Compendium of Plant Genomes Philipp Simon Massimo Iorizzo Dariusz Grzebelus Rafal Baranski Editors The Carrot Genome Philipp Simon • Massimo Iorizzo • Dariusz Grzebelus • Rafal Baranski Editors The Carrot Genome 123 [email protected] Editors Philipp Simon Massimo Iorizzo Vegetable Crops Research Unit Plants for Human Health Institute USDA-ARS North Carolina State University Madison, WI, USA Kannapolis, NC, USA Dariusz Grzebelus Rafal Baranski University of Agriculture in Krakow Faculty of Biotechnology and Kraków, Poland Horticulture University of Agriculture in Krakow Kraków, Poland ISSN 2199-4781 ISSN 2199-479X (electronic) Compendium of Plant Genomes ISBN 978-3-030-03388-0 ISBN 978-3-030-03389-7 (eBook) https://doi.org/10.1007/978-3-030-03389-7 Library of Congress Control Number: 2019934354 © Springer Nature Switzerland AG 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland [email protected] Daucus: Taxonomy, Phylogeny, Distribution 2 David M. Spooner Abstract 2.1 Taxonomy of the Apiaceae Cultivated carrot (Daucus carota subsp. sativus) (Umbelliferae) is the most important member in the Apiaceae family in terms of economy and nutrition and is The Apiaceae (Umbelliferae) family contains considered the second most popular vegetable in 466 genera and 3820 species (Plunkett et al. in the world after potato. Despite its global impor- press) and is one of the largest families of seed Daucus tance, the systematics of remains under plants. It is nearly cosmopolitan in distribution, active revision at the species, genus, and but most diverse in temperate regions of the subtribal levels. The phylogenetic relationships northern hemisphere (Downie et al. 2000a, b, c; Daucus among the species of and close relatives Heywood 1983). It is well supported as a fi in the Apioideae have been clari ed recently monophyletic family, closely related to the fam- by a series of molecular studies using DNA ilies Araliaceae, Pittosporaceae, and Myo- rbcL matK sequences of the plastid genes and ; docarpaceae, and these, along with three smaller plastid introns rpl16, rps16, rpoC1; nuclear families, constitute the order Apiales, containing ribosomal DNA internal transcribed spacer about 5400 species (Judd et al. 2016; Plunkett (ITS) sequences; and plastid DNA restriction et al. 1996b). sites. Of these DNA markers, the ITS region The Apiaceae is well defined morphologically consisting of ITS1, the intervening spacer, and by a suite of characters, typically including herbs ITS2 has served as the main marker used. with compound leaves, stems usually hollow in Recently, next-generation DNA sequencing the internodes and with secretory canals con- methodologies have been used. We review these taining ethereal oils, resins, and other com- techniques and how they are impacting the pounds; alternate compound leaves or simple and Daucus taxonomy of the genus . deeply divided or lobed leaves with sheathing petioles; determinate inflorescences containing simple to compound umbels often subtended by involucral bracts; small flowers with 5 sepals, 5 petals, 5 stamens, and 2 connate carpels with an inferior ovary; 2 small stigmas; with the fruit a D. M. Spooner (&) schizocarp (dry fruits breaking into one-seeded USDA-Agricultural Research Service, Vegetable segments) with each of the two mericarps Crops Research Unit, Department of Horticulture, attached to an entire and deeply divided forked University of Wisconsin–Madison, 1575 Linden Dr, 53706-1590 Madison, WI, USA central stalk (carpophone) (Judd et al. 2016). e-mail: [email protected] © Springer Nature Switzerland AG 2019 9 P. Simon et al. (eds.), The Carrot Genome, Compendium of Plant Genomes, https://doi.org/10.1007/978-3-030-03389-7_2 [email protected] 10 D. M. Spooner [email protected] 2 Daucus: Taxonomy, Phylogeny, Distribution 11 b Fig. 2.1 Reproduction of the upper part of the Daucus numbers above the branches representing bootstrap maximum likelihood phylogeny of Banasiak et al. (2016), support and posterior probability values. The arrows using combined nuclear internal transcribed spacer region show