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Molecular insights into the non-recombining nature of the spinach male-determining region

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Abstract

Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species’ sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars. These observations suggest that, in spinach, a Y-chromosomal region around the male-determining locus does not (or almost not) recombine with a counterpart region on the X chromosome. Using five of the seven DNA markers, five bacterial artificial chromosome (BAC) clone contigs with a total length of approximately 690 kbp were constructed. Full sequencing of six representative BAC clones (total insert length 504 kbp) from the five contigs and a transcriptome analysis by RNA-seq revealed that the Y-chromosomal region around the male-determining locus contains large amounts of repetitive elements, suggesting that the region might be poor in gene content. Most of the repeats found in this region are novel Ty1-copia-like and its derivative elements that accumulate predominantly in heterochromatic regions. Our findings may provide valuable insight into spinach genome structure and clues for future research into the evolution of the sex determining locus.

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References

  • Akamatsu T, Suzuki T, Uchimiya H (1998) Determination of male or female of spinach by using DNA marker. Japanese patent JP 1998052284

  • Altschul SF, Madden TL, Schäer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bachtrog D (2013) Evolution of Sex Chromosomes. In: Losos J (ed) The Princeton guide to evolution. Princeton University Press, Princeton, pp 387–396

    Google Scholar 

  • Brandes A, HeslopHarrison J, Kamm A, Kubis S, Doudrick R, Schmidt T (1997) Comparative analysis of the chromosomal and genomic organization of Ty1-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol Biol 33:11–21

    Article  CAS  PubMed  Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden T (2009) BLAST plus: architecture and applications. Bmc Bioinformatics 10:421

    Article  PubMed  PubMed Central  Google Scholar 

  • Cermak T, Kubat Z, Hobza R, Koblizkova A, Widmer A, Macas J, Vyskot B, Kejnovsky E (2008) Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes. Chromosome Res 16:961–976

    Article  CAS  PubMed  Google Scholar 

  • Charlesworth D (2016) Plant sex chromosomes. Annu Rev Plant Biol 67:397–420

    Article  CAS  PubMed  Google Scholar 

  • Charlesworth B, Charlesworth D (1978) Model for evolution of dioecy and gynodioecy. Am Nat 112:975–997

    Article  Google Scholar 

  • Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215–220

    Article  CAS  PubMed  Google Scholar 

  • Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H (2014) The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505:546–549

    Article  CAS  PubMed  Google Scholar 

  • Ellis JR, Janick J (1960) The chromosomes of Spinacia oleracea. Am J Bot 47:210–214

    Article  Google Scholar 

  • Fuentes-Bazan S, Mansion G, Borsch T (2012a) Towards a species level tree of the globally diverse genus Chenopodium (Chenopodiaceae). Mol Phylogenet Evol 62:359–374

    Article  PubMed  Google Scholar 

  • Fuentes-Bazan S, Uotila P, Borsch T (2012b) A novel phylogeny-based generic classification for Chenopodium sensu lato, and a tribal rearrangement of Chenopodioideae (Chenopodiaceae). Willdenowia 42:5–24

    Article  Google Scholar 

  • Fujito S, Takahata S, Suzuki R, Hoshino Y, Ohmido N, Onodera Y (2015) Evidence for a common origin of homomorphic and heteromorphic sex chromosomes in distinct Spinacia species. G3 (Bethesda) 5:1663–1673

    Article  PubMed Central  Google Scholar 

  • Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QC (2015) Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Mol Ecol 24:3243–3256

    Article  CAS  PubMed  Google Scholar 

  • Hammer K (2001) Chenopodiaceae, Spinacia oleracea L. In: Hanelt P, Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben Germany (eds) Mansfeld’s encyclopedia of agricultural and horticultural crops (except ornamentals), 1st English edn. Springer, Berlin, pp 249–251

    Google Scholar 

  • Heslop-Harrison J, Brandes A, Taketa S, Schmidt T, Vershinin A, Alkhimova E, Kamm A, Doudrick R, Schwarzacher T, Katsiotis A, Kubis S, Kumar A, Pearce S, Flavell A, Harrison G (1997) The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution. Genetica 100:197–204

    Article  CAS  PubMed  Google Scholar 

  • Hobza R, Lengerova M, Svoboda J, Kubekova H, Kejnovsky E, Vyskot B (2006) An accumulation of tandem DNA repeats on the Y chromosome in Silene latifolia during early stages of sex chromosome evolution. Chromosoma 115:376–382

    Article  CAS  PubMed  Google Scholar 

  • Hobza R, Kubat Z, Cegan R, Jesionek W, Vyskot B, Kejnovsky E (2015) Impact of repetitive DNA on sex chromosome evolution in plants. Chromosome Res 23:561–570

