Asaf S., Khan A.L., Khan M.A., Shahzad R., Lubna, Kang S.M., Al-Harrasi A., Al-Rawahi A., Lee I.J. 2018. Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species. PLoS ONE 13(3): e0192966. https://doi.org/10.1371/journal.pone.0192966
Azuma T., Kajita T., Yokoyama J., Ohashi H. 2000. Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data. Am. J. Bot. 87(1): 67-75. https:// doi.org/10.2307/2656686
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17: 540-552. https://doi. org/10.1093/oxfordjournals.molbev.a026334
Chen J.H., Hao Z.D., Xu H.B., Yang L.M., Liu G.X.,Sheng Y., Zheng C., Zheng W.W., Cheng T.L., Shi J.S. 2015. The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng. Front. Plant Sci. 6: 447. https://doi.org/10.3389/ fpls.2015.00447
Chen J.H., Sun H., Wen J., Yang Y.P. 2010. Molecular phylogeny of Salix L. (Salicaceae) inferred from three chloroplast datasets and its systematic implications. Taxon 59: 29-37. https://doi.org/10.1002/tax.591004
Chen Y.N., Hu N., Wu H.T. 2019. Analyzing and characterizing the chloroplast genome of Salix wilsonii. BioMed Res. Int. Article ID: 5190425. https://doi. org/10.1155/2019/5190425
Cronn R., Liston A., Parks M., Gernandt D.S., Shen R., Mockler T. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by- synthesis technology. Nucleic Acids Res. 36: e122. https://doi.org/10.1093/nar/gkn502
Daniell H., Lin C.S., Yu M., Chang W.J. 2016. Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol. 17: 134. https://doi. org/10.1186/s13059-016-1004-2
Darriba D., Taboada G.L., Doallo R., Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 9: 772. https://doi. org/10.1038/nmeth.2109
De Las Rivas J., Lozano J.J., Ortiz A.R. 2002. Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome Res. 12(4): 567-583. https://doi. org/10.1101/gr.209402
Drescher A., Ruf S., Calsa Jr T., Carrer H., Bock R. 2000. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J. 22(2): 97-104. https://doi.org/10.1046/j.1365- 313X.2000.00722.x
Ebert D., Peakall R. 2009. Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol. Ecol. Resour. 9(3): 673-690. https://doi.org/10.1111/j.1755- 0998.2008.02319.x
Eguiluz M., Rodrigues N.F., Guzman F., Yuyama P., Margis R. 2017. The chloroplast genome sequence from Eugenia uniflora, a Myrtaceae from Neotropics. Plant Syst. Evol. 303: 1199-1212. https://doi.org/10.1007/ s00606-017-1431-x
Feng C. H., He C. Y., Wang Y., Zeng Y. F., Zhang J. G. 2019. Phylogenetic position of Chosenia arbutifolia in the Salicaceae inferred from whole chloroplast genome. Forest Res. 32(2): 73-77. https://doi.org/10.13275/j. cnk.lykxyj.2019.02.011
Guisinger M.M., Kuehl J.V., Boore J.L., Jansen R.K. 2011. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol. Biol. Evol. 28: 583-600. https://doi.org/10.1093/molbev/msq229
Hardig T.M., Anttila C.K., Brunsfeld S.J. 2010. A phylogenetic analysis of Salix (Salicaceae) based on matK and ribosomal DNA sequence data. J. Bot. Article ID: 197696. https://doi.org/10.1155/2010/197696
Ingvarsson P.K., Ribstein S., Taylor D.R. 2003. Molecular revolution of insertions and deletion in the chloroplast genome of Silene. Mol. Biol. Evol. 20: 1737-1740. https://doi.org/10.1093/molbev/msg163
Jheng C.F., Chen T.C., Lin J.Y., Chen T.C., Wu W.L., Chang C.C. 2012. The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. Plant Sci. 190:62-73. https://doi.org/10.1016/j. plantsci.2012.04.001
Kadis I. 2005. Chosenia: an amazing tree of Northeast Asia. Arnoldia 63: 8-17.
