Botanica Pacifica. A journal of plant science and conservation 2014. 3(1): 3-19.
Article first published online: 30 APR 2014 | DOI: 10.17581/bp.2014.03101
Phylogenetic Analysis of the Far Eastern Salix (Salicaceae) Based on Sequence Data from Chloroplast DNA Regions and ITS of Nuclear Ribosomal DNA
Vyacheslav Y. Barkalov & Marina M. Kozyrenko
Institute of Biology & Soil Science FEB RAS, Vladivostok 690022 Russia
In order to further elucidate the relationships in the Salix genus, phylogenetic analysis was conducted based on comparison of the nucleotide sequences of the chloroplast DNA regions (petG-trnP, petN-psbM, psaA-ycf3, psbM-trnD, rpoB-trnC, trnC-petN, trnD-trnT, trnS-psbZ, rbcL, matK) and the ITS region (ITS1-5.8S rRNA-ITS2) of nuclear ribosomal DNA of 86 Salix species from three subgenera: Salix, Chamaetia, Vetrix, 27 sections and Chosenia arbutifolia. The previously recognized genera Chosenia and Toisusu merged with Salix. The divergence of species in the Salix genus (according to ITS and cpDNA data) was very low. In most species from Chamaetia and Vetrix subgenera, the sequences differed by several substitutions or were identical. Molecular differences were identified mainly in species belonging to the subgenus Salix in its previous broad meaning. ITS-phylogeny generally agrees with the most-recent infrageneric classification of Salix: the isolation of subgenera Pleuradenia, Chosenia, Salix (for exception sect. Triandrae), Longifoliae has been well supported, but the isolation of subgenera Protitea and Chamaetia is not supported. Relationships between the subgenera Chamaetia and Vetrix remain unresolved. High similarity of the plastid and nuclear genomes revealed in the majority of Salix species included in the analysis may indicate that they have relatively recently diverged from a common ancestor or there is a result of lineage sorting through hybridization.
Баркалов В.Ю., Козыренко М.М. Филогенетический анализ дальневосточных Salix (Salicaceae), основанный на данных секвенирования регионов хлоропластной ДНК и ITS ядерной рибосомной ДНК. С целью дальнейшего выяснения взаимоотношений в роде Salix проведен филогенетический анализ на основе сравнения нуклеотидных последовательностей регионов хлоропластной ДНК (petG-trnP, petN-psbM, psaA-ycf3, psbM-trnD, rpoB-trnC, trnC-petN, trnD-trnT, trnS-psbZ, rbcL, matK ) и ITS региона (ITS1-5.8S rRNA-ITS2) ядерной рибосомной ДНК 86 видов Salix из трёх подродов: Salix, Chamaetia, Vetrix и 27 секций, а также Chosenia arbutifolia. Дивергенция видов внутри рода Salix по данным ITS и хпDNA была очень низкой, у большинства видов из подродов Chamaetia и Vetrix последовательности различались несколькими заменами или были идентичны. Молекулярные различия выявлены главным образом у видов, принадлежащих подроду Salix в прежнем широком его понимании. ITS-филогения согласуется, в основном, с современными классификационными схемами рода Salix на уровне подродов: хорошо поддерживает выделение подродов Pleuradenia, Chosenia, Salix (за исключением sect. Triandrae), Longifoliae, но не поддерживает выделение подродов Protitea и Chamaetia. Взаимоотношения подродов Chamaetia и Vetrix остаются не разрешенными. Высокое сходство пластидного и ядерного геномов, выявленное у большинства включенных в анализ видов Salix, может указывать на их относительно недавнюю дивергенцию от общего предка или на пересечение генеалогических линий через гибридизацию.
Keywords: chloroplast DNA, ITS, phylogenetic analysis, Salicaceae, Salix, хлоропластная ДНК, филогенетический анализ
References
Abdollahzadeh A, Kazempour Osaloo S & Maassoumi AA 2011. Molecular phylogeny of the genus Salix (Salicaceae) with an emphasize to its species in Iran. Iranian Journal of Botany 17: 244-253.
