References
- Ahuja MR (2005) Polyploidy in gymnosperms revisited. Silvae Genetica 54: 59-69. https://doi.org/10.1515/sg-2005-001010.1515/sg-2005-0010
- Ahuja MR, Neale DB (2005) Evolution of Genome Size in Conifers. Silvae Genetica 54: 126-137. https://doi.org/10.1515/sg-2005-002010.1515/sg-2005-0020
- Ahuja MR, Devey ME, Grover AT, Jermstad KD, Neale DB (1994) Mapped DNA probes from loblolly pine can be used for restriction fragment length polymorphism mapping in other conifers. Theor. Appl.Genet. 88: 279–282. https://doi.org/10.1007/bf0022363210.1007/BF0022363224186006
- Armenise L, Simeone M, Piredda R, Schirone B (2012) Validation of DNA barcoding as an efficient tool for taxon identification and detection of species diversity in Italian conifers. Eur. J. Forest Res. 131: 1337-1353. https://doi.org/10.1007/s10342-012-0602-010.1007/s10342-012-0602-0
- Aronen T, Ryynanen L (2012) Variation in telomere repeats of scots pine (Pinus sylvestris L.). Tree Genetics and Genomes 8: 267-275. https://doi.org/10.1007/s11295-011-0438-710.1007/s11295-011-0438-7
- Auckland L, Johnston J, Price H, Bridgwater F, (2001) Stability of nuclear DNA content among divergent and isolated populations of Fraser fir. Can. J. Bot. 79: 1375–1378. https://doi.org/10.1139/b01-10410.1139/b01-104
- Bagal UR, Leebens-Mack JH, Lorenz WW, Dean JF (2012) The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage. BMC Genomics 13: S1. https://doi.org/10.1186/1471-2164-13-s3-s110.1186/1471-2164-13-S3-S1339442422759610
- Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82: 247–277. https://doi.org/10.2307/239988010.2307/2399880
- Bateman RM, Hilton J, Rudall PJ (2006) Morphological and molecular phylogenetic context of the angiosperms: Contrasting the ’top-down’ and ’bottom-up’ approaches used to infer the likely characteristics of the first flowers. J. Exp. Bot. 57: 3471–3503. https://doi.org/10.1093/jxb/erl12810.1093/jxb/erl12817056677
- Bautista R, Villalobos DP, Díaz-Moreno S, Cantón FR, Cánovas FM, Claros MG (2007) Toward a Pinus pinaster bacterial artificial chromosome library. Ann. For. Sci. 64:855–864. https://doi.org/10.1051/forest:200706010.1051/forest:2007060
- Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95:127–132. https://doi.org/10.1093/aob/mci00810.1093/aob/mci008
- Berube Y, Zhuang J, Rungis D, Ralph S, Bohlmann J, Ritland K (2007) Characterization of EST SSRs in loblolly pine and spruce. Tree Genet Genomes 3 :251– 259. https://doi.org/10.1007/s11295-006-0061-110.1007/s11295-006-0061-1
- Bogunic F, Muratovic E, Brown SC, Siljak-Yakovlev S (2003) Genome size and base composition of five Pinus species from the Balkan region. Plant Cell Reports 22:59-63. https://doi.org/10.1007/s00299-003-0653-210.1007/s00299-003-0653-2
- Bogunic F, Muratovic E, Ballian D, Siljak-Yakovlev SS, Brown SC (2007) Genome size stability among five subspecies of Pinus nigra Arnold s.l. Environmental and Experimental Botany 59: 354-360. https://doi.org/10.1016/j.envexpbot.2006.04.00610.1016/j.envexpbot.2006.04.006