hard incongruence between Banasiak et al. (2016) of ribosomal DNA (ITS) and plastid (rps16 intron, rpoC1 and the nuclear ortholog phylogenies of Arbizu et al. intron, and rpoB-trnC intergenic spacer) data, with (2014b, 2016b) This large suite of distinctive characters 2000a, b, c, 2001, 2010; Katz-Downie et al. makes the Apiaceae and its constituent species 1999; Lee 2002; Lee and Downie 1999, 2000, easily recognized to family, but divisions within 2006; Plunkett et al. 1996a; Spalik and Downie the family have been the subject of long dispute 2007; Spalik et al. 2001a, b; Weitzel et al. 2014). including circumscription and relationships of Of these DNA markers, the ITS region consisting the genus Daucus (Constance 1971; Plunkett and of ITS1, the intervening spacer, and ITS2 has Downie 1999) Traditionally, the Apiaceae has served as the main marker. A recent study of ITS, been divided into three subfamilies, the Sanicu- and other DNA regions proposed as standard loideae, Hydrocotyloideae, and Apioideae, with barcodes (psbA-trnH, matK, and rbcL) in 1957 the Apioideae, containing the genus Daucus,by species in 385 diverse genera in the Apiaceae far the largest of these three traditional subfam- have shown ITS to serve to identify species ilies. Drude (1898) recognized 8 tribes and 10 73.3% of the time, higher than any of the other subtribes within the Apioideae. Molecular phy- individual markers tested (Liu et al. 2014). logenetic studies have confirmed the monophyly A study by Banasiak et al. (2016) using DNA of the subfamily Apioideae but not many of its sequences from nuclear ribosomal ITS and three tribes and subtribes (Downie et al. 2001). plastid markers (rps16 intron, rpoC1 intron, and Downie et al. (2001) recognized nine tribes in the rpoB-trnC intergenic spacer) is the latest of a Apiaceae subfamily Apioideae, and placed series of studies to investigate ingroup and out- Daucus, and 12 other genera, in tribe Scan- group relationships of Daucus (Fig. 2.1). This diceae Spreng., subtribe Daucinae Dumort. (the study redefined and expanded the genus Daucus other 12 genera being Agrocharis Hochst., to include the following genera and species into Ammodaucus Coss. and Durieu, Cuminum L., its synonymy: Agrocharis Hochst. (4 species), Laser Borkh. ex P. Gaertn., B. Mey. and Schreb., Melanoselinum Hoffm. (1 species), Monizia Laserpitium L., Melanoselinum Hoffm., Monizia Lowe (1 species), Pachyctenium Maire and Lowe, Orlaya Hoffm., Pachyctenium Maire and Pamp. (1 species), Pseudorlaya (Murb.) Murb. Maire and Polemannia Eckl. and Zeyh., Poly- (2 species), Rouya Coincy (1 species), Torn- lophium Boiss., Pseudorlaya (Murb.) Murb., and abenea Parl. (6 species), Athamanta dellacellae Thapsia L.). E. A. Durand and Barratte, and Cryptotaenia A genus-level treatment of Daucus by Sáenz elegans Webb ex Bolle (these latter two genera Laín(1981) used morphological and anatomical with only some of its members transferred to data and recognized 20 species. Rubatzky et al. Daucus). (1999) later estimated 25 species of Daucus. The Banasiak et al. (2016) made the relevant phylogenetic relationships among the species of nomenclatural transfers into Daucus (Table 2.1) genus Daucus and close relatives in the Api- and following this classification, the genus oideae have been clarified by a series of molec- Daucus contains ca. 40 species and now includes ular studies using DNA sequences of the plastid winged and completely unadorned (“obsolete”) genes rbcL and matK; plastid introns rpl16, fruits in addition to its traditionally recognized rps16, rpoC1; nuclear ribosomal DNA internal spiny fruits. As summarized in Banasiak et al. transcribed spacer (ITS) sequences; and plastid (2016) and presented in graphic form in Fig. 5 DNA restriction sites (e.g., Arbizu et al. 2014b, of this paper, winged versus spiny versus obso- 2016a, b; Banasiak et al. 2016; Downie and lete fruits presented major traditional taxonomic Katz-Downie 1996; Downie et al. 1996, 1998, characters at higher levels in the Apiaceae (e.g., [email protected] 12 Table 2.1 Taxonomic circumscription of