Argus GW 1997. Infrageneric classification of Salix (Salicaceae) in the New World. Systematic Botany Monographs 52: 1-121. CrossRef
Argus GW 2010. Salix. In: Flora of North America North of Mexico. (Flora of North America Editorial Committee, eds.). Vol. 7, pp. 23-162. Oxford University Press, New York, NY, and Oxford, UK.
Azuma T, Kajita T, Yokoyama J & Ohashi H 2000. Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data. American Journal of Botany 87: 67-75. CrossRef
Barkalov VY 2012. New Salix (Salicaceae) from the Russian Far East. Botanicheskii Zhurnal 97(6): 797-806 (in Russian with English summary). [Баркалов В.Ю. Новые виды Salix (Salicaceae) с российского Дальнего Востока//Ботанический журнал. 2012. Т. 97, № 6. С. 797-806 (с вклейкой).]
Bolshakov NM 1992. Salicaceae. In: Flora of Siberia (Krasnoborov I.M. & Malyschev L.I. eds.). Vol. 5, pp. 8-59 (in Russian). Nauka, Novosibirsk. [Большаков Н.М. 1992. Salicaceae//Флора Сибири/под ред. Красноборова И.М., Малышева Л.И. Новосибирск: Наука. Т. 5. С. 8-59.]
Bonfield JK, Smith KF & Staden R 1995. A new DNA sequence assembly program. Nucleic Acids Research 23: 4992-4999. CrossRef
Borchsenius F 2009. FastGap 1.2. Department of Biological Sciences, University of Aarhus, Denmark. Published online at http://192.38.46.42/aubot/fb/FastGap_home.htm
Brunsfeld SJ, Miller TR & Carstens BC 2007. Insights into the Biogeography of the Pacific Northwest of North America: Evidence from the Phylogeography of Salix melanopsis. Systematic Botany 32: 129-139. CrossRef
Brunsfeld SJ & Antilla CK 2004. Complexities in the phylogeny of Salix (Salicaceae). Botany. Systematic section/ASPT. Cottonwood B (Snowbird Center). Abstract ID: 791.
Brunsfeld SJ, Soltis DE & Soltis PS 1992. Evolutionary patterns and processes in Salix sect. Longifoliae: evidence from chloroplast DNA. Systematic Botany 17: 239-256. CrossRef
Chao N 1996. On the problems of the classification of Toisusu Kimura (Salicaceae) in Northeastern Asia. Journal of Sichuan Forestry Science and Technology 17(2): 12-15.
Chao N, Gong GT & Liu J 1998. On the classification and distribution of the family Salicaceae. Journal of Sichuan Forestry Science and Technology 19(4): 9-20.
Chao N, Gong GT & Liu J 2010. On the subdivision of the genus Pleiarina Rafin. [sic] (Salicaceae). Journal of Sichuan Forestry Science and Technology 31(5): 8-20.
Chen JH, Sun H, Wen J & Yang YP 2008. Cladistic analysis of the genus Salix (Salicaceae). Acta Metallurgica Sinica 30: 1-7.
Chen JH, Wen J & Yang YP 2010. Molecular phylogeny of Salix L. (Salicaceae) inferred from three chloroplast datasets and its systematic implications. Taxon 59: 29-37.
Clement M, Posada D & Crandall KA 2000. TCS: A computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659. CrossRef
Demesure B, Sodzi N & Petit RJ 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4: 129-131. CrossRef
Dorn RD 1976. A synopsis of American Salix. Canadian Journal of Botany 54: 2769-2789. CrossRef
Fang CF, Zhao SD & Skvortsov AK 1999. Salicaceae. In: Flora of China. (Wu Z.Y, Raven P.H., eds.). Vol. 4, pp. 139-274. Science Press, Beijing; Missouri Botanical Garden Press, St. Louis
Felsenstein J 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791. CrossRef
Galtier N, Gouy M & Gautier C 1996. SeaView and Phylowin, two graphic tools for sequence alignment and molecular phylogeny. Computer Applications in the Biosciences 12: 543-548.
