http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1025257
MITOGENOME ANNOUNCEMENT
The complete chloroplast genome of Cynara humilis Pasquale Luca Curci and Gabriella Sonnante
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/02/15. For personal use only.
Institute of Biosciences and BioResources (IBBR) – National Research Council (CNR), Bari, Italy
Abstract
Keywords
The complete chloroplast genome of the wild thistle Cynara humilis L. (Asteraceae) is presented in this study. The genome is 152,585 bp in length and has a quadripartite structure composed by a large single-copy (LSC) of 83,622 bp, a small single-copy (SSC) of 18,651 bp and two inverted repeats (IRb/a) of 25,156 bp each. The GC content corresponds to 37.7%. The amount of unique genes is 114, in which 17 are duplicated in the IRs, for a total of 131 genes. A maximum parsimony phylogenetic analysis revealed that C. humilis chloroplast genome is closely related to that of the globe artichoke within the Carduoideae subfamily.
Asteraceae, Carduoideae, chloroplast genome, Cynara humilis, phylogeny
Cynara L. is a small genus native to the Mediterranean region, belonging to the Asteraceae family. The genus comprises: (i) the complex species C. cardunculus L. containing the ‘‘wild cardoon’’ as well as the globe artichoke and the cultivated cardoon; (ii) seven (or six according to some authors) additional wild species (Rottenberg, 2014; Wiklund, 1992). Cynara humilis L. is a relatively small thistle, native to southern Spain and Portugal, northern Morocco and western Algeria. Some botanists placed this species in a distinct genus, Bourgaea, due to its revoluted leaf margins and winged achens, which distinguishes it from all the other Cynara species. Eventually, C. humilis was included within Cynara based on morphological and genetic data, and is considered a member of the secondary gene pool of C. cardunculus (Rottenberg & Zohary, 1996; Wiklund, 1992). In the Asteraceae family, the monophyly or polyphyly of the Cynara complex is still a matter of debate (Barres et al., 2013). Cynara humilis has often been analyzed for cp DNA markers and/or ITS-ETS sequences in order to infer phylogeny at the genus or at higher taxonomic levels (Barres et al., 2013; Sonnante et al., 2007). In this study, we amplified and sequenced the whole chloroplast genome of C. humilis, to contribute to
Correspondence: Gabriella Sonnante, Institute of Biosciences and BioResources (IBBR) – National Research Council (CNR), Via Amendola, 165/A - 70126 Bari, Italy. Tel: (+39) 0805583400. E-mail: [email protected]
History Received 27 January 2015 Revised 24 February 2015 Accepted 28 February 2015 Published online 26 March 2015
the current understanding of phylogenetic relationships within the genus Cynara and, at a higher level, with other Asteraceae species. Cynara humilis DNA, obtained from fresh leaves (Sonnante et al., 2002), was used for cp DNA isolation using long-range PCR with primers designed on C. cardunculus cp genome (Curci et al., in press). DNA sample is stored at the CNR-IBBR DNA bank. Chloroplast fragments were sent to IGA Technology Services (Udine) for Miseq/Illumina sequencing. The complete sequence was annotated with DOGMA software (Wyman et al., 2004); coding sequences, tRNAs and rRNAs were confirmed and, in some cases, manually adjusted after BLASTn searches. The annotated sequence was then submitted to GenBank (accession number KP299292). The complete cp genome sequence of C. humilis is 152,585 bp in length. The GC content corresponds to 37.7%. The cp typical quadripartite structure involves two inverted repeats (IRb and IRa) of 25,156 bp each, a large single-copy (LSC) region of 83,622 bp and a small single-copy (SSC) region of 18,651 bp. The whole cp genome is made of 114 unique genes: 80 protein-coding, 30 tRNA and 4 rRNA genes. Total number of genes sums up to 131, when considering gene duplication in the IRs. The complete sequence was used to infer phylogenetic relationships among the main representatives of Asteraceae, for which the cp genome is available, including the globe artichoke (Figure 1). A maximum parsimony analysis was performed with Mega 6.0 (Tamura et al., 2013) using 500 bootstrap replicates and setting Panax ginseng (Araliaceae) as the outgroup. The phylogenetic tree delivered bootstrap values higher than 89 in all nodes and grouped all considered species in the three main Asteraceae subfamilies: Asteroideae, Cichorioideae and Carduoideae. The monophyletic group of Asteroideae is related to Lactuca sativa (Cichorioideae), whereas C. cardunculus and C. humilis (Carduoideae) are more distantly related.