- Bobola MS, Smith DE, Klein AS (1992) Five major nuclear ribosomal repeats represent a large and variable fraction of the genomic DNA of Picea rubens and P. mariana. Mol. Biol. Evol. 9: 125–137. https://doi.org/10.1093/oxfordjournals.molbev.a04070210.1093/oxfordjournals.molbev.a040702
- Brodribb TJ, Pitterman J, Coomes DA (2012) Elegance versus speed: examining the competition between conifer and angiosperm trees. International Journal of Plant Sciences 173: 673-694. https://doi.org/10.1086/66600510.1086/666005
- Brown GR, Newton CH, Carlson JE (1998) Organization and distribution of a Sau3A tandem repeated DNA sequence in Picea (Pinaceae) species. Genome 41: 560–565. https://doi.org/10.1139/g98-05410.1139/g98-054
- Cafasso D, Chinali G (2014) An ancient satellite DNA has maintained repetitive units of the original structure in most species of the living fossil plant genus Zamia. Genome 57: 125-135. https://doi.org/10.1139/gen-2013-013310.1139/gen-2013-0133
- Cafasso D, Cozzolino S, De Luca P, Chinali G (2003) An unusual satellite DNA from Zamia paucijuga (Cycadales) characterised by two different organizations of the repetitive unit in the plant genome. Gene: 311: 71–79. https://doi.org/10.1016/s0378-1119(03)00555-910.1016/S0378-1119(03)00555-9
- Cafasso D, Cozzolino S, Vereecken NJ, De Luca P, Chinali G (2009) Organization of a dispersed repeated DNA element in the Zamia genome. Biologia Plantarum 53: 28–36. https://doi.org/10.1007/s10535-009-0005-310.1007/s10535-009-0005-3
- Campbell CS, Wright WA, Cox M, Vining TF, Majorc CS, Arsenaulta MP (2005) Nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in Picea (Pinaceae): sequence divergence and structure. Molecular Phylogenetics and Evolution 35: 165–185. https://doi.org/10.1016/j.ympev.2004.11.01010.1016/j.ympev.2004.11.01015737589
- Chagne D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera MT, Vendramin GG, Garcia V, Frigerio JMM, Echt C, Richardson T, Plomion C (2004) Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor. Appl. Genet. 109:1204–1214. https://doi.org/10.1007/s00122-004-1683-z10.1007/s00122-004-1683-z15448894
- Chase MW, Reveal JL (2009) A phylogenetic classification of the land plants to accompany APGIII. Bot. J. Linnean Soc. 161: 122-127. https://doi.org/10.1111/j.1095-8339.2009.01002.x10.1111/j.1095-8339.2009.01002.x
- Christenhusz MJM, Reveal JL, Farjon A, Gardner MF, Mill RR, Chase MW (2011) A new classification and linear sequence of extant gymnosperms. Phytotaxa 19: 55-70. https://doi.org/10.11646/phytotaxa.19.1.310.11646/phytotaxa.19.1.3
- Christiakov DA, Hellemans B, Volckaert FAM (2006) Microsatellites and their genomic distribution, evolution, function and applications: A review with special reference to fish genetics. Aquqculture 255: 1–29. https://doi.org/10.1016/j.aquaculture.2005.11.03110.1016/j.aquaculture.2005.11.031
- Cullis CA, Griessem GP, Gorman SW, Teasdale RD (1988) The 25S, 18S, and 5S ribosomal RNA genes from Pinus radiata D. Don. In: Molecular Genetics of Forest Trees. Proc. 2nd Workshop IUFRO Working Party s2.04.06. Cheliak W M, Yapa A C (Eds).Canadian Forestry Service PNFI Inf. Rep. PI-X-80, pp.34–40.