    Article  CAS  PubMed  Google Scholar 

  • Iizuka M, Janick J (1962) Cytogenetic analysis of sex determination in Spinacia oleracea. Genetics 47:1225–1241

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ito M, Ohmido N, Akiyama Y, Fukui K, Koba T (2000) Characterization of spinach chromosomes by condensation patterns and physical mapping of 5S and 45S rDNAs by FISH. J Am Soc Hortic Sci 125:59–62

    CAS  Google Scholar 

  • Janick J (1998) Hybrids in horticultural crops. In: Lamkey KR, Staub JE (eds) Concepts and breeding of heterosis in crop plants. Crop Science Society of America, Madison, pp 45–56

    Google Scholar 

  • Janick J, Stevenson E (1954) A genetic study of the heterogametic nature of the staminate plant in spinach. Proc Am Soc Hortic Sci 63:444–446

    Google Scholar 

  • Janick J, Stevenson E (1955) Genetics of the monoecious character in spinach. Genetics 40:429–437

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jukes T, Cantor C (1969) Evolution of protein molecules. In: Munro H (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132

    Chapter  Google Scholar 

  • Kadereit G, Mavrodiev E, Zacharias E, Sukhorukov A (2010) Molecular phylogeny of Atripliceae (Chenopodioideae, Chenopodiaceae): implications for systematics, biogeography, flower and fruit evolution, and the origin of C4 photosynthesis. Am J Bot 97:1664–1687

    Article  PubMed  Google Scholar 

  • Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH (2004) Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166:1437–1450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kataoka R, Hara M, Kato S, Isobe S, Sato S, Tabata S, Ohmido N (2012) Integration of linkage and chromosome maps of red clover (Trifolium pratense L.). Cytogenet Genome Res 137:60–69

    Article  CAS  PubMed  Google Scholar 

  • Katayama Y, Shida S (1956) Development of intersexual flowers and their location on the stalk in spinach. Jpn J Breed 6:19–22

    Article  Google Scholar 

  • Kumar A, Bennetzen J (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  Google Scholar 

  • Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, Antonescu C, Salzberg S (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu Z, Moore PH, Ma H, Ackerman CM, Ragiba M, Yu Q, Pearl HM, Kim MS, Charlton JW, Stiles JI, Zee FT, Paterson AH, Ming R (2004) A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427:348–352

    Article  CAS  PubMed  Google Scholar 

  • Na JK, Wang J, Ming R (2014) Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes. BMC Genom 15:335

    Article  Google Scholar 

  • Naeger J, Golenberg E (2016) Mode and tempo of sequence and floral evolution within the Anserineae. Plant Syst Evol 302:385–398

    Article  Google Scholar 

  • Onodera Y, Yamamoto PM, Kubo T, Tetsuo M (1999) Heterogeneity of the atp6 presequences in normal and different sources of male-sterile cytoplasms of sugar beet. J Plant Physiol 155:656–660

    Article  CAS  Google Scholar 

  • Onodera Y, Yonaha I, Niikura S, Yamazaki S, Mikami T (2008) Monoecy and gynomonoecy in Spinacia oleracea L.: morphological and genetic analyses. Sci Hortic 118:266–269

    Article  Google Scholar 

  • Onodera Y, Yonaha I, Masumo H, Tanaka A, Niikura S, Yamazaki S, Mikami T (2011) Mapping of the genes for dioecism and monoecism in Spinacia oleracea L.: evidence that both genes are closely linked. Plant Cell Rep 30:965–971

    Article  CAS  PubMed  Google Scholar 

  • Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92–94

    Article  CAS  PubMed  Google Scholar 

  • Picq S, Santoni S, Lacombe T, Latreille M, Weber A, Ardisson M, Ivorra S, Maghradze D, Arroyo-Garcia R, Chatelet P, This P, Terral JF, Bacilieri R (2014) A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines. BMC Plant Biol 14:229

    Article  PubMed  PubMed Central  Google Scholar 

  • Renner S, Ricklefs R (1995) Dioecy and its correlates in the flowering plants. Am J Bot 82:596–606

    Article  Google Scholar 

  • Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rogers S, Bendich A (1987) Ribosomal-RNA genes in plants—variability in copy number and in the intergenic spacer. Plant Mol Biol 9:509–520

    Article  CAS  PubMed  Google Scholar 

  • Sakamoto K, Ohmido N, Fukui K, Kamada H, Satoh S (2000) Site-specific accumulation of a LINE-like retrotransposon in a sex chromosome of the dioecious plant Cannabis sativa. Plant Mol Biol 44:723–732

