Abstract
A first assembly of globe artichoke genome was released in 2016 and the project required the adoption of a set of strategies to overcome the lack of a homozygous reference genotype. Moreover, the inability to exploit standard genotyping methods, normally adopted in inbred species where homozygous segregating progenies can be more easily obtained, posed some challenges. A low-pass genotyping-by-sequencing strategy for heterozygous individuals was implemented for the first time and required the development of dedicated tools. The method allowed to leverage very low coverage to impute genotypic states of F1 segregating individuals and use this information to arrange scaffolds in pseudomolecules. The availability of a chromosome-scale reference sequence allowed to depict, for the first time, the genomic landscape of globe artichoke. The work shed lights on its genes, their structure and function, orthology and synteny with other species, repeats and the timing of their expansion, age of speciation and whole-genome duplications. All the features revealed in this study expanded the knowledge base for comparative genomics across all plants. More importantly, the genome sequence of globe artichoke will facilitate transferability of genomic and genetic findings in the Compositae family, hence accelerating the discovery of the molecular mechanism at the base of economically important traits and their exploitation for selection, genetic engineering or utilization in biotechnological processes, in the light of the richness of nutraceutical properties of this species and its overall economic importance for the Mediterranean horticulture.
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Acquadro A, Lanteri S, Scaglione D, Arens P, Vosman B, Portis E (2009) Genetic mapping and annotation of genomic microsatellites isolated from globe artichoke. Theor Appl Genet, 1573–1587
Andolfatto P, Davison D, Erezyilmaz D, Hu T, Mast J, Sunayama-Morita T, Stern D (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21:610–617
Bansal V, Bafna V (2008) HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24:I153–I159
Barker M, Kane N, Matvienko M, Kozik A, Michelmore W, Knapp S, Rieseberg L (2008) Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol 25:2445–2455
Barrett L, Fletcher S, Wilton S (2012) Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell Mol Life Sci 69:3613–3634
Curci P, De Paola D, Danzi D, Vendramin G, Sonnante G (2015) Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae. PLoS ONE 10
Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E, Mitchell S (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6
Etter P, Preston J, Bassham S, Cresko W, Johnson E (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE 6
Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H (2014) Draft genome sequence of eggplant (Solanum melongena L.): the representative Solanum species indigenous to the old world. DNA Res
Kesseli RV, Michelmore RW (1997) The Compositae: systematically fascinating but specifically neglected. In: Paterson AH (ed) Genome mapping in plants. R.G. Landes Co. Georgetown, TX, pp 179–191
Kim S, Park M, Yeom S-I, Kim Y-M, Lee JM, Lee H-A, Seo E, Choi J, Cheong K, Kim K-T, Jung K, Lee G-W, Oh S-K, Bae C, Kim S-B, Lee H-Y, Kim S-Y, Kim M-S, Kang B-C, Jo YD, Yang H-B, Jeong H-J, Kang W-H, Kwon J-K, Shin C, Lim JY, Park JH, Huh JH, Kim J-S, Kim B-D, Cohen O, Paran I, Suh MC, Lee SB, Kim Y-K, Shin Y, Noh S-J, Park J, Seo YS, Kwon S-Y, Kim HA, Park JM, Kim H-J, Choi S-B, Bosland PW, Reeves G, Jo S-H, Lee B-W, Cho H-T, Choi H-S, Lee M-S, Yu Y, Do Choi Y, Park B-S, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai H-S, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sorensen I, Lee S-J, Kim RW, Choi I-Y, Choi B-S, Lim J-S, Lee Y-H, Choi D (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278
Lanteri S, Acquadro A, Comino C, Mauro R, Mauromicale G, Portis E (2006) A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers. Theor Appl Genet 112:1532–1542
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder O, Leung F, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner C, Lam T, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford M, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam T, Yiu S, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong G, Olson M, Zhang X, Li S, Yang H, Wang J (2010) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317
