Abstract
Pepper (Capsicum spp.) belongs to the Solanaceae, which is an economically important family of flowering plants consisting of about 102 genera and over 2500 species. The Solanaceae family includes crops of agronomic importance for which the efforts in genome sequencing are ongoing by almost 10 years (https://www.solgenomics.net/organism/sol100/view). Since the beginning of 2014, various consortia have released the genome sequences of domesticated and wild Capsicum species. The first effort was focused on the whole-genome sequencing of Capsicum annuum CM334 and of Capsicum chinense PI159236, which were widely used as founders of mapping populations and carry important disease resistance traits. Just a couple of months later, the genome sequences of C. annuum Zunla-1 and of the wild species Chiltepin (C. annuum var. glabriusculum) were published. Both studies reported a pepper genome size of ~3–3.5 Gb, rich in repetitive elements (over 80%) with about 35 thousand genes. The improved version of the reference genome CM334 as well as of C. chinense PI159236 together with the sequencing of the domesticated Capsicum baccatum revealed evolutionary relationships and estimated lineage divergence times occurring in Capsicum. Recently, the linked-read sequencing technology has been applied for the sequencing of a C. annuum accession that was an F1 cross hybrid of CM334 and a non-pungent pepper breeding line. Furthermore, genome resequencing studies have been performed with the aim to analyze loci of interest related to biotic/abiotic stresses and to qualitative features. In this chapter, we provide an overview of the genome sequencing and annotation strategies and describe the main results disclosed by all the whole and targeted genome sequencing projects in Capsicum.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ahn YK, Manivannanbinaya A, Sandeep K, Jun TH, Yang EY, Choi S, Kim JH, Kim DS, Lee E-S (2018) Whole genome resequencing of Capsicum baccatum and Capsicum annuum to discover single nucleotide polymorphism related to powdery mildew resistance. Sci Rep 8:5188. https://doi.org/10.1038/s41598-018-23279-5
Barchi L, Acquadro A, Portis E, Comino C, Nourdine M, Borras D, Bustos Lopez M, Giordano R, Monge S, Carli C, Lanteri S (2017) Genome re-sequencing of piedmontese pepper ecotypes. In: The XIV Solanaceae and III cucurbitaceae genomics joint conference, 3–6 Sept, Valencia, Spain
Bombarely A, Moser M, Amrad A, Bao M, Bapaume L et al (2016) Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nat Plants 2(6):16074. https://doi.org/10.1038/nplants.2016.74
Caranta C, Palloix A, Gebre-Selassie G, Lefebvre V, Moury B, Daubeze AM (1996) A complementation of two genes originating from susceptible Capsicum annuum lines confers a new and complete resistance to pepper veinal mottle virus. Phytopathology 86:739–743. https://doi.org/10.1094/Phyto-86-739
Caranta C, Thabuis A, Palloix A (1999) Development of a CAPS marker for the Pvr4 locus: a tool for pyramiding potyvirus resistance genes in pepper. Genome 42:1111–1116. https://doi.org/10.1139/gen-42-6-1111
Chunthawodtiporn J, Hill T, Stoffel K, Van Deynze A (2018) Quantitative trait Loci controlling fruit size and other horticultural traits in bell pepper (Capsicum annuum). Plant Genome 11(1)
Coleman C, Copetti D, Cipriani G, Hoffmann S, Kozma P, Kovács L, Morgante M, Testolin R, Di Gaspero G (2009) The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines. BMC Genet 10:89
D’Agostino N, Traini A, Frusciante L, Chiusano ML (2007) Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome. BMC Bioinf 8(Suppl 1):S9–S9. https://doi.org/10.1186/1471-2105-8-S1-S9
Devran Z, Kahveci E, Özkaynak E, Studholme DJ, Tör M (2015) Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing. Mol Breed 35(4):101
Harris RS (2007) Improved pairwise alignment of genomic DNA. Ph.D. thesis, The Pennsylvania State University, University Park, USA
Hulse-Kemp AM, Maheshwari S, Stoffel K, Hill TA, Jaffe D, Williams S et al (2018) Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Hort Res. https://doi.org/10.1038/s41438-017-0011-0
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30(9):1236–1240. https://doi.org/10.1093/bioinformatics/btu031
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucl Acids Res 45(Database issue), D353–D361. https://doi.org/10.1093/nar/gkw1092
Kang YJ, Ahn YK, Kim KT, Jun TH (2016) Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance. BMC Plant Biol 16:235
Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278
Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT et al (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 18:210. https://doi.org/10.1186/s13059-017-1341-9
Leonore R, Shabari S, Donghui L, Eva H (2017) Using the arabidopsis information resource (TAIR) to find information about arabidopsis genes. Curr Prot Bioinformat 60(1):11111–111145. https://doi.org/10.1002/cpbi36
Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Richter J et al (2002) Apollo: a sequence annotation editor. Genome Biol 3(12). https://doi.org/10.1186/gb-2002-3-12-research0082
Li YH, Zhao SC, Ma JX, Li D, Yan L, Li J et al (2013) Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genom 14:579. https://doi.org/10.1186/1471-2164-14-579
Maumus F, Quesneville H (2016) Impact and insights from ancient repetitive elements in plant genomes. Curr Opin Plant Biol 30:41–46. https://doi.org/10.1016/jpbi201601003
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS-LRR–encoding genes in Arabidopsis. Plant Cell 15:809–834
Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457(7231):843–848
Qin C, Yu C, Shen Y, Fang X, Chen L, Min J et al (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111:5135–5140
The Gene Ontology Consortium (2017) Expansion of the gene ontology knowledgebase and resources. Nucl Acids Res 45(Database issue):D331–D338. https://doi.org/10.1093/nar/gkw1108
The UniProt Consortium (2015) UniProt: a hub for protein information. Nucl Acids Res 43(Database issue):D204–D212. https://doi.org/10.1093/nar/gku989
Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 30,485(7400):635–641. https://doi.org/10.1038/nature11119
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276. https://doi.org/10.1016/0040-5809(75)90020-9
Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB (2017) Direct determination of diploid genome sequences. Genome Res 27:757–767
Wu F, Eanetta NT, Xu Y, Durrett R, Mazourek M, Jahn MM, Tanksley SD (2009) A COSII genetic map of the pepper genome provides a detailed picture synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. Theor Appl Genet 118:1279–1293. https://doi.org/10.1007/s00122-009-0980-y
Yandell M, Ence D (2012) A beginners guide to eukaryotic genome annotation. Nat Rev Gen 13:329. https://doi.org/10.1038/nrg3174
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Tripodi, P., Acquadro, A., Lanteri, S., D’Agostino, N. (2019). Genome Sequencing of Capsicum Species: Strategies, Assembly, and Annotation of Genes. In: Ramchiary, N., Kole, C. (eds) The Capsicum Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-97217-6_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-97217-6_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-97216-9
Online ISBN: 978-3-319-97217-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)