Chromosome restructuring and number change during the evolution of Morus notabilis and Morus alba

Abstract

Mulberry (Morus spp .) is an economically important plant as the main food plant used for rearing domesticated silkworm and it has multiple uses in traditional Chinese medicine. Two basic chromosome numbers (Morus notabilis, n = 7, and Morus alba, n = 14) have been reported in the genus Morus, but the evolutionary history and relationship between them remain unclear. In the present study, a 335-Mb high-quality chromosome-scale genome was assembled for the wild mulberry species M. notabilis. Comparative genomic analyses indicated high chromosomal synteny between the 14 chromosomes of cultivated M. alba and the six chromosomes of wild M. notabilis. These results were successfully verified by fluorescence in situ hybridization. Chromosomal fission/fusion events played crucial roles in the chromosome restructuring process between M. notabilis and M. alba. The activity of the centromere was another key factor that ensured the stable inheritance of chromosomes. Our results also revealed that long terminal repeat retrotransposons were a major driver of the genome divergence and evolution of the mulberry genomes after they diverged from each other. This study provides important insights and a solid foundation for studying the evolution of mulberry, allowing the accelerated genetic improvement of cultivated mulberry species.

References

[1] Nepal MP, Ferguson CJ . Phylogenetics of Morus (Moraceae) inferred from ITS and trnL-trnF sequence data . Syst Bot. 2012; 37: 442-50.

[2] He N, Zhang N, Qi W et al. Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun. 2013;4:2445.

[3] Yu YF, Li H, Zhang B et al. Nutritional and functional components of mulberry leaves from different varieties: evaluation of their potential as food materials. Int J Food Prop. 2018; 21: 1495-507.

[4] Li D, Ma B, Xu X et al. MMHub, a database for the mulberry metabolome. Database (Oxford). 2020; 2020. https://doi.org/10.1093/database/baaa011.

[5] Li D, Chen G, Ma B et al. Metabolic profiling and transcriptome analysis of mulberry leaves provide insights into flavonoid biosynthesis. J Agr Food Chem. 2020; 68: 1494-504.

[6] Li H, Yang Z, Zeng Q et al. Abnormal expression of bHLH3 disrupts a flavonoid homeostasis network, causing differences in pigment composition among mulberry fruits. Hortic Res. 2020; 7: 83.

[7] Liu J, Wan J, Wang D et al. Comparative transcriptome analysis of key reductase genes involved in the 1-Deoxynojirimycin biosynthetic pathway in mulberry leaves and cloning, prokaryotic expression, and functional analysis of MaSDR1 and MaSDR2 . J Agric Food Chem. 2020; 68: 12345-57.

[8] Sattler MC, Carvalho CR, Clarindo WR . The polyploidy and its key role in plant breeding. Planta. 2016; 243: 281-96.

[9] Xuan Y, Li C, Wu Y et al. FISH-based mitotic and meiotic diakinesis karyotypes of Morus notabilis reveal a chromosomal fusion-fission cycle between mitotic and meiotic phases. Sci Rep. 2017; 7: 9573.

[10] Xuan YH, Wu Y, Li P et al. Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences. Peerj. 2019; 7: e8158.

[11] Venkatesh KH, Nijagunaiah R, Munirajappa. Cytogenetical studies in some diploid mulberry varieties (Moraceae). Cytologia. 2013; 78: 69-72.

[12] Schneider, CK . In: Plantae Wilsonianae: An Enumeration of the Woody Plants Collected in Western China for the Arnold Arboretum of Harvard University during the Years 1907, 1908, and 1910 (ed. by Charles Sprague Sargent). Cambridge: The University Press, 1916, 293-4.

[13] Jiao F, Luo R, Dai X et al. Chromosome-level reference genome and population genomic analysis provide insights into the evolution and improvement of domesticated mulberry (Morus alba) . Mol Plant. 2020; 13: 1001-12.

[14] Zeng Q, Chen H, Zhang C et al. Definition of eight mulberry species in the genus Morus by internal transcribed spacer-based phylogeny. PLoS One. 2015; 10: e0135411.

[15] Wang X, Xu Y, Zhang S et al. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet. 2017; 49: 765-72.

[16] Zhou Z, Jiang Y, Wang Z et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol. 2015; 33: 408-14.

[17] Lin T, Zhu G, Zhang J et al. Genomic analyses provide insights into the history of tomato breeding. Nat Genet. 2014; 46: 1220-6.

[18] Zeng L, Tu XL, Dai H et al. Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biol. 2019; 20: 79.

[19] Lisch D . How important are transposons for plant evolution? Nat Rev Genet. 2013; 14: 49-61.

[20] Daccord N, Celton JM, Linsmith G et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet. 2017; 49: 1099-106.

[21] Butelli E, Licciardello C, Zhang Y et al. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell. 2012; 24: 1242-55.

[22] Kobayashi S, Goto-Yamamoto N, Hirochika H . Retrotransposon-induced mutations in grape skin color. Science. 2004; 304: 982-2.

[23] McCann J, Schneeweiss GM, Stuessy TF et al. The impact of reconstruction methods, phylogenetic uncertainty and branch lengths on inference of chromosome number evolution in American daisies (Melampodium, Asteraceae) . PLoS One. 2016; 11: e0162299.