Katoh K., Kuma K.I., Toh H., Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518. https://doi.org/10.1093/nar/gki198
Kurtz S., Choudhuri J.V., Ohlebusch E., Schleiermacher C., Stoye J., Giegerich R. 2001. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29: 4633-4642. https://doi. org/10.1093/nar/29.22.4633
Leskinen E., Alström-Rapaport C. 1999. Molecular phylogeny of Salicaceae and closely related Flacourtiaceae: evidence from 5.8 S, ITS 1 and ITS 2 of the rDNA. Plant Syst. Evol. 215: 209-227. https://doi. org/10.1007/BF00984656
Li X., Li Y.F., Zang M.Y., Li M.Z., Fang Y.M. 2018. Complete chloroplast genome sequence and phylogenetic analysis of Quercus acutissima. Int. J. Mol. Sci. 19: 2443. https://doi.org/10.3390/ijms19082443
Lohse M., Drechsel O., Bock R. 2007. OrganellarGenomeDRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52: 267-274. https://doi.org/10.1007/s00294-007-0161-y
Lu D.Y., Zhang L., Zhang G.S., Hao L. 2020. Chloroplast genome structure and variation of Salicaceae plants.
J. Northwest A&F Univ. (Nat. Sci. Ed.), 48(2): 87-94. https://doi.org/10.13207/j.cnki.jnwafu.2020.02.011
Mader M., Pakull B., Blanc-Jolivet C., Paulini-Drewes M., Bouda Z.H.N., Degen B., Small I., Kersten B. 2018. Complete chloroplast genome sequences of four Meliaceae species and comparative analyses. Int. J. Mol. Sci. 19: 701. https://doi.org/10.3390/ijms19030701
Mayor C., Brudno M., Schwartz J.R., Poliakov A., Rubin E.M., Frazer K.A., Pachter L.S., Dubchak I. 2000. Vista: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047. https:// doi.org/10.1093/bioinformatics/16.11.1046
McPherson H., van der Merwe M., Delaney S.K., Edwards M.A., Henry R.J., McIntosh E., Rymer P.D., Milner M.L., Siow J., Rossetto M. 2013. Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol. 13: 8. https://doi.org/10.1186/1472-6785-13-8
Moskalyuk T.A. 2016. Chosenia arbutifolia (Salicaceae): life strategies and introduction perspectives. Sibirskij Lesnoj Zurnal (Sib J For Sci) 3: 34-45 (in English with Russian abstract).
Nakai T. 1920. Chosenia, a new genus of Salicaceae. Bot. Mag. (Tokyo) 34: 66-69.
Neuhaus H.E., Emes M.J. 2000. Nonphotosynthetic metabolism in plastids. Annu. Rev. Plant Biol. 51: 111-140. https://doi.org/10.1146/annurev.arplant.51.1.111 Ohashi H. 2001. Salicaceae of Japan. Sci. Rep. Tôhoku Imp. Univ. Ser. 4 40: 269-396.
Palmer J.D. 1985. Comparative organization of chloroplast genomes. Annu. Rev. Genet. 19: 325-354. https://doi. org/10.1146/annurev.ge.19.120185.001545
Powell W., Morgante M., Andre C., McNicol J.W., Machray G.C., Doyle J.J., Tingey S.V., Rafalski
J.A. 1995. Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr. Biol. 5: 1023-1029. https:// doi.org/10.1016/S0960-9822(95)00206-5
Provan J., Powell W., Hollingsworth P.M. 2001. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol. Evol. 16(3): 142-147. https://doi.org/10.1016/S0169-5347(00)02097-8
Raubeson L.A., Peery R., Chumley T.W., Dziubek C., Fourcade H.M., Boore J.L., Jansen R.K. 2007. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8(1): 174. https://doi.org/10.1186/1471-2164-8-174
Skvortsov A.K. 1999. Willows of Russia and adjacent countries. Taxonomical and geographical revision (English translation with additions). Univ. Joensuu. Fac. Math. Nat. Sci. Rep. Ser. 39: 1-307.
