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The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa

Year 2021, Volume: 11 Issue: 2, 1504 - 1518, 01.06.2021

Aykut Yılmaz

https://doi.org/10.21597/jist.791414
Cited By: 1

Abstract

The genus Crocus L. (Iridaceae) consists of about 200 species distributed from western Europe and north west Africa to western China. The genus is taxonomically very problematic and day after day it becomes more difficult to understand the relationships between Crocus species because of the identification of new species. Recently, the studies based on DNA sequences are frequently used for the solution of taxonomic problems, the determination of species diversity and especially the evaluation of phylogenetic relationships among the studied taxa. The use of the regions belonging to nuclear DNA and especially chloroplast genome and the combinations of these regions are frequently recommended in many studies. However, there is no information about suitable barcoding regions that can be used for all plant groups. This study focuses on determination of the most succesful barcoding regions, understanding the species discrimination abilities and finally evaluation of phylogenetic relationships among the Crocus taxa using one region from nuclear DNA (ITS1-5.8S rRNA gene-ITS2) and four regions from chloroplast DNA (1. trnK-matK IGS, 2. partial psbA gene-psbA/trnH IGS-partial trnH gene, 3. rpoC1 gene, 4. partial trnL gene-trnL/trnF IGS-partial trnF gene). Sequence informations for related DNA regions were obtained from NCBI. As a result, it can be stated that the region which is only covering ITS1-5.8S rRNA gene-ITS2 separated the all taxa in species level and it is more beneficial for the phylogenetically evaluation of Crocus taxa. Furthermore, dendrogram show taxonomic problems belonging to some species in the genus such as C. biflorus taxa.