[24] Udall JA, Long E, Ramaraj T et al. The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants. Front Plant Sci. 2019; 10: 1541.

[25] Yang L, Koo DH, Li D et al. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis . Plant J. 2014; 77: 16-30.

[26] Cheng YB, Shang D, Lup M et al. Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome. Cell Biosci. 2020; 10: 67.

[27] Mayrose I, Lysak MA . The evolution of chromosome numbers: mechanistic models and experimental approaches. Genome Biol Evol. 2021; 13: evaa220.

[28] Wang ZY, Wang XY. Evolutionary genomics model of chromosome number reduction and B chromosome production (in Chinese). Sci Sin Vitae. 2020; 50: 524-37.

[29] Wang XY, Jin D, Wang Z et al. Telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes. New Phytol. 2015; 205: 378-89.

[30] Fishman L, Willis JH, Wu CA et al. Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae) . Heredity. 2014; 112: 562-8.

[31] Gao Z, Fu S, Dong Q et al. Inactivation of a centromere during the formation of a translocation in maize. Chromosome Res. 2011; 19: 755-61.

[32] Zhang W, Friebe B, Gill BS et al. Centromere inactivation and epigenetic modifications of a plant chromosome with three functional centromeres. Chromosoma. 2010; 119: 553-63.

[33] Han F, Gao Z, Birchler JA . Reactivation of an inactive centromere reveals epigenetic and structural components for centromere specification in maize. Plant Cell. 2009; 21: 1929-39.

[34] Casacuberta E, Gonzalez J . The impact of transposable elements in environmental adaptation. Mol Ecol. 2013; 22: 1503-17.

[35] Ungerer MC, Strakosh SC, Zhen Y . Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Curr Biol. 2006; 16: R872-3.

[36] Parisod C, Badaeva ED . Chromosome restructuring among hybridizing wild wheats. New Phytol. 2020; 226: 1263-73.

[37] Bariah I, Keidar-Friedman D, Kashkush K . Where the wild things are: transposable elements as drivers of structural and functional variations in the wheat genome. Front Plant Sci. 2020; 11: 585515.

[38] Ma B, Xin Y, Kuang L et al. Distribution and characteristics of transposable elements in the mulberry genome. Plant Genome. 2019; 12: 180094.

[39] Rao SSP, Huntley MH, Durand NC et al. A 3D map of the human genome at Kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159: 1665-80.

[40] Ranallo-Benavidez TR, Jaron KS et al. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun. 2020; 11: 1432.

[41] Koren S, Walenz BP, Berlin K et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017; 27: 722-36.

[42] Vaser R, Sovic I, Nagarajan N et al. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017; 27: 737-46.

[43] Walker BJ, Abeel T, Shea T et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9: e112963.

[44] Simao FA, Waterhouse RM, Ioannidis P et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31: 3210-2.

[45] Servant N, Varoquaux N, Lajoie BR et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015; 16: 259.

[46] Burton JN, Adey A, Patwardhan RP et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol. 2013; 31: 1119-25.

[47] Durand NC, Robinson JT, Shamim MS et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited Zoom. Cell Syst. 2016; 3: 99-101.

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

[49] Gremme G, Steinbiss S, Kurtz S . GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Trans Comput Biol Bioinform. 2013; 10: 645-56.

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

[51] Rho M, Tang H . MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes. Nucleic Acids Res. 2009; 37: e143.

[52] Wicker T, Sabot F, Hua-Van A et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007; 8: 973-82.

[53] Yang Z . PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007; 24: 1586-91.

[54] Ma J, Bennetzen JL . Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 2004; 101: 12404-10.

[55] Grabherr MG, Haas BJ, Yassour M et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29: 644-U130.

[56] Stanke M, Diekhans M, Baertsch R et al. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008; 24: 637-44.

[57] Ter-Hovhannisyan V, Lomsadze A, Chernoff YO et al. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 2008; 18: 1979-90.

[58] Jones P, Binns D, Chang HY et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014; 30: 1236-40.

[59] Kurtz S, Phillippy A, Delcher AL et al. Versatile and open software for comparing large genomes. Genome Biol. 2004; 5: R12.

[60] Chen C, Chen H, Thomas HR et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020; 13: 1194-202.

[61] Emms DM, Kelly S . OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20: 238.

[62] Zhang D, Gao F, Jakovlić I et al. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 2020; 20: 348-55.

[63] Katoh K, Standley DM . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30: 772-80.

[64] Ranwez V, Douzery EJP, Cambon C et al. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Mol Biol Evol. 2018; 35: 2582-4.

[65] Talavera G, Castresana J . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007; 56: 564-77.

[66] Kalyaanamoorthy S, Minh BQ, Wong TKF et al. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017; 14: 587-9.

[67] Nguyen LT, Schmidt HA, von Haeseler A et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32: 268-74.

[68] Han MV, Thomas GWC, Lugo-Martinez J et al. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol Biol Evol. 2013; 30: 1987-97.

[69] Suyama M, Torrents D, Bork P . PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006; 34: W609-12.

[70] Benson G . Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27: 573-80.