2
P. L. Curci & G. Sonnante
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/02/15. For personal use only.
Figure 1. Maximum parsimony phylogenetic tree based on chloroplast genome sequences from ten Asteraceae and one Araliaceae species. Accession numbers: Guizotia abyssinica EU549769, Ageratina adenophora NC_015621, Helianthus annuus NC007977, Parthenium argentatum NC_013553, Jacobaea vulgaris HQ234669, Chrysanthemum morifolium JQ362483, Artemisia frigida NC_020607, Lactuca sativa DQ383816, Cynara cardunculus KM035764, C. humilis KP299292, Panax ginseng KF431956.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Barres L, Sanmartı´n I, Anderson CL, Susanna A, Buerki S, GalbanyCasals M, Vilatersana R. (2013). Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae). Am J Botany 100:867–82. Curci PL, De Paola D, Danzi D, Vendramin GG, Sonnante G. (2015). Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae. PLoS ONE 10:e0120589. doi: 10.1371/journal.pone.0120589. Rottenberg A, Zohary D. (1996). The wild ancestry of the cultivated artichoke. Genet Resour Crop Evol 43:53–8.
Rottenberg A. (2014). The wild gene pool of globe artichoke. Israel J Plant Sci DOI: 10.1080/07929978.2014.887379. Sonnante G, Carluccio AV, Vilatersana R, Pignone D. (2007). On the origin of artichoke and cardoon from the Cynara gene pool as revealed by rDNA sequence variation. Genet Resour Crop Evol 54: 483–95. Sonnante G, De Paolis A, Lattanzio V, Perrino P. (2002). Genetic variation in wild and cultivated artichoke revealed by RAPD markers. Genet Resour Crop Evol 49:247–52. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–9. Wiklund A. (1992). The genus Cynara L. (Asteraceae-Cardueae). Bot J Linn Soc 109:75–123. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
MITOGENOME ANNOUNCEMENT
The complete chloroplast genome of Cynara humilis Pasquale Luca Curci and Gabriella Sonnante
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/02/15. For personal use only.
Institute of Biosciences and BioResources (IBBR) – National Research Council (CNR), Bari, Italy
Abstract
Keywords
The complete chloroplast genome of the wild thistle Cynara humilis L. (Asteraceae) is presented in this study. The genome is 152,585 bp in length and has a quadripartite structure composed by a large single-copy (LSC) of 83,622 bp, a small single-copy (SSC) of 18,651 bp and two inverted repeats (IRb/a) of 25,156 bp each. The GC content corresponds to 37.7%. The amount of unique genes is 114, in which 17 are duplicated in the IRs, for a total of 131 genes. A maximum parsimony phylogenetic analysis revealed that C. humilis chloroplast genome is closely related to that of the globe artichoke within the Carduoideae subfamily.