Marie D, Brown S (1993) A cytometric exercise in plant DNA histograms, with 2C-values for 70 species. Biol Cell 78:41–51
Martinez M, Diaz I (2008) The origin and evolution of plant cystatins and their target cysteine proteinases indicate a complex functional relationship. BMC Evol Biol 8
Mascher M, Wu S, St Amand P, Stein N, Poland J (2013) Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS ONE 8(10):e76925
Ohta T (1991) Multigene families and the evolution of complexity. J Mol Evol 33:34–41
Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes. Bioinformatics 23:1061–1067
Peterson B, Weber J, Kay E, Fisher H, Hoekstra H (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7(5):e37135
Portis E, Barchi L, Acquadro A, Macua JI, Lanteri S (2005) Genetic diversity assessment in cultivated cardoon by AFLP (amplified fragment length polymorphism) and microsatellite markers. Plant Breed 124(3):299–304
Portis E, Mauro RP, Barchi L, Acquadro A, Mauromicale G, Lanteri S (2014) Mapping yield-associated QTL in globe artichoke. Mol Breed 34:615–630
Portis E, Mauromicale G, Mauro R, Acquadro A, Scaglione D, Lanteri S (2009) Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus). Theor Appl Genet, 59–70
Portis E, Portis F, Valente L, Moglia A, Barchi L, Lanteri S, Acquadro A (2016) A genome-wide survey of the microsatellite content of the globe artichoke genome and the development of a web-based database. PLoS ONE 11(9):e016284
Portis E, Scaglione D, Acquadro A, Mauromicale G, Mauro R, Knapp SJ, Lanteri S (2012) Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex. BMC Res Notes 5:252
Portis E, Acquadro A, Tirone M, Pesce GR, Mauromicale G, Lanteri S (2018) Mapping the genomic regions encoding biomass-related traits in Cynara cardunculus L. Mol Breed 38(5):64
Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y, Wu Z, Mao L, Wu H, Ling-Hu C, Zhou H, Lin H, González-Morales S, Trejo-Saavedra DL, Tian H, Tang X, Zhao M, Huang Z, Zhou A, Yao X, Cui J, Li W, Chen Z, Feng Y, Niu Y, Bi S, Yang X, Li W, Cai H, Luo X, Montes-Hernández S, Leyva-González MA, Xiong Z, He X, Bai L, Tan S, Tang X, Liu D, Liu J, Zhang S, Chen M, Zhang L, Zhang L, Zhang Y, Liao W, Zhang Y, Wang M, Lv X, Wen B, Liu H, Luan H, Zhang Y, Yang S, Wang X, Xu J, Li X, Li S, Wang J, Palloix A, Bosland PW, Li Y, Krogh A, Rivera-Bustamante RF, Herrera-Estrella L, Yin Y, Yu J, Hu K, Zhang Z (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci 111:5135–5140
Raven PH, Axelrod DI (1974) Angiosperm biogeography and past continental movements. Ann Mo Bot Gard 61:539–637
Rotino GL, Lanteri S, Sala T, Toppino L, Acquadro A, Barchi L, Portis E, Rinaldi R, Scaglione D, Dal Molin A, Minio A, Ferrarini A, Tononi P, Zamperin G, Fantini E, Pietrella M, Giuliano G, Delledonne M (2014) An eggplant (Solanum melongena L.) high quality genome draft. In: Plant and animal genome XXIInd conference, January 11–15, 2014, San Diego, CA, USA
Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, Xu X, Pan S, Cheng S, Liu X, Ren Y, Wang J, Albiero A, Dal Pero F, Todesco S, Van Eck J, Buels R, Bombarely A, Gosselin J, Huang M, Leto J, Menda N, Strickler S, Mao L, Gao S, Tecle I, York T, Zheng Y, Vrebalov J, Lee J, Zhong S, Mueller L, Stiekema W, Ribeca P, Alioto T, Yang W, Huang S, Du Y, Zhang Z, Gao J, Guo Y, Wang X, Li Y, He J, Li C, Cheng Z, Zuo J, Ren J, Zhao J, Yan L, Jiang H, Wang B, Li H, Li Z, Fu F, Chen B, Han B, Feng Q, Fan D, Wang Y, Ling H, Xue Y, Ware D, McCombie W, Lippman Z, Chia J, Jiang K, Pasternak S, Gelley L, Kramer M, Anderson L, Chang S, Royer S, Shearer L, Stack S, Rose J, Xu Y, Eannetta N, Matas A, McQuinn R, Tanksley S, Camara F, Guigo R, Rombauts S, Fawcett J, Van de Peer Y, Zamir D, Liang C, Spannagl M, Gundlach H, Bruggmann R, Mayer K, Jia Z, Zhang J, Ye Z, Bishop G, Butcher S, Lopez-Cobollo R, Buchan D, Filippis I, Abbott J, Dixit R, Singh M, Singh A, Pal J, Pandit A, Singh P, Mahato A, Dogra V, Gaikwad K, Sharma T, Mohapatra T, Singh N, Causse M, Rothan C, Schiex T, Noirot C, Bellec A, Klopp C, Delalande C, Berges H, Mariette J, Frasse