Keywords

Crocus nuclear DNA chloroplast DNA C. biflorus

References

  • Addam K, Bou-Hamdan M, Sabbagh N, Takkoush J, Hout K, 2019. Crocus baalbekensis K. Addam and M. Bou Hamdan sp. Nov and its three forms (IRIDACEAE), new endemic species and forms from Lebanon, joined the Lebanese Flora. MOJ Eco Environ Sci., 4(2): 75-83.
  • Alvarez I, Wendel JF, 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29: 417-434.
  • Baytop T, Mathew B, Brıghton C, 1975. Four New Taxa in Turkish Crocus (Iridaceae). Kew Bulletin, 30(2): 241-246.
  • Brıghton CA, Mathew B, Marchant CJ, 1973. Choromosome counts in the genus Crocus (Iridaceae). Kew Bulletin, 28: 451-464.
  • Candan F, 2015. Morphological and Leaf Anatomical Investigations on 2 Yellow Flowered Endemic Taxa of Crocus L. (Crocus ancyrensis, Crocus siehenaus) fromTurkey. International Journal of Agriculture, Forestry and Fisheries, 3(3): 93-98.
  • Chase MW, Cowan RS, Hollıngsworth PM et al., 2007. A proposal for a standardised protocol to barcode all land plants. Taxon, 56(2): 295-299.
  • Coleman AW, 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisions. Trends Genet., 19(7): 370-375.
  • Denk, T. and Grimm, G.W. 2010. The oaks of western Eurasia: Traditional classifications and evidence from two nuclear markers. Taxon. 59(2): 351 ̶ 366.
  • Erol O, Şık L, Kaya HB, Tanyolaç B, Kuçuker O, 2011. Genetic diversity of Crocus antalyensis B. Mathew (Iridaceae) and a new subspecies from southern Anatolia. Plant Syst Evol., 294: 281-287.
  • Erol O, Kaya HB, Şık L, Tuna M, Can L, Tanyolaç MB, 2014. The genus Crocus, series Crocus (Iridaceae) in Turkey and 2 East Aegean islands: a genetic approach. Turk J Biol., 38: 48-62.
  • Erol O, Harpke D, Yıldırım H, 2015. A new Crocus L.(Iridaceae) species from SE Turkey, based on morphological and molecular data. Phytotaxa, 239(3): 223-232.
  • Fılız E, Koç I, 2012. Bitkilerde DNA Barkodları. AKÜ FEBİD, 12: 53-57.
  • Harpke D, 2012. Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466 Gatersleben/Germany.
  • Harpke D, Meng S, Rutten T, Kerndorff H, Blattner FR, 2013. Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: ancient hybridization and chromosome number evolution. Molecular Phylogenetics and Evolution, 66(3): 617-627.
  • Harpke D, 2014. Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466 Gatersleben/Germany.
  • Harpke D, Peruzzı L, Kerndorff H, Karamplıanıs T, Constantınıdıs T, Ranđelovıć V, Ranđelovıć N, Juškovıć M, Pasche E, Blattner FR, 2014. Phylogeny, geographic distribution and new taxonomic circumscription of the Crocus reticulatus species group (Iridaceae). Turkish Journal of Botany, 38: 1182-1198.
  • Harpke D, Carta A, Tomovıć G, Ranđelovıć V, Ranđelovıć N, Blattner FR, Peruzzı L, 2015. Phylogeny, karyotype evolution and taxonomy of Crocus series Verni (Iridaceae). Plant Systematics and Evolution, 301: 309-325.
  • Harpke D, Kerndorff H, Pasche E, Peruzzı L, 2016. Neotypification of the name Crocus biflorus Mill. (Iridaceae) and its consequences in the taxonomy of the genus. Phytotaxa, 260(2): 131-143.
  • Harpke D, 2018. IPK-Gatersleben, Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466 Gatersleben/Germany.
  • Harrıson RG, Larson EL, 2014. Hybridization, Introgression, and the Nature of Species Boundaries. Journal of Heredity, 105: 795-809.
  • Hurkan K, 2017. Karasal bitkilerde DNA barkodlama: Bazı DNA barkod bölgelerinin incelenmesi. The International Journal of Innovative Approaches in Science Research, vol. 1, no. 1.
  • Jonah PM, Bello LL, Lucky O, Mıdau A, Moruppa SM, 2011. Review: the importance of molecular markers in plant breeding programmes. Global Journal of Science Frontier Research, 11: 0975-5896.
  • Karasawa K, 1950. Note on the Cytology of Crocus. Genetica, 25(1): 188-192.
  • Kerndorff H, Pasche E, Harpke D, 2016. The Genus Crocus (Liliiflorae, Iridaceae): Taxonomical Problems and How to Determine a Species Nowadays? STAPFIA, 105: 42-50.
  • Kumar S, Stecher G, Lı M, Knyaz C, Tamura K, 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35: 1547-1549.
  • Mathew B, 1982. The Crocus: a revision of the genus Crocus. BT Batsford Ltd. London 127 pp.
  • Mathew B, 1984. Crocus L. in Davis PH, Flora of Turkey and The East Aegean Islands. Edinburgh University Press, Edinburgh, 8: 413-438.
  • Mosolygo-Lukacs A, Sramko G, Barabas S, Czegledı L, Javor A, Molnar VA, Suranyı G, 2016. Molecular genetic evidence for allotetraploid hybrid speciation in the genus Crocus L. (Iridaceae). Phytotaxa, 258(2): 121-136.
  • NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/genbank.
  • Petersen G, Seberg O, Thorsøe S, Jørgensen T, Mathew B, 2008. A phylogeny of the genus Crocus (Iridaceae) based on sequence data from five plastid regions. Taxon, 57(2): 487-499.
  • Roma-Marzıo F, Harpke D, Peruzzı L, 2018. Rediscovery of Crocus biflorus var. estriatus (Iridaceae) and its taxonomic characterisation. Italian Botanist, 6: 23-30.
  • Saxena RB, 2016. Botany, Taxonomy and Cytology of Crocus Series Intertexti. Indo. American Journal of Pharmaceutical Sciences, 3(4): 321-323.
  • Schorı M, Emch K, Kıtko AR, Shınwarı ZK, Showalter AM, 2018. National Germplasm Resourches Laboratory, Agricultural Research Service, USDA, 10300 Baltimore Ave., Beltsville, MD 20705 USA.
  • Seberg O, Petersen G, 2009. How many loci does it take to DNA barcode a Crocus? PLoS One, 4(2): E4598.
  • Sramko G, 2008. Sequence variability of the nrITS in the Ophrys fuciflora species-complex of the Mediterranean bee-orchid (Ophrys L.) genus. Department of Botany. University of Debrecen, Debrecen.
  • Sramko G, Attıla MV, Hawkıns JA, Bateman RM, 2014. Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae). Annals of Botany, 114(8): 1609-1626.
  • Tamura K, Neı M, Kumar S, 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101: 11030-11035.
  • Uslu E, Babaç MT, Yılmaz A (2012). Karyological Studies On Some Crocus L. Taxa From Turkey. Caryologia: Caryologia: International Journal of Cytology, Cytosystematics and Cytogenetics, 65(1): 7–10.