    Article  CAS  PubMed  Google Scholar 

  • Sassa H (2007) A technique to isolate DNA from woody and herbaceous plants by using a silica-based plasmid extraction column. Anal Biochem 363:166–167

    Article  CAS  PubMed  Google Scholar 

  • Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644

    Article  CAS  PubMed  Google Scholar 

  • Takahata S, Yago T, Iwabuchi K, Hirakawa H, Suzuki Y, Onodera Y (2016) Comparison of spinach sex chromosomes with sugar beet autosomes reveals extensive synteny and low recombination at the male-determining locus. J Hered 107:679–685

    Article  PubMed  Google Scholar 

  • Trapnell C, Pachter L, Salzberg S (2009) TopHat: discovering splice junctions with RNA-SEq. Bioinformatics 25:1105–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • VanBuren R, Zeng F, Chen C, Zhang J, Wai CM, Han J, Aryal R, Gschwend AR, Wang J, Na JK, Huang L, Zhang L, Miao W, Gou J, Arro J, Guyot R, Moore RC, Wang ML, Zee F, Charlesworth D, Moore PH, Yu Q, Ming R (2015) Origin and domestication of papaya Yh chromosome. Genome Res 25:524–533

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vyskot B, Hobza R (2015) The genomics of plant sex chromosomes. Plant Sci 236:126–135

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Na JK, Yu Q, Gschwend AR, Han J, Zeng F, Aryal R, VanBuren R, Murray JE, Zhang W, Navajas-Pérez R, Feltus FA, Lemke C, Tong EJ, Chen C, Wai CM, Singh R, Wang ML, Min XJ, Alam M, Charlesworth D, Moore PH, Jiang J, Paterson AH, Ming R (2012) Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc Natl Acad Sci USA 109:13710–13715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Westergaard M (1958) The mechanism of sex determination in dioecious flowering plants. Adv Genet Incorp Mol Genet Med 9:217–281

    CAS  Google Scholar 

  • Wicker T, Keller B (2007) Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res 17:1072–1081

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu Z, Wang H (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35:W265–W268

    Article  PubMed  PubMed Central  Google Scholar 

  • Xu C, Jiao C, Sun H, Cai X, Wang X, Ge C, Zheng Y, Liu W, Sun X, Xu Y, Deng J, Zhang Z, Huang S, Dai S, Mou B, Wang Q, Fei Z (2017) Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nat Commun 8:15275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamamoto K, Oda Y, Haseda A, Fujito S, Mikami T, Onodera Y (2014) Molecular evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at different loci in a chromosomal region. Heredity 112:317–324

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors thank Tohoku Seed Co. Ltd. (Utsunomiya, Tochigi, Japan) very much for providing the spinach breeding lines used in this study. We appreciate the technical assistance provided by Mrs. H. Yokomoto. The work presented here was supported by the Interuniversity Bio-Backup Project (IBBP) as an application code (Hokkaido 0001). We used the DNA Sequencing Facility of Research Faculty of Agriculture, Hokkaido University.

Funding

This work was supported by the Japan Society for the Promotion of Science (Grants-in-Aid for Scientific Research (KAKENHI) Grant Numbers 26292001 and 16H06279), Ministry of Education, Culture, Sports, Science and Technology (KAKENHI Grant Number 221S0002), and the Takeda Science Foundation.

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Authors and Affiliations

  1. The Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo, 060-8589, Japan

    Tomohiro Kudoh, Mitsuhiko Takahashi, Takayuki Osabe & Yasuyuki Onodera

  2. Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan

    Atsushi Toyoda

  3. The Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan

    Hideki Hirakawa

  4. The Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan

    Yutaka Suzuki

  5. Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan

    Nobuko Ohmido

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  1. Tomohiro Kudoh
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  2. Mitsuhiko Takahashi
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  3. Takayuki Osabe
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  4. Atsushi Toyoda
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  5. Hideki Hirakawa
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  8. Yasuyuki Onodera
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Correspondence to Yasuyuki Onodera.

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The authors declare that they have no conflict of interest.

Data availability

The BAC clone sequences (AP017636–AP017641) and the RNA-seq reads (DRA006107) generated during and/or analyzed during the current study are available in the DNA Data Bank of Japan (DDBJ). The primer sequences of the SP_0018 marker developed by Tohoku Seed Co., Ltd. is not publicly available because it remains a trade secret.

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Communicated by S. Hohmann.

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Kudoh, T., Takahashi, M., Osabe, T. et al. Molecular insights into the non-recombining nature of the spinach male-determining region. Mol Genet Genomics 293, 557–568 (2018). https://doi.org/10.1007/s00438-017-1405-2

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  • DOI: https://doi.org/10.1007/s00438-017-1405-2

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