Compendium of Plant Genomes Philipp Simon Massimo Iorizzo Dariusz Grzebelus Rafal Baranski Editors The Carrot Genome Compendium of Plant Genomes Series Editor Chittaranjan Kole, ICAR-National Research Center on Plant Biotechnology, Pusa, Raja Ramanna Fellow, Government of India, New Delhi, India [email protected] 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. 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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] Carrot Organelle Genomes: Organization, Diversity, 12 and Inheritance David M. Spooner, Philipp W. Simon, Douglas Senalik and Massimo Iorizzo Abstract 12.1 Plastid Structure, Mutational Cultivated carrot (Daucus carota subsp. sativus) Rates, and Inheritance is one of about 25–40 related wild species in the in Angiosperms genus Daucus depending on the classification. It is part of a widely distributed and taxonomically Palmer (1985) provided an early review of complex family Apiaceae (Umbelliferae) con- plastid structure and gene content, documenting, taining 466 genera and 3820 species that is one in angiosperms, (1) its relatively small size of the largest families of seed plants. Members of (generally 120–160 knt); (2) high copy number Daucus the Apiaceae, particularly the genus , (as many as 1000 per cell); (3) quadripartite have been the subject of intensive recent molec- circular structure comprising two inverted repeats ular studies on the structure and genetics of (IR), flanking a large single-copy (LSC) region plastids and mitochondria. This chapter sum- and a small single-copy (SSC) region; (4) labile marizes organellar (plastids and mitochondria) structure of the IR region variously shrinking and structure, function, mutational rates, and expanding in different lineages with the junction inter-organelle DNA transfer in the Apiaceae between the inverted repeat and the large Daucus and inheritance in the genus ,witha single-copy region located in a generally fixed wider focus on the Apiaceae and the sister family position within the 276-nt rps 19 gene; Araliaceae, and places these data in the context (5) repertoire of a complete set of rRNA, tRNA, of other studies in the angiosperms. and protein-encoding genes (Fig. 12.1); (6) only rare modifications of this basic structure in par- asitic plants with reduced gene content, deletion of the IR region in the Fabaceae, or extensive gene rearrangements in the Geraniaceae. In summary, most of the over 200 angiosperm chloroplast genomes examined at that time were D. M. Spooner (&) Á P. W. Simon Á D. Senalik USDA-Agricultural Research Service, Vegetable overwhelmingly similar in size, conformation, Crops Research Unit, Department of Horticulture, repeat structure, gene content, and gene order University of Wisconsin-Madison, 1575 Linden Dr., and arrangement, with the predominant mode of Madison, WI 53706, USA structural evolution consisting of small deletions e-mail: [email protected] and insertions occurring in intergenic spacers, 5′ M. Iorizzo and 3′ untranslated regions, and in the few Department of Horticultural Sciences, North Carolina State University, 600 Laureate Way, introns found in their genes. Kannapolis, NC 28081, USA © Springer Nature Switzerland AG 2019 205 P. Simon et al. (eds.), The Carrot Genome, Compendium of Plant Genomes, https://doi.org/10.1007/978-3-030-03389-7_12 [email protected] 206 D. M. Spooner et al. (a) Photosystem I and II trnP(ugg) orf41 nad7 7 rpl16 rps3 cox3 ccmB 5 f ATP synthase, NADH dehydrogenase r rps12 nad3 rps1 orf39a o trnM(cau) orf42 trnK(uuu) orf43 mttB orf45 orf38 rpl10 cox2 Ribosomal Proteins orf37 orf47 nad1 orf48 orf55 ccmC nad2 trnM(cau) nad2 orf60 Non coding RNA trnS(uga) trnC(gca) ccmFNatp1 trnN(guu) trnY(gua) 125 kb nad2 ycf and ORFs nad2 orf36 nad4L rps13 rps4 Other genes nad1 orf34 150 kb rps7 Dc cox1 nad1 100 kb cob MP→ atp4 orf50 175 kb nad6 Mitochondrion atp8 orf33 NC_017855 orf39b ccmFc rps12 nad3 orf32 rps1 75 kb 200 kb orf31 rpl5 trnP(ugg) cox3 nad4 nad5 trnE(uuc)nad5 nad5 trnH(gug) rrn26 orf51a