Song Y., Dong W.P., Liu B., Xu C., Yao X., Gao J., Corlett R.T. 2015. Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae. Front. Plant Sci. 6: 662. https://doi. org/10.3389/fpls.2015.00662
Soranzo N., Provan J., Powell W. 1999. An example of microsatellite length variation in the mitochondrial genome of conifers. Genome 42: 158-161. https://doi. org/10.1139/g98-111
Sun C.R., Li J., Dai X.J., Chen Y.N. 2018. Analysis and characterization of the Salix suchowensis chloroplast genome. J. For. Res. 29(4): 1003-1011. https://doi. org/10.1007/s11676-017-0531-3
Tangphatsornruang S., Uthaipaisanwong P., Sangsrakru D., Chanprasert J., Yoocha T., Jomchai N., Tragoonrung S. 2011. Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships. Gene 475: 104-112. https://doi. org/10.1016/j.gene.2011.01.002
Tian X.Y., Zheng J.W., Jiao Z.Y., Zhou J., He K.Y., Wang B.S., He X.D. 2019. Transcriptome sequencing and EST-SSR marker development in Salix babylonica and S. suchowensis. Tree Genet. Genomes 15: 9. https://doi. org/10.1007/s11295-018-1315-4
Tóth G., Gáspári Z., Jurka J. 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10: 967-98. https://doi.org/10.1101/ gr.10.7.967
Tu Z.Y. 1982. Breeding and cultivation of Salix. Jiangsu Science and Technology Press, Nanjing, p. 154-196.
Varshney R.K., Graner A., Sorrells M.E. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23(1): 48-55. https:// doi.org/10.1016/j.tibtech.2004.11.005
Walker J.F., Zanis M.J., Emery N.C. 2014. Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae). Am. J. Bot. 101: 722-729. https://doi. org/10.3732/ajb.1400049
Wang R.J., Cheng C.L., Chang C.C., Wu C.L., Su T.M., Chaw S.M. 2008. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol. Biol. 8: 36. https://doi.org/10.1186/1471-2148-8-36
Wang Z., Fang C.F. 1984. Salicaceae. In: Flora Reipublicae Popularis Sinicae. Science Press, Beijing, pp 79-81.
Wicke S., Schneeweiss G.M., DePamphilis C.W., Müller K.F., Quandt D. 2011. The evolution of the plastid chromosome in land plants: Gene content, gene order, gene function. Plant Mol. Biol. 76: 273-297. https://doi. org/10.1007/s11103-011-9762-4
Wu Z.Q. 2015. The new completed genome of purple willow (Salix purpurea) and conserved chloroplast genome structure of Salicaceae. JNSCI 1(3): e49.
Wullschleger S.D., Weston D.J., DiFazio S.P., Tuskan G.A. 2013. Revisiting the sequencing of the first tree genome: Populus trichocarpa. Tree Physiol. 33: 357-364. https:// doi.org/10.1093/treephys/tps081
Wyman S.K., Jansen R.K., Boore J.L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. https://doi.org/10.1093/ bioinformatics/bth352
Zhang L., Xi Z.X., Wang M.C., Guo X.Y., Ma T. 2018.
Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows. Ecol. Evol. 8: 7817-7823. https://doi.org/10.1002/ece3.4261
Zhao J.T., Xu Y., Xi L.J., Yang J.W., Chen H.W., Zhang
J. 2018. Characterization of the chloroplast genome sequence of
Acer miaotaiense: comparative and phylogenetic analyses. Molecules 23: 1740. https://doi. org/10.3390/molecules23071740