P, Vautrin S, Zouine M, Latche A, Rousseau C, Regad F, Pech J, Philippot M, Bouzayen M, Pericard P, Osorio S, del Carmen A, Monforte A, Granell A, Fernandez-Munoz R, Conte M, Lichtenstein G, Carrari F, De Bellis G, Fuligni F, Peano C, Grandillo S, Termolino P, Pietrella M, Fantini E, Falcone G, Fiore A, Giuliano G, Lopez L, Facella P, Perrotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, van Schriek K, Feron R, van Oeveren J, de Heer P, daPonte L, Jacobs-Oomen S, Cariaso M, Prins M, van Eijk M, Janssen A, van Haaren M, Jo S, Kim J, Kwon S, Kim S, Koo D, Lee S, Hur C, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jocker A, Warfsmann J, Gobel U, Kawamura S, Yano K, Sherman J, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen E, van de Belt J, van Haarst J, Peters S, van Staveren M, Henkens M, Mooyman P, Hesselink T, van Ham R, Jiang G, Droege M, Choi D, Kang B, Kim B, Park M, Yeom S, Lee Y, Choi Y, Li G, Gao J, Liu Y, Huang S, Fernandez-Pedrosa V, Collado C, Zuniga S, Wang G, Cade R, Dietrich R, Rogers J, Knapp S, Fei Z, White R, Thannhauser T, Giovannoni J, Botella M, Gilbert L, Gonzalez R, Goicoechea J, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Schoof H, Meyers B, Gurazada A, Green P, Mathur S, Vyas S, Solanke A, Kumar R, Gupta V, Sharma A, Khurana P, Khurana J, Tyagi A, Dalmay T, Mohorianu I, Walts B, Chamala S, Barbazuk W, Li J, Guo H, Lee T, Wang Y, Zhang D, Paterson A, Wang X, Tang H, Barone A, Chiusano M, Ercolano M, D’Agostino N, Di Filippo M, Traini A, Sanseverino W, Frusciante L, Seymour G, Elharam M, Fu Y, Hua A, Kenton S, Lewis J, Lin S, Najar F, Lai H, Qin B, Qu C, Shi R, White D, White J, Xing Y, Yang K, Yi J, Yao Z, Zhou L, Roe B, Vezzi A, D’Angelo M, Zimbello R, Schiavon R, Caniato E, Rigobello C, Campagna D, Vitulo N, Valle G, Nelson D, De Paoli E, Szinay D, de Jong H, Bai Y, Visser R, Lankhorst R, Beasley H, McLaren K, Nicholson C, Riddle C, Gianese G, Consortium TG, Consortium TG (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641
Scaglione D, Acquadro A, Portis E, Taylor C, Lanteri S, Knapp S (2009) Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database. BMC Genom 10:454
Scaglione D, Acquadro A, Portis E, Tirone M, Knapp S, Lanteri S (2012a) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genom 13:3
Scaglione D, Lanteri S, Acquadro A, Lai Z, Knapp SJ, Rieseberg L, Portis E (2012b) Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa. Plant Biotechnol J 10:956–969
Scaglione D, Reyes-Chin-Wo S, Acquadro A, Froenicke L, Portis E, Beitel C, Tirone M, Mauro R, Lo Monaco A, Mauromicale G, Faccioli P, Cattivelli L, Rieseberg L, Michelmore R, Lanteri S (2016) The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci Rep 6:19427
Staton S, Bakken B, Blackman B, Chapman M, Kane N, Tang S, Ungerer M, Knapp S, Rieseberg L, Burke J (2012) The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant J 72:142–153
van Os H, Stam P, Visser R, van Eck H (2005) SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor Appl Genet 112:187–194
Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA 107:10578–10583
Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti S, Patil V, Skryabin K, Kuznetsov B, Ravin N, Kolganova T, Beletsky A, Mardanov A, Di Genova A, Bolser D, Martin D, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop G, Sagredo B, Mejia N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera M, Giuliano G, Pietrella M, Perrotta G, Facella P, O’Brien K, Feingold S, Barreiro L, Massa G, Diambra L, Whitty B, Vaillancourt B, Lin H, Massa A, Geoffroy M, Lundback S, DellaPenna D, Buell C, Sharma S, Marshall D, Waugh R, Bryan G, Destefanis M, Nagy I, Milbourne D, Thomson S, Fiers M, Jacobs J, Nielsen K, Sonderkaer M, Iovene M, Torres G, Jiang J, Veilleux R, Bachem C, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert B, Goverse A, van Ham R, Visser R, Consortium PGS (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–U194
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Scaglione, D., Acquadro, A., Portis, E., Lanteri, S. (2019). Genomics. In: Portis, E., Acquadro, A., Lanteri, S. (eds) The Globe Artichoke Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-20012-1_9
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