Hamza-Babiker N, Heinze B, Glössl J & Arnold C 2009. Chloroplast DNA identification of eight closely related European Salix species. Austrian Journal of Forest Science 126: 175-193.
Hardig TM, Anttila CK & Brunsfeld SJ 2010. A phylogenetic analysis of Salix (Salicaceae) based on matK and ribosomal DNA sequence data. Journal of Botany 2010: 1-12 (Article ID 197696, 12 pages, 2010). CrossRef
Hardig TM, Brunsfeld SJ, Fritz RS, Morgan M & Orians CM 2000. Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone. Molecular Ecolology 9: 9-24. CrossRef
Heinze B 2007. A database of PCR primers for the chloroplast genomes of higher plants. Plant Methods 3-4: 1-7.
Huang SSF, Hwang SY & Lin TP 2002. Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia. Molecular Ecology 11: 2349-2358. CrossRef
Kimura A 1928. Über Toisusu -eine neue Salicaceen-Gattung und die systematische Stellung derselben. Botanical Magazine (Tokyo) 42: 287-290.
Kimura A 1931. The scientific name of Japanese "Salix viminalis (non L.)". Botanical Magazine (Tokyo) 45: 28 (in Japanese).
Kimura A 1937. Symbolae Iteologicae IV. Science Reports of the Tohoku Imperial University, Series 4, Biology 12: 311-321.
Kimura A 1938. Symbolae Iteologicae VI. Science Reports of the Tohoku Imperial University, Series 4, Biology 13: 390-394.
Kimura A 1988. De Salicis subgenera Pleuradenia commentation. Science Reports of the Tohoku University, Series 4, Biology 39(3): 143-147.
Kimura A 1989. Salicaceae. In: Wild flowers of Japan woody plants. (Satake Y., Hara H., Watari S. & Tominari T. eds.). Vol. 1, pp. 31-51, pls. 39-58. Heibonsha Ltd. Publisher, Tokyo (in Japanese).
Leskinen E & Alström-Rapoport C 1999. Molecular phylogeny of Salicaceae and closely related Flacourtiaceae: Evidence from 5.8 S, ITS 1 and ITS 2 of the rDNA. Plant Systematics and Evolution 215: 209-227. CrossRef
Lim GS & Carvalho MR 2013. A reconsideration of the typification of Rafinesque generic names allied to Salix L. Rhodora 115(962):170-190, doi: http://dx.doi.org/10.3119/12-11. DOI: 10.3119/12-11 CrossRef
Liu M, Zhu F, Liu Z, Zhang H 2012. Phylogenetic relationship among Salix species based on ITS sequences. Guizhou Forestry Science and Technology 4: 30-35.
Mir BA, Koul S, Kumar A, Kaul MK, Soodan AS & Raina SN 2010. Intraspecific variation in the internal transcribed spacer (ITS) regions of rDNA in Withania somnifera (Linn.) Dunal. Indian Journal of Biotechnology 9: 325-328.
Mosseler A 1989. Interspecific pollen-pistil incongruity in Salix. Canadian Journal of Forestry Research 19: 1161-1168. CrossRef
Mosseler A 1990. Hybrid performance and species crossability relationships in willows (Salix). Canadian Journal of Botany 68: 2329-2338. CrossRef
Nasarow MI 1936. Salix. In: Flora of the USSR. (Komarov V.L. ed.). Vol. 5, pp. 24-216, 707-713 (in Russian). [Назаров М.И. 1936. Salix//Флора СССР/под ред. Комарова В.Л. Т. 5. М., Л.: Издательство АН СССР. С. 24-216, 707-713.]
Nedoluzhko VA 1995. Salicaceae. In: Plantae Vasculares Orientis Extremi Sovietici. (Kharkevich S.S. ed.). Vol. 7, pp. 145-212. Nauka, Saint-Petersburg (in Russian). [Недолужко В.А. 1995а. Salicaceae//Сосудистые растения советского Дальнего Востока/под ред. Харкевича С.С. Т. 7. Санкт-Петербург: Наука. С. 145-212.]