- Davies BJ, O‘Brien IEW, Murray BG (1997) Karyotypes, chromosome bands and genome size variation in New Zealand endemic gymnosperms. Plant Systematics and Evolution 208: 169-185. https://doi.org/10.1007/bf0098544010.1007/BF00985440
- De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I (2020) Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evolutionary Applications 13:210–227. https://doi.org/10.1111/eva.1283910.1111/eva.12839693558631892953
- Devey ME, Fiddler TA, Liu BH, Knapp SJ, Neale DB (1994) An RFLP linkage map for loblolly pine based on three generation outbred pedigree. Theor. Appl. Genet. 88: 273–278. https://doi.org/10.1007/bf0022363110.1007/BF0022363124186005
- Echt CS, May-Marquardt TP (1997) Survey of microsatellite DNA in pine. Genome 40: 9–17. https://doi.org/10.1139/g97-00210.1139/g97-0029061909
- Echt CS, Saha S, Krutovsky KV, Wimalanathan K, Erpelding JE, Chun Liang C, Nelson CD (2011) An annotated genetic map of loblolly pine basedon micro-satellite and cDNA markers. BMC Genetics 12:17. https://doi.org/10.1186/1471-2156-12-1710.1186/1471-2156-12-17303814021269494
- Elsik CG, Williams CG (2000) Retroelements contribute to the excess of low-cop number DNA in pine. Mol. Genet. Genomics 264: 47–55. https://doi.org/10.1007/s00438000027910.1007/s00438000027911016832
- Elsik CG, Williams CG (2001) Families of clustered microsatellites in a conifer genome. Mol. Genet. Genomics 265: 535-542. https://doi.org/10.1007/s00438010044310.1007/s00438010044311405637
- Farhat P, Hidalgo O, Robert T, Siljak-Yakovlev S, Leitch I, Adams RP, Daghar Kharrat MB (2019a) Polyploidy in the genus Juniperus: an unexpectedly high rate. Frontiers in Plant Science 10: Article 676. https://doi.org/10.3389/fpls.2019.0067610.3389/fpls.2019.00676654100631191584
- Farhat P, Siljak-Yakovlev S, Adams RP, Daghar Kharrat MB, Robert T (2019b) Genome size variation and polyploidy in the geographical range of Juniperus sabina L. (Cupressaceae). Botany Letters. https://doi.org/10.1080/23818107.2019.161326210.1080/23818107.2019.1613262
- Farhat P, Siljak-Yakovlev S, Hidalgo O, Rushforth K, Bartel JA, Valentin N, Leitch IJ, Adams RP (2021) Polyploidy in Cupressaceae: Discovery of a new naturally occurring tetraploid, Xanthocyparis vietnamensis. Journal of Systematics and Evolution. https://doi.org/10.1111/jse.1275110.1111/jse.12751
- Flanary BE, Kletetschka G (2005) Analysis of telomere length and telomerase activity in tree species of various life-spans, and with age in the bristlecone pine Pinus longaeva. Biogerontology 6:101–111. https://doi.org/10.1007/s10522-005-3484-410.1007/s10522-005-3484-416034678
- Fragniere Y, Betrisey S, Cardinaux L, Stoffe IM, Kozlowski L (2015) Fighting the last strand? A global analysis of the distribution and conservation status of gymnosperms. Journal of Biogeography 42: 809-820. https://doi.org/10.1111/jbi.1248010.1111/jbi.12480
- Friesen N, Brandes A, Heslop-Harrison JS (2001) Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Molecular Biology and Evolution 18: 1176–1188. https://doi.org/10.1093/oxfordjournals.molbev.a00390510.1093/oxfordjournals.molbev.a00390511420359
- Friis EM, Pedersen KR, Crane PR (2010) Diversity in obscurity: Fossil flowers and the early history of angiosperms. Philos. Trans. R. Soc. B Biol. Sci. 365: 369– 382. https://doi.org/10.1098/rstb.2009.022710.1098/rstb.2009.0227283825720047865
- Fuchs J, Brandes A, Schubert I (1995) Telomere sequence localization and karyo-type evolution in higher plants. Plant Systematics and Evolution 196: 227– 241. https://doi.org/10.1007/bf0098296210.1007/BF00982962
- Garcia S, Ales Kova A, Leitch AR, Garnatje T (2017) Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. The Plant Journal 89: 1020–1030. https://doi.org/10.1111/tpj.1344210.1111/tpj.1344227943584
