Copenhagen, Denmark: Council for Nordic Publications in Botany; 1987

[18] Marhold K. Brassicaceae. In: Euro+Med Plantbase - the Information Resource for Euro-Mediterranean Plant Diversity. date last accessed).

[19] Tutin TG. Flora Europaea. Cambridge, UK: Cambridge University Press; 1968

[20] POWO. Plants of the World Online. Facilitated by Royal Botanic Gardens, Kew. https://powo.science.kew.org/taxon/1085072-2 (6 November 2024, date last accessed).

[21] Ben Akacha B, Michalak M, Ben Romdhane W. et al. Recent advances in phytochemistry, pharmaceutical, biomedical, phy-toremediation, and bio-preservative applications of Lobularia maritima. S Afr J Bot. 2024; 165:202-16

[22] Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop domestication. Cell. 2006; 127:1309-21

[23] Meyer RS, Purugganan MD. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet. 2013; 14: 840-52

[24] Zhou C, McCarthy SA, Durbin R. YaHS: yet another hi-C scaf-folding tool. Bioinformatics. 2023; 39:btac808

[25] Huang L, Ma Y, Jiang J. et al. A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance. Hortic Res. 2020; 7:197

[26] Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34:3094-100

[27] Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011; 475: 493-6

[28] Beichman AC, Phung TN, Lohmueller KE. Comparison of single genome and allele frequency data reveals discordant demo-graphic histories. G3 ( Bethesda). 2017; 7:3605-20

[29] Liu J, Ji X, Chen H. Beta-PSMC: uncovering more detailed population history using beta distribution. BMC Genomics. 2022; 23:785

[30] Terhorst J, Kamm JA, Song YS. Robust and scalable infer-ence of population history from hundreds of unphased whole genomes. Nat Genet. 2017; 49:303-9

[31] Iwata Y, Koizumi N. An Arabidopsis transcription factor, AtbZIP60, regulates the endoplasmic reticulum stress response in a manner unique to plants. Proc Natl Acad Sci USA. 2005; 102: 5280-5

[32] Lu D-P, Christopher DA. Endoplasmic reticulum stress acti-vates the expression of a sub-group of protein disulfide iso-merase genes and AtbZIP60 modulates the response in Ara-bidopsis thaliana. Mol Gen Genomics. 2008; 280:199-210

[33] Tajima H, Iwata Y, Iwano M. et al. Identification of an Arabidopsis transmembrane bZIP transcription factor involved in the endo-plasmic reticulum stress response. Biochem Biophys Res Commun. 2008; 374:242-7

[34] Konstantinova N, Hoermayer L, Glanc M. et al. WAVY GROWTH Arabidopsis E 3 ubiquitin ligases affect apical PIN sorting deci-sions. Nat Commun. 2022; 13:5147

[35] Sakai T, Mochizuki S, Haga K. et al. The WAVY GROWTH 3 E3 ligase family controls the gravitropic response in Arabidopsis roots. Plant J. 2012; 70:303-14

[36] Wang J-L, Wang M, Zhang L. et al. WAV E3 ubiquitin ligases mediate degradation of IAA32/34 in the TMK1-mediated auxin signaling pathway during apical hook development. Proc Natl Acad Sci. 2024;

[37]

[38] Jali SS, Rosloski SM, Janakirama P. et al. A plant-specific HUA2-LIKE gene family in Arabidopsis thaliana is essential for develop-ment. Plant J. 2014; 80:242-54

[39] Lemus T, Mason GA, Bubb KL. et al. AGO1 and HSP 90 buffer different genetic variants in Arabidopsis thaliana. Genetics. 2023; 223:iyac163

[40] Ilk N, Ding J, Ihnatowicz A. et al. Natural variation for antho-cyanin accumulation under high-light and low-temperature stress is attributable to the ENHANCER OF AG-4 2 (HUA2) locus in combination with production of anthocyanin pigment 1 (PAP1) and PAP2. New Phytol. 2015; 206:422-35

[41] Wang F, Gao Y, Liu Y. et al. BES1-regulated BEE1 controls photoperiodic flowering downstream of blue light signaling pathway in Arabidopsis. New Phytol. 2019; 223:1407-19

[42] Petridis A, Döll S, Nichelmann L. et al. Arabidopsis thaliana G2-like flavonoid regulator and Brassinosteroid enhanced expres-sion1 are low-temperature regulators of flavonoid accumula-tion. New Phytol. 2016; 211:912-25

[43] Moreno JE, Moreno-Piovano G, Chan RL. The antagonistic basic helix-loop-helix partners BEE and IBH1 contribute to control plant tolerance to abiotic stress. Plant Sci. 2018; 271:143-50

[44] Xue Y, Zhong Z, Harris CJ. et al. Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation. Nat Commun. 2021; 12:4292

[45] He Q, Lu Q, He Y. et al. Dynamic changes of the anthocyanin biosynthesis mechanism during the development of heading Chinese cabbage (Brassica rapa L.) and Arabidopsis under the control of BrMYB2. Front Plant Sci. 2020; 11:593766