The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa

Year 2021, Volume: 11 Issue: 2, 1504 - 1518, 01.06.2021

Aykut Yılmaz

https://doi.org/10.21597/jist.791414
Cited By: 1

Abstract

The genus Crocus L. (Iridaceae) consists of about 200 species distributed from western Europe and north west Africa to western China. The genus is taxonomically very problematic and day after day it becomes more difficult to understand the relationships between Crocus species because of the identification of new species. Recently, the studies based on DNA sequences are frequently used for the solution of taxonomic problems, the determination of species diversity and especially the evaluation of phylogenetic relationships among the studied taxa. The use of the regions belonging to nuclear DNA and especially chloroplast genome and the combinations of these regions are frequently recommended in many studies. However, there is no information about suitable barcoding regions that can be used for all plant groups. This study focuses on determination of the most succesful barcoding regions, understanding the species discrimination abilities and finally evaluation of phylogenetic relationships among the Crocus taxa using one region from nuclear DNA (ITS1-5.8S rRNA gene-ITS2) and four regions from chloroplast DNA (1. trnK-matK IGS, 2. partial psbA gene-psbA/trnH IGS-partial trnH gene, 3. rpoC1 gene, 4. partial trnL gene-trnL/trnF IGS-partial trnF gene). Sequence informations for related DNA regions were obtained from NCBI. As a result, it can be stated that the region which is only covering ITS1-5.8S rRNA gene-ITS2 separated the all taxa in species level and it is more beneficial for the phylogenetically evaluation of Crocus taxa. Furthermore, dendrogram show taxonomic problems belonging to some species in the genus such as C. biflorus taxa.