- Gernandt DS, Liston A, Pinerod (2001) Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes. Molecular. Phylogenetics and Evolution 21: 449–467. https://doi.org/10.1006/mpev.2001.102610.1006/mpev.2001.102611741386
- Gorelick R, Fraser D, Zonneveld BJM, Little DP (2014) Cycad (Cycadales) chromo-some numbers are not correlated with genome size. Int. J. Plant Sci. 175:986-997. https://doi.org/10.1086/67808510.1086/678085
- Greilhuber J (2005) Intraspecific variation in genome size in angiosperms: identifying its existence. Ann. Bot. 95: 91-98. https://doi.org/10.1093/aob/mci00410.1093/aob/mci004424670915596458
- Greilhuber J, Leitch I (2013) Genome size and the phenotype. In: I.J. Leitch et al. (eds.), Plant Genome Diversity Volume 2, pp 323-344. https://doi.org/10.1007/978-3-7091-1160-4_2010.1007/978-3-7091-1160-4_20
- Grotkopp E, Rejmanek M, Rost TL (2002) Toward a causal explanation of plant invasiveness: seedling growth and life-history strategies of 29 pine (Pinus) species. Am. Nat. 159:396–419. https://doi.org/10.2307/307924910.1086/33899518707424
- Grotkopp E, Rejmanek M, Sanderson MJ, Rost TL (2004) Evolution of genome size in pines (Pinus) and its life-history correlates: supertree analysis. Evolution 58: 1705–1729. https://doi.org/10.1111/j.0014-3820.2004.tb00456.x10.1111/j.0014-3820.2004.tb00456.x15446425
- Guan R, Zhao Y, Zhang H, Fan G et al. (2016) Draft genome of the living fossil Ginkgo biloba. GigaScience 5: 49. https://doi.org/10.1186/s13742-016-0154-110.1186/s13742-016-0154-1511889927871309
- Hall SE, Dvorak WS, Johnston JS, Price HJ, Williams CG (2000) Flow cytometric analysis of DNA content for tropical and temperate New World pines. Ann. Bot. (Lond.) 86:1081–1086. https://doi.org/10.1006/anbo.2000.127210.1006/anbo.2000.1272
- Hamberger B, Hall D, Yuen M, Oddy C, Hamberger B et al. (2009) Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome. BMC Plant Biol. 9: 106. https://doi.org/10.1186/1471-2229-9-10610.1186/1471-2229-9-106272907719656416
- Herbinger CM, Gordost K, Allen H (2011) Tetranucleotide and dinucleotide microsatellite markers for red spruce (Picea rubens). The Americas Journal of Plant Science and Biotechnology 5 (Sp. Issue 2): 105-111.
- Hidalgo O, Vallès J, Romo A, Canela MA, Garnatje T (2015) Genome size variation in gymnosperms under different growth conditions. Caryologia. 68: 92–96. https://doi.org/10.1080/00087114.2015.102454610.1080/00087114.2015.1024546
- Hill K (2005) Diversity and evolution of gymnosperms. In: Henry RJ (ed.), Plant Diversity and evolution : Diversity and phenotypic Variation in Higher Plants CABI Publishing Wallingford, Oxfordshire UK. https://doi.org/10.1079/9780851999043.002510.1079/9780851999043.0025
- Hizume M, Shibata F, Matsusakii Y, Kondo T (2000) Chromosomal localization of telomere sequence repeats in five gymnosperm species. Chromosome Science 4: 39-42
- Hizume M, Shibata F, Murayama Y, Kondo T (2001) Cloning of DNA sequences localized on proximal fluorescent chromosome bands by microdissection in Pinus densiflora Sieb. Zucc. Chromosoma 110: 345-351. https://doi.org/10.1007/s00412010014910.1007/s00412010014911685534
- Hizume M, Shibata F, Matsusaki Y, Garajova Z (2002a) Chromosome identification and comparative karyotype analysis of Pinus species. Theoretical and Applied Genetics 105: 491-497. https://doi.org/10.1007/s00122-002-0975-410.1007/s00122-002-0975-412582496
- Hizume M, Shibata F, Matsumoto A, Maruyama Y, Hayashi E, Kondo T, Kondo K, Zhang S (2002b) Tandem repeat DNA localising on the proximal DAPI bands of chromosomes of Larix, Pinaceae. Genome 45:777-783. https://doi.org/10.1139/g02-04110.1139/g02-04112175082
- Hizume M, Shibata F, Kondo K, Hoshi Y, Kondo T, Ge S, Yang Q, Hong D (1999) Identification of chromosomes in two Chinese spruce species by multicolor fluorescence in situ hybridization. Chromosome Sci. 3: 37–41.