Asteraceae, Carduoideae, chloroplast genome, Cynara humilis, phylogeny
Cynara L. is a small genus native to the Mediterranean region, belonging to the Asteraceae family. The genus comprises: (i) the complex species C. cardunculus L. containing the ‘‘wild cardoon’’ as well as the globe artichoke and the cultivated cardoon; (ii) seven (or six according to some authors) additional wild species (Rottenberg, 2014; Wiklund, 1992). Cynara humilis L. is a relatively small thistle, native to southern Spain and Portugal, northern Morocco and western Algeria. Some botanists placed this species in a distinct genus, Bourgaea, due to its revoluted leaf margins and winged achens, which distinguishes it from all the other Cynara species. Eventually, C. humilis was included within Cynara based on morphological and genetic data, and is considered a member of the secondary gene pool of C. cardunculus (Rottenberg & Zohary, 1996; Wiklund, 1992). In the Asteraceae family, the monophyly or polyphyly of the Cynara complex is still a matter of debate (Barres et al., 2013). Cynara humilis has often been analyzed for cp DNA markers and/or ITS-ETS sequences in order to infer phylogeny at the genus or at higher taxonomic levels (Barres et al., 2013; Sonnante et al., 2007). In this study, we amplified and sequenced the whole chloroplast genome of C. humilis, to contribute to
Correspondence: Gabriella Sonnante, Institute of Biosciences and BioResources (IBBR) – National Research Council (CNR), Via Amendola, 165/A - 70126 Bari, Italy. Tel: (+39) 0805583400. E-mail: [email protected]
History Received 27 January 2015 Revised 24 February 2015 Accepted 28 February 2015 Published online 26 March 2015
the current understanding of phylogenetic relationships within the genus Cynara and, at a higher level, with other Asteraceae species. Cynara humilis DNA, obtained from fresh leaves (Sonnante et al., 2002), was used for cp DNA isolation using long-range PCR with primers designed on C. cardunculus cp genome (Curci et al., in press). DNA sample is stored at the CNR-IBBR DNA bank. Chloroplast fragments were sent to IGA Technology Services (Udine) for Miseq/Illumina sequencing. The complete sequence was annotated with DOGMA software (Wyman et al., 2004); coding sequences, tRNAs and rRNAs were confirmed and, in some cases, manually adjusted after BLASTn searches. The annotated sequence was then submitted to GenBank (accession number KP299292). The complete cp genome sequence of C. humilis is 152,585 bp in length. The GC content corresponds to 37.7%. The cp typical quadripartite structure involves two inverted repeats (IRb and IRa) of 25,156 bp each, a large single-copy (LSC) region of 83,622 bp and a small single-copy (SSC) region of 18,651 bp. The whole cp genome is made of 114 unique genes: 80 protein-coding, 30 tRNA and 4 rRNA genes. Total number of genes sums up to 131, when considering gene duplication in the IRs. The complete sequence was used to infer phylogenetic relationships among the main representatives of Asteraceae, for which the cp genome is available, including the globe artichoke (Figure 1). A maximum parsimony analysis was performed with Mega 6.0 (Tamura et al., 2013) using 500 bootstrap replicates and setting Panax ginseng (Araliaceae) as the outgroup. The phylogenetic tree delivered bootstrap values higher than 89 in all nodes and grouped all considered species in the three main Asteraceae subfamilies: Asteroideae, Cichorioideae and Carduoideae. The monophyletic group of Asteroideae is related to Lactuca sativa (Cichorioideae), whereas C. cardunculus and C. humilis (Carduoideae) are more distantly related.
2
P. L. Curci & G. Sonnante
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/02/15. For personal use only.
Figure 1. Maximum parsimony phylogenetic tree based on chloroplast genome sequences from ten Asteraceae and one Araliaceae species. Accession numbers: Guizotia abyssinica EU549769, Ageratina adenophora NC_015621, Helianthus annuus NC007977, Parthenium argentatum NC_013553, Jacobaea vulgaris HQ234669, Chrysanthemum morifolium JQ362483, Artemisia frigida NC_020607, Lactuca sativa DQ383816, Cynara cardunculus KM035764, C. humilis KP299292, Panax ginseng KF431956.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Barres L, Sanmartı´n I, Anderson CL, Susanna A, Buerki S, GalbanyCasals M, Vilatersana R. (2013). Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae). Am J Botany 100:867–82. Curci PL, De Paola D, Danzi D, Vendramin GG, Sonnante G. (2015). Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae. PLoS ONE 10:e0120589. doi: 10.1371/journal.pone.0120589. Rottenberg A, Zohary D. (1996). The wild ancestry of the cultivated artichoke. Genet Resour Crop Evol 43:53–8.
Rottenberg A. (2014). The wild gene pool of globe artichoke. Israel J Plant Sci DOI: 10.1080/07929978.2014.887379. Sonnante G, Carluccio AV, Vilatersana R, Pignone D. (2007). On the origin of artichoke and cardoon from the Cynara gene pool as revealed by rDNA sequence variation. Genet Resour Crop Evol 54: 483–95. Sonnante G, De Paolis A, Lattanzio V, Perrino P. (2002). Genetic variation in wild and cultivated artichoke revealed by RAPD markers. Genet Resour Crop Evol 49:247–52. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–9. Wiklund A. (1992). The genus Cynara L. (Asteraceae-Cardueae). Bot J Linn Soc 109:75–123. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