rpl2 225 kb trnfM(cau) trnM(cau) orf52a 50 kb orf54 nad1 orf53 matR nad5 nad5 nad5 orf59 atp8 orf28 rrn18 250 kb rrn5 orf39c atp9 25 kb rps12 nad3 orf27 rps1 rpl5 trnD(guc) trnP(ugg) orf26 cox3 trnG(gcc) nad5 275 kb nad5 trnQ(uug) rrn26 atp6 0 kb orf51b trnM(cau) trnW(cca)nad9 orf52b 0 kb 150 kb psbA rpl2 matK Plastid rps16 ycf2 NC_008325 25 kb atpA ndhB rps7 atpF atpI rps12 rps2 125 kb rpoC2 rrn16 50 kb rpoC1 rpoB rrn23 75 kb ycf1 psbD ndhH 100 kb psbC ndhAndhI rps14 psaB ndhG psaA ndhE ycf3 ndhD rps4 ccsA ndhJ ndhK ndhC Duplications within genome ndhF atpE atpB rbcL accD ycf4 petA rps18 rpl20 rrn23 clpP psbB petB Duplications between genomes rrn16 rps7 rps12 ndhB ycf2 rpl2 rps8 rpl16 rpoA petD (b) ORF a ORF bORF c cox1 Fig. 12.1 Structure of the carrot mitochondrial and annotations were obtained from NCBI accessions plastid genomes and inter-organelle DNA transfer; NC_017855 (mitochondrion) and NC_008325 (plastid). genome coordinates every 25 kb are listed inside the Duplicated regions were detected using BLAST+ version figure. a Mitochondrial (top) and plastid (bottom) 2.6.0 megablast program (Camacho et al. 2009) with genomes (visualized using Circos version 0.69-6; Krzy- minimum alignment length of 50, minimum percentage winski et al. 2009) and gene annotations of Daucus carota; similarity of 80, and no dust filtering. b Structure of the these circularized genomes are drawn open to show gene plastid D. carota DcMP sequence. Open reading frames transfers between them. For the plastid, only genes over (ORFs) were detected using Open Reading Frame Finder 300 nt are annotated for space limitations, but these are (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). The collinear with those fully annotated in Ruhlman et al. sequence was oriented according to 5′–3′ (indicated by (2006). Duplications within (blue) and between arrows); ORF orientation is in opposite direction as related (red) genomes are shown by connected lines or ribbons. to other figures. Thick vertical blue lines indicate target The direction of all duplications between genomes is site duplication (TSD). Thin red vertical lines indicate presumed to be from plastid to mitochondrion except relative position of P1, P2, and P3 tnrV promoters. The red DcMP from mitochondrion to plastid (Iorizzo et al. 2012a, box indicates the region comprising partial sequence of b) as labeled by the arrow. Organellar sequences and gene cox1 gene. The scheme is drawn to scale [email protected] 12 Carrot Organelle Genomes: Organization, Diversity, … 207 Palmer (1985) mentioned the maternal inheri- to over 3000 (https://www.ncbi.nlm.nih.gov/ tance of plastid DNA, documented for most spe- genomes/GenomesGroup.cgi?taxid=2759&opt= cies by Tilney-Bassett (1978). Corriveau and plastid), allowing for finer comparisons of plastid Coleman (1988) developed a rapid cytological DNA sequences. Raubeson and Jansen (2005) screen based on epifluorescence microscopy for documented varying rates of change in different maternal inheritance and examined 235 plant regions of the plastid genome, favoring phylo- species from 80 angiosperm families. They genetic studies at different taxonomic levels. detected putative plastid DNA in the generative Plastid DNA analyses (first DNA restriction site and/or sperm cells of pollen from 43 species in 26 studies, and then DNA sequences from portions genera of 15 families, but not in the generative or of the genome) dominated much of the molecular sperm cells of pollen from the remaining 192 phylogenetic literature in the 1980s and 1990s. species (82%), strongly suggesting that they have Jansen and Ruhlman (2012) documented addi- only maternal inheritance. Their results corrobo- tional lineages of both gymnosperms and rated most reports of maternal plastid inheritance, angiosperms (the Campanulaceae) deviating and suggested that biparental inheritance of from stability of plastid architecture, gene and plastids is rare, occurring in about 14% of flow- intron content, and gene order across seed plants.