[46] He Q, Wu J, Xue Y. et al. The novel gene BrMYB2, located on chromosome A07, with a short intron 1 controls the purple-head trait of Chinese cabbage (Brassica rapa L.). Hortic Res. 2020; 7:1-19

[47] Chhon S, Jeon J, Kim J. et al. Accumulation of anthocyanins through overexpression of AtPAP 1 in Solanum nigrum Lin. (black nightshade). Biomol Ther. 2020; 10:277

[48] Zvi MMB, Shklarman E, Masci T. et al. PAP1 transcription factor enhances production of phenylpropanoid and terpenoid scent compounds in rose flowers. New Phytol. 2012; 195:335-45

[49] Drake N, Breeze P.Climate change and modern human occupa-tion of the Sahara from MIS 6-2. In: Jones SC, StewartBA.eds. Africa from MIS 6-2: Population Dynamics and Paleoenvironments. Springer Netherlands: Dordrecht, 2016,103-22

[50] Tjallingii R, Claussen M, Stuut J-BW. et al. Coherent high-and low-latitude control of the northwest African hydrological balance. Nat Geosci. 2008; 1:670-5

[51] Tisserand A, Malaizé B, Jullien E. et al. African monsoon enhancement during the penultimate glacial period (MIS 6.5 ∼ 170 ka) and its atmospheric impact. Palaeogeogr. Palaeoclimatol. 2009; 24: PA2220

[52] Gross BL, Olsen KM. Genetic perspectives on crop domestica-tion. Trends Plant Sci. 2010; 15:529-37

[53] Meyer RS, DuVal AE, Jensen HR. Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. New Phytol. 2012; 196:29-48

[54] Cowan RK, Hoen DR, Schoen DJ. et al. MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms. Mol Biol Evol. 2005; 22:2084-9

[55] Morales J, Pérez-Jordà G, Peña-Chocarro L. et al. The origins of agriculture in North-West Africa: macro-botanical remains from Epipalaeolithic and Early Neolithic levels of Ifri Oudadane (Morocco). JArchaeolSci. 2013; 40:2659-69

[56] Lucarini G, Bokbot Y, Broodbank C. New light on the silent millennia: Mediterranean Africa, ca. 4000-900 BC. Afr Archaeol Rev. 2021; 38:147-64

[57] Ben NJ. Les peintures rupestres de l’abri de Zamla (Jebel Ous-selat - Tunisie Centrale) : la représentation d’une planimétrie agraire? Antiq Afr. 2021; 57:19-32

[58] Altman A, Shennan S, Odling-Smee J. Ornamental plant domestication by aesthetics-driven human cultural niche con-struction. Trends Plant Sci. 2022; 27:124-38

[59] Hernández Bermejo JEH. García Sánchez EG. Economic botany and ethnobotany in Al-Andalus (Iberian Peninsula: tenth-fifteenth centuries), an unknown heritage of mankind. Econ Bot. 1998; 52:15-26

[60] Hernández Bermejo JE, Carabaza Bravo JM, García Sánchez E. et al. Landscapes and forest flora of al-Andalus: a reconstruc-tion from textual historical documentation. Mediterr Botany. 2019; 40:71-80

[61] García Sánchez E, Hernández Bermejo JE. Ornamental plants in agricultural and botanical treatises from al-Andalus. In: ConanM, D. C.ed. Middle East Garden Traditions:Unity and Diversity. Dumbarton Oaks: Washington, 2007,75-94

[62] Busche M, Pucker B, Weisshaar B. et al. Three R2R3-MYB transcription factors from banana (Musa acuminata)activate structural anthocyanin biosynthesis genes as part of an MBW complex. BMC Res Notes. 2023; 16:103

[63] Guo Y, Li D, Liu T. et al. Genome-wide identification of PAP 1 direct targets in regulating seed anthocyanin biosynthesis in Arabidopsis. Int J Mol Sci. 2023; 24:16049

[64] Espley RV, Hellens RP, Putterill J. et al. Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10. Plant J. 2007; 49:414-27

[65] Wei K, Wang L, Zhang Y. et al. A coupled role for CsMYB75 and CsGSTF1 in anthocyanin hyperaccumulation in purple tea. Plant J. 2019; 97:825-40

[66] Liu X, Zhao T, Yuan L. et al. A fruit-expressed MYB transcription factor regulates anthocyanin biosynthesis in Atropa belladonna. Int J Mol Sci. 2024; 25:4963

[67] Yang W, Zhang L, Mandáková T. et al. The chromosome-level genome sequence and karyotypic evolution of Megadenia pyg-maea (Brassicaceae). Mol Ecol Resour. 2021; 21:871-9

[68] Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30:2114-20

[69] van Berkum NL, Lieberman-Aiden E, Williams L. et al. Hi-C: a method to study the three-dimensional architecture of genomes. JVisExp. 2010; 39: e1869

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

[71] Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta. 2023; 2:e107

[72] Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009; 25: 1754-60

[73] Durand NC, Shamim MS, Machol I. et al. Juicer provides a one-click system for analyzing loop-resolution hi-C experiments. Cell Syst. 2016; 3:95-8