- Hung KH, Lin CY, Huang CC, Hwang CC, Hsu TW, Kuo YL, Wang WK, Hung CY, Chiang TY (2012) Isolation and characterization of microsatellite loci from Pinus massoniana (Pinaceae). Botanical Studies (2012) 53: 191-196.
- Ickert-Bond SM, Wojciechowski MF (2004) Phylogenetic Relationships in Ephedra (Gnetales): Evidence from Nuclear and Chloroplast DNA Sequence Data. Systematic Botany 29: 834–849. https://doi.org/10.1600/036364404245114310.1600/0363644042451143
- Ickert-Bond SM, Sousa A, Min Y, Loera I, Metzgar J, Pellicer J, Hidalgo O, Leitch I (2020) Polyploidy in gymnosperms-Insight into the genomic and evolutionary consequences of polyploidy in Ephedra. Molecular Phylogenetics and Evolution 147: 106786. https://doi.org/10.1016/j.ympev.2020.10678610.1016/j.ympev.2020.10678632135310
- Joyner KL, Wang X-R, Johnston JS, Price HJ, Williams CG (2001) DNA content for Asian pines parallels New World relatives. Canadian Journal of Botany 79:192–196. https://doi.org/10.1139/b00-15110.1139/b00-151
- Kamm A, Doudrick RL, Heslop-Harrison JS, Schmidt T (1996) The genomic and physical organizationof Ty1-Copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proceedings National Academy of Sciences USA 93: 2708–2713. https://doi.org/10.1073/pnas.93.7.270810.1073/pnas.93.7.2708396958610105
- Kan XZ, Wang SS, Ding X, Wang XQ (2007) Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications. Molecular Phylogenetics and Evolution 44:765-477. https://doi.org/10.1016/j.ympev.2007.05.00410.1016/j.ympev.2007.05.00417596969
- Kelly LJ, Renny-Byfield S, Pellicer J, Macas J, Novak P, Neumann P, Lysak MA, Day PD, Berger M, Fay MF, Nichols RA, Leitch AR, Leitch IJ (2015) Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytol 208:596– 607. https://doi.org/10.1111/nph.1347110.1111/nph.13471474468826061193
- Kenrick P, Crane PR (1997) The origin and early evolution of plants on land. Nature 389: 33–39. https://doi.org/10.1038/3791810.1038/37918
- Kejnovsky E, Hawkins J, Feschotte C (2012) Plant transposable elements: biology and evolution. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien, New York, pp 17-34. https://doi.org/10.1007/978-3-7091-1130-7_210.1007/978-3-7091-1130-7_2
- Khoshoo TN (1959) Polyploidy in gymnosperms. Evolution 13: 24-39. https://doi.org/10.1111/j.1558-5646.1959.tb02991.x10.1111/j.1558-5646.1959.tb02991.x
- Kinlaw CS, Gertulla SM, Carter MC (1994) Lipid transfer protein genes of loblolly pine are members of a complex gene family. Plant Molecular Biology 26:1213–1216. https://doi.org/10.1007/bf0004070210.1007/BF000407027811979
- Kossack DS, Kinlaw CS (1999) IFG, a gypsy-like retrotransposon in Pinus (Pinaceae) has an extensive history in pines. Plant Mol. Biol. 39: 417–426. https://doi.org/10.1023/a:100611573262010.1023/A:1006115732620
- Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE et al. (2010) The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11: 420. https://doi.org/10.1186/1471-2164-11-42010.1186/1471-2164-11-420299694820609256
- Kriebel HB (1985) DNA sequence components of the Pinus strobus nuclear genome. Can. J. For. Res. 15:1–4. https://doi.org/10.1139/x85-00110.1139/x85-001