Nedoluzhko VA 1995. Conspectus of dendroflora of the Russian Far East (Baranov V.I. ed.). 208 p. Dal'nauka, Vladivostok (in Russian). [Недолужко В.А. 1995б. Конспект дендрофлоры российского Дальнего Востока/под ред. Баранова В.И. 208 с. Владивосток: Дальнаука.]
Ohashi H 2000. A systematic enumeration of Japanese Salix (Salicaceae). Journal of Japanese Botany 75(1):1—41.
Ohashi H 2001. Salicaceae of Japan. Science Reports of the Tohoku University, Series 4, Biology 40(4): 269-396.
Pleines T, Jakob SS & Blattnerl FR 2009. Application of noncoding DNA regions in intraspecific analyses. Plant Systematics and Evolution 282: 281-294. CrossRef
Probatova NS, Kazanovsky SG, Rudyka EG, Barkalov VY, Seledets VP & Nechaev VA 2011. In: IAPT/IOPB chromosome data 12 (K. Marhold ed.) Taxon 60(6): 1790-1794.
Rozas J, Sanchez-Delbarrio JC, Messeguer X & Rozas R 2003. DnaSP, DNApolymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497. CrossRef
Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE & Small RL 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-166. CrossRef
Simmons MP & Ochoterena H 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381. CrossRef
Skvortsov AK 1966. Salicaceae. In: Flora Arctica URSS. (Tolmatchev A.I., ed.). Vol. 5, pp. 7-118. Nauka Publishers, Moscow, Leningrad (in Russian). [Скворцов А.К. 1966. Salicaceae//Арктическая флора СССР/под ред. А.И. Толмачева. Т. 5. С. 7-118. М., Л.: Наука]
Skvortsov AK 1999. Willows of Russia and adjacent countries. Taxonomical and geographical revision. University of Joensuu Report. Series No 39 Biology. Joensuu, Finland. P. 1-307.
Skvortsov AK 1968. Willows of the USSR. A taxonomic and geographic revision. In: Proceedings of the study of the fauna and flora of the USSR, published by Moscow Society of Naturalists (V.N. Tikhomirov ed.). New ser., Sect. Bot. 15 (XXIII). 263 с. Nauka, Moscow (in Russian). [Скворцов А.К. 1968. Ивы СССР: систематический и географический обзор//Материалы к познанию фауны и флоры СССР, издаваемые Московским обществом испытателей природы/под ред. В.Н. Тихомирова. Новая серия, Отд. ботанический. Вып. 15 (XXIII). 263 с. Москва: Наука.]
Sohma K 1993. Pollen diversity in Salix (Salicaceae). Science Reports of the Tohoku University, ser. 4, Biology 40: 77-178.
Sourdis J & Nei M 1988. Relative efficiencies of the maximum and distance-matrix methods in obtaining the correct phylogenetic tree. Molecular Biology and Evolution 5: 298-311.
Staden R, Beal KF & Bonfield JK 1999. The Staden Package 1998. Computer Methods in Molecular Biology 132: 115-130.
Suda Y 1958. The number of chromosomes in Japanese salicaceous plants. Science Reports of the Tohoku University, ser. 4, Biology 24: 1-4.
Swofford DL, Olsen JL, Waddell PJ & Hillis DM 1996. Phylogenetic inference. In: Molecular systematic. (Hillis D.M., Moritz C., Mable B.K. eds.). P. 407-514. Sinauer Associates, Sunderland, MA.
Swofford DL 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.04. MA: Sinauer Associates, Sunderland.
Trybush S, Jahodová Š, Macalpine W & Karp A 2008. A genetic study of a Salix germplasm resource reveals new insights into relationships among subgenera, sections and species. BioEnergy Research 1: 67-79. CrossRef
Wang C. & Fang CF 1984. Salicaceae. In: Flora Reipublicae Popularis Sinicae. (Wu Z.Y. ed.). Vol. 20, issue 2. P. 79—403. Science Press, Beijing (in Chinese).
Zhang ML 1994. A preliminary cladistic study on the multistaminal willows (Salix) in China. Bulletin of Botanical Research 14: 299-305.
|
|