[74] Seppey M, Manni M, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness. Methods Mol Biol. 2019; 1962:227-45

[75] Ou S, Chen J, Jiang N. Assessing genome assembly quality using the LTR assembly index (LAI). Nucleic Acids Res. 2018; 46:e126

[76] Xiao M, Hao G, Guo X. et al. A high-quality chromosome-level Eutrema salsugineum genome, an extremophile plant model. BMC Genomics. 2023; 24:174

[77] Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinfor-matics. 2009; 25:4-10

[78] Flynn JM, Hubley R, Goubert C. et al. RepeatModeler2 for auto-mated genomic discovery of transposable element families. Proc Natl Acad Sci USA. 2020; 117:9451-7

[79] Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008; 9:18

[80] Xu Z, Wang H. LTR-FINDER: an efficient tool for the pre-diction of full-length LTR retrotransposons. Nucleic Acids Res. 2007; 35:W265-8

[81] Ou S, Jiang N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotrans-posons. Plant Physiol. 2018; 176:1410-22

[82] Ou S, Su W, Liao Y. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehen-sive pipeline. Genome Biol. 2019; 20:275

[83] Stanke M, Steinkamp R, Waack S. et al. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004; 32: W309-12

[84] Birney E, Clamp M, Durbin R. GeneWise and Genomewise. Genome Res. 2004; 14:988-95

[85] Bairoch A, Apweiler R.The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 2000; 28:45-8

[86] Zdobnov EM, Apweiler R. InterProScan - an integration plat-form for the signature-recognition methods in InterPro. Bioin-formatics. 2001; 17:847-8

[87] Conesa A, Götz S, García-Gómez JM. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21:3674-6

[88] Huerta-Cepas J, Szklarczyk D, Heller D. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019; 47:D309-14

[89] Kanehisa M, Goto S, Sato Y. et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012; 40:D109-14

[90] Wang Y, Tang H, Debarry JD. et al. MCScanX: a toolkit for detec-tion and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40:e49-9

[91] Krzywinski M, Schein J, Birol ˙I. et al. Circos: an informa-tion aesthetic for comparative genomics. Genome Res. 2009; 19: 1639-45

[92] Li H. A statistical framework for SNP calling, mutation dis-covery, association mapping and population genetical param-eter estimation from sequencing data. Bioinformatics. 2011; 27: 2987-93

[93] Van der Auwera GA, O’Connor B. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. Sebastopol, USA: O’Reilly Media; 2020

[94] Yang W, Feng L, Jiao P. et al. Out of the Qinghai-Tibet plateau: genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae). Mol Ecol. 2023; 32: 492-503

[95] Purcell S, Neale B, Todd-Brown K. et al. PLINK: a tool set for whole-genome association and population-based linkage anal-yses. Am J Hum Genet. 2007; 81:559-75

[96] Zheng X, Levine D, Shen J. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics. 2012; 28:3326-8

[97] Alexander DH, Novembre J, Lange K. Fast model-based estima-tion of ancestry in unrelated individuals. Genome Res. 2009; 19: 1655-64

[98] Jin J-J, Yu W-B, Yang J-B. et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21:241

[99] Kozlov AM, Darriba D, Flouri T. et al., eds. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylo-genetic inference. Bioinformatics. 2019; 35:4453-5

[100] Ossowski S, Schneeberger K, Lucas-Lledó JI. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science. 2010; 327:92-4

[101] Excoffier L, Marchi N, Marques DA. et al. Fastsimcoal2: demo-graphic inference under complex evolutionary scenarios. Bioin-formatics. 2021; 37:4882-5

[102] Chen C, Yang W, Liu J. et al. Population transcriptomics reveals gene flow and introgression between two non-sister Alpine gentians. Front Ecol Evol. 2021; 9:638230

[103] Excoffier L, Dupanloup I, Huerta-Sánchez E. et al. Robust demo-graphic inference from genomic and SNP data. PLoS Genet. 2013; 9:e1003905

[104] Li K, Zhang S, Song X. et al. Genome evolution of blind subter-ranean mole rats: adaptive peripatric versus sympatric specia-tion. Proc Natl Acad Sci USA. 2020; 117:32499-508

[105] Alexa A, Rahnenfuhrer J.topGO: enrichment analysis for gene ontologyR package version 2480. 2022;

[106] Camacho C, Coulouris G, Avagyan V. et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10:1-9

[107] Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012; 44:821-4

[108] Li M-X, Yeung JMY, Cherny SS. et al. Evaluating the effective numbers of independent tests and significant p-value thresh-olds in commercial genotyping arrays and public imputation reference datasets. Hum Genet. 2012; 131:747-56

[109] Patro R, Duggal G, Love MI. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017; 14:417-9

[110] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15:550

[111] Lou S, Guo X, Liu L. et al. Allelic shift in cis-elements of the transcription factor RAP2.12 underlies adaptation asso-ciated with humidity in Arabidopsis thaliana. Sci Adv. 2022; 8: eabn8281