- Kubis S, Schmidt T, Heslop-Harrison JS (1998) Repetitive DNA elements as a major component of plant genomes. Ann. Bot. 82:45-56. https://doi.org/10.1006/anbo.1998.077910.1006/anbo.1998.0779
- Kurdi-Haider B, Shalhoub V, Dib-Hajj S, Deeb S (1983) DNA sequence organization in the genome of Cycas revoluta. Chromosoma 88: 319-327. https://doi.org/10.1007/bf0028585410.1007/BF00285854
- Kuzmin D, Feranchuk S, Sharov VV, Krutovsky KV (2019) Stepwise large genome assembly approach: A case of Siberian larch (Larix sibirica Ledeb). BMC Bioinformatics 20(Suppl 1):37. https://doi.org/10.1186/s12859-018-2570-y10.1186/s12859-018-2570-y636258230717661
- L’Homme Y, Segun A, Trembley FM (2000) Different classes of retrotransposons in coniferous spruce species. Genome 43: 1084–1089. https://doi.org/10.1139/g00-07710.1139/g00-077
- Leitch AR, Leitch IJ (2012) Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytologist 194:629–646. https://doi.org/10.1111/j.1469-8137.2012.04105.x10.1111/j.1469-8137.2012.04105.x22432525
- Leitch IJ, Hanson L, Winfield M, Parker J, Bennett MD (2001) Nuclear DNA C-values complete familial representation in gymnosperms. Annals of Botany 88: 843-849. https://doi.org/10.1006/anbo.2001.152110.1006/anbo.2001.1521
- Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007. https://doi.org/10.1093/molbev/msh07310.1093/molbev/msh07314963101
- Lin X, Faridi N, Casola C (2016) An Ancient Transkingdom Horizontal Transfer of Penelope. Like Retroelements from Arthropods to Conifers. Genome Biol. Evol. 8:1252–1266. https://doi.org/10.1093/gbe/evw07610.1093/gbe/evw076486070427190138
- Liston A, Robinson WA, Oliphant JM, Alvarezbuylla ER (1996) Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seed plants. Systematic Botany 21: 109–120. https://doi.org/10.2307/241974210.2307/2419742
- Liu W, Thummasuwan S, Sehgal SK, Chouvarine P, Peterson DG (2011) Characterization of the genome of bald cypress. BMC Genomics 12:553. https://doi.org/10.1186/1471-2164-12-55310.1186/1471-2164-12-553322885822077969
- Liu Y, El-Kassaby YA (2019) Novel insights into plant genome evolution and adaptation as revealed through transposable elements and non-coding RNAs in conifers. Genes 10:228. https://doi.org/10.3390/genes1003022810.3390/genes10030228647072630889931
- Magbanua, ZV, Ozkan S, Bartlett BD, Chouvarine P, Saski CA et al. (2011) Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS ONE 6: e16214. https://doi.org/10.1371/journal.pone.001621410.1371/journal.pone.0016214302502521283709
- Maggini F, Baldassini S (1995) Ribosomal RNA genes in the genus Pinus. I. Caryologia 48: 17–25. https://doi.org/10.1080/00087114.1995.1079731410.1080/00087114.1995.10797314
- Maomao Yan XD, Shuxian L, Tongming Y (2012) A meta-analysis of EST-SSR sequences in the genomes of pine, poplar and eucalyptus. Tree Genetics and Molecular Breeding 2:1–7. https://doi.org/10.5376/tgmb.2012.02.000110.5376/tgmb.2012.02.0001