Keywords

Crocus nuclear DNA chloroplast DNA C. Biflorus

References

  • Addam K, Bou-Hamdan M, Sabbagh N, Takkoush J, Hout K, 2019. Crocus baalbekensis K. Addam and M. Bou Hamdan sp. Nov and its three forms (IRIDACEAE), new endemic species and forms from Lebanon, joined the Lebanese Flora. MOJ Eco Environ Sci., 4(2): 75-83.
  • Alvarez I, Wendel JF, 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29: 417-434.
  • Baytop T, Mathew B, Brıghton C, 1975. Four New Taxa in Turkish Crocus (Iridaceae). Kew Bulletin, 30(2): 241-246.
  • Brıghton CA, Mathew B, Marchant CJ, 1973. Choromosome counts in the genus Crocus (Iridaceae). Kew Bulletin, 28: 451-464.
  • Candan F, 2015. Morphological and Leaf Anatomical Investigations on 2 Yellow Flowered Endemic Taxa of Crocus L. (Crocus ancyrensis, Crocus siehenaus) fromTurkey. International Journal of Agriculture, Forestry and Fisheries, 3(3): 93-98.
  • Chase MW, Cowan RS, Hollıngsworth PM et al., 2007. A proposal for a standardised protocol to barcode all land plants. Taxon, 56(2): 295-299.
  • Coleman AW, 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisions. Trends Genet., 19(7): 370-375.
  • Denk, T. and Grimm, G.W. 2010. The oaks of western Eurasia: Traditional classifications and evidence from two nuclear markers. Taxon. 59(2): 351 ̶ 366.
  • Erol O, Şık L, Kaya HB, Tanyolaç B, Kuçuker O, 2011. Genetic diversity of Crocus antalyensis B. Mathew (Iridaceae) and a new subspecies from southern Anatolia. Plant Syst Evol., 294: 281-287.
  • Erol O, Kaya HB, Şık L, Tuna M, Can L, Tanyolaç MB, 2014. The genus Crocus, series Crocus (Iridaceae) in Turkey and 2 East Aegean islands: a genetic approach. Turk J Biol., 38: 48-62.
  • Erol O, Harpke D, Yıldırım H, 2015. A new Crocus L.(Iridaceae) species from SE Turkey, based on morphological and molecular data. Phytotaxa, 239(3): 223-232.
  • Fılız E, Koç I, 2012. Bitkilerde DNA Barkodları. AKÜ FEBİD, 12: 53-57.
  • Harpke D, 2012. Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466 Gatersleben/Germany.
  • Harpke D, Meng S, Rutten T, Kerndorff H, Blattner FR, 2013. Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: ancient hybridization and chromosome number evolution. Molecular Phylogenetics and Evolution, 66(3): 617-627.
  • Harpke D, 2014. Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466 Gatersleben/Germany.
  • Harpke D, Peruzzı L, Kerndorff H, Karamplıanıs T, Constantınıdıs T, Ranđelovıć V, Ranđelovıć N, Juškovıć M, Pasche E, Blattner FR, 2014. Phylogeny, geographic distribution and new taxonomic circumscription of the Crocus reticulatus species group (Iridaceae). Turkish Journal of Botany, 38: 1182-1198.
  • Harpke D, Carta A, Tomovıć G, Ranđelovıć V, Ranđelovıć N, Blattner FR, Peruzzı L, 2015. Phylogeny, karyotype evolution and taxonomy of Crocus series Verni (Iridaceae). Plant Systematics and Evolution, 301: 309-325.
  • Harpke D, Kerndorff H, Pasche E, Peruzzı L, 2016. Neotypification of the name Crocus biflorus Mill. (Iridaceae) and its consequences in the taxonomy of the genus. Phytotaxa, 260(2): 131-143.
  • Harpke D, 2018. IPK-Gatersleben, Taxonomy and Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, D-06466 Gatersleben/Germany.
  • Harrıson RG, Larson EL, 2014. Hybridization, Introgression, and the Nature of Species Boundaries. Journal of Heredity, 105: 795-809.
  • Hurkan K, 2017. Karasal bitkilerde DNA barkodlama: Bazı DNA barkod bölgelerinin incelenmesi. The International Journal of Innovative Approaches in Science Research, vol. 1, no. 1.
  • Jonah PM, Bello LL, Lucky O, Mıdau A, Moruppa SM, 2011. Review: the importance of molecular markers in plant breeding programmes. Global Journal of Science Frontier Research, 11: 0975-5896.
  • Karasawa K, 1950. Note on the Cytology of Crocus. Genetica, 25(1): 188-192.
  • Kerndorff H, Pasche E, Harpke D, 2016. The Genus Crocus (Liliiflorae, Iridaceae): Taxonomical Problems and How to Determine a Species Nowadays? STAPFIA, 105: 42-50.
  • Kumar S, Stecher G, Lı M, Knyaz C, Tamura K, 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35: 1547-1549.
  • Mathew B, 1982. The Crocus: a revision of the genus Crocus. BT Batsford Ltd. London 127 pp.
  • Mathew B, 1984. Crocus L. in Davis PH, Flora of Turkey and The East Aegean Islands. Edinburgh University Press, Edinburgh, 8: 413-438.
  • Mosolygo-Lukacs A, Sramko G, Barabas S, Czegledı L, Javor A, Molnar VA, Suranyı G, 2016. Molecular genetic evidence for allotetraploid hybrid speciation in the genus Crocus L. (Iridaceae). Phytotaxa, 258(2): 121-136.
  • NCBI, National Centre of Biotechnology Information, https://www.ncbi.nlm.nih.gov/genbank.
  • Petersen G, Seberg O, Thorsøe S, Jørgensen T, Mathew B, 2008. A phylogeny of the genus Crocus (Iridaceae) based on sequence data from five plastid regions. Taxon, 57(2): 487-499.
  • Roma-Marzıo F, Harpke D, Peruzzı L, 2018. Rediscovery of Crocus biflorus var. estriatus (Iridaceae) and its taxonomic characterisation. Italian Botanist, 6: 23-30.
  • Saxena RB, 2016. Botany, Taxonomy and Cytology of Crocus Series Intertexti. Indo. American Journal of Pharmaceutical Sciences, 3(4): 321-323.
  • Schorı M, Emch K, Kıtko AR, Shınwarı ZK, Showalter AM, 2018. National Germplasm Resourches Laboratory, Agricultural Research Service, USDA, 10300 Baltimore Ave., Beltsville, MD 20705 USA.
  • Seberg O, Petersen G, 2009. How many loci does it take to DNA barcode a Crocus? PLoS One, 4(2): E4598.
  • Sramko G, 2008. Sequence variability of the nrITS in the Ophrys fuciflora species-complex of the Mediterranean bee-orchid (Ophrys L.) genus. Department of Botany. University of Debrecen, Debrecen.
  • Sramko G, Attıla MV, Hawkıns JA, Bateman RM, 2014. Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae). Annals of Botany, 114(8): 1609-1626.
  • Tamura K, Neı M, Kumar S, 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101: 11030-11035.
  • Uslu E, Babaç MT, Yılmaz A (2012). Karyological Studies On Some Crocus L. Taxa From Turkey. Caryologia: Caryologia: International Journal of Cytology, Cytosystematics and Cytogenetics, 65(1): 7–10.
There are 38 citations in total.

Details

Primary Language English
Journal Section Moleküler Biyoloji ve Genetik / Moleculer Biology and Genetic
Authors

Aykut Yılmaz 0000-0002-0327-8388

Publication Date June 1, 2021
Submission Date September 7, 2020
Acceptance Date December 3, 2020
Published in Issue Year 2021 Volume: 11 Issue: 2

Cite

APA Yılmaz, A. (2021). The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa. Journal of the Institute of Science and Technology, 11(2), 1504-1518. https://doi.org/10.21597/jist.791414
AMA Yılmaz A. The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa. J. Inst. Sci. and Tech. June 2021;11(2):1504-1518. doi:10.21597/jist.791414
Chicago Yılmaz, Aykut. “The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa”. Journal of the Institute of Science and Technology 11, no. 2 (June 2021): 1504-18. https://doi.org/10.21597/jist.791414.
EndNote Yılmaz A (June 1, 2021) The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa. Journal of the Institute of Science and Technology 11 2 1504–1518.
IEEE A. Yılmaz, “The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa”, J. Inst. Sci. and Tech., vol. 11, no. 2, pp. 1504–1518, 2021, doi: 10.21597/jist.791414.
ISNAD Yılmaz, Aykut. “The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa”. Journal of the Institute of Science and Technology 11/2 (June 2021), 1504-1518. https://doi.org/10.21597/jist.791414.
JAMA Yılmaz A. The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa. J. Inst. Sci. and Tech. 2021;11:1504–1518.
MLA Yılmaz, Aykut. “The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa”. Journal of the Institute of Science and Technology, vol. 11, no. 2, 2021, pp. 1504-18, doi:10.21597/jist.791414.
Vancouver Yılmaz A. The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa. J. Inst. Sci. and Tech. 2021;11(2):1504-18.

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