- Miksche JP, Hotta Y (1973) DNA base composition and repetitious DNA in several conifers. Chromosoma 41: 29–36. https://doi.org/10.1007/bf0028407210.1007/BF00284072
- Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics 30: 194-200. https://doi.org/10.1038/ng82210.1038/ng82211799393
- Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD et al. (2009) Evolution of genome size and complexity in Pinus. PLoS ONE 4: e4332. https://doi.org/10.1371/journal.pone.000433210.1371/journal.pone.0004332263304019194510
- Mosca E, Cruz F, Gómez-Garrido J, Bianco L, Rellstab C, Brodbeck S, Csilléry K, Fady B, Fladung M et al. (2019) A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource. G3 Genes/Genomes/Genetics 9:2039. https://doi.org/10.1534/g3.119.40008310.1534/g3.119.400083664387431217262
- Murray BG (1998) Nuclear DNA amounts in gymnosperms. Annals of Botany 82: 3-14. https://doi.org/10.1006/anbo.1998.076410.1006/anbo.1998.0764
- Murray BG (2005) When does intraspecific C-value variation become taxonomically significant? Annals of Botany 95: 119-126. https://doi.org/10.1093/aob/mci00710.1093/aob/mci007424671215596461
- Murray BG (2013) Karyotype Variation and Evolution in Gymnosperms. In: I.J. Leitch et al. (eds.), Plant Genome Diversity Volume 2, pp. 231-242. https://doi.org/10.1007/978-3-7091-1160-4_1410.1007/978-3-7091-1160-4_14
- Murray BG, Friesen N, Heslop-Harrison JS (2002) Molecular cytogenetic analysis of Podocarpus and comparison with other gymnosperm species. Annals of Botany 89: 483–489. https://doi.org/10.1093/aob/mcf04710.1093/aob/mcf047423386512096809
- Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D et al. (2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology 2014, 15:R59. doi:10.1186/gb-2014-15-3-r59. https://doi.org/10.1186/gb-2014-15-3-r5910.1186/gb-2014-15-3-r59405375124647006
- Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Steven L. Salzberg SL, Jill L, Wegrzyn JL (2017) The Douglas-Fir Genome sequence reveals specialization of the photosynthetic Apparatus in Pinaceae. G3 Genes/Genomes/Genetics 7:3157. https://doi.org/10.1534/g3.117.30007810.1534/g3.117.300078559294028751502
- Nunes JD, Torres GA, Davide LC, de Campos JMS (2009) Chromosome banding and DNA content in tropical Pinus species. Scientia Forestalis, Piracicaba 37: 213-218.
- Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A et al. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497: 579–584. https://doi.org/10.1038/nature1221110.1038/nature1221123698360
- Ohri D (1998) Genome size variation and plant systematic. Annals of Botany 82: 75-84. https://doi.org/10.1006/anbo.1998.076510.1006/anbo.1998.0765
- Ohri D (2005) Climate and growth form: the consequences for genome size in plants. Plant Biology 7: 449-458. https://doi.org/10.1055/s-2005-86587810.1055/s-2005-86587816163609
- Ohri D (2015) How small and constrained is the genome size of angiosperm woody species. Silvae Genetica 64: 20-32. https://doi.org/10.1515/sg-2015-000210.1515/sg-2015-0002
- Ohri D (2021a) Polyploidy in gymnosperms – a reappraisal. Silvae Genetica 70: 22-38. https://doi.org/10.2478/sg-2021-000310.2478/sg-2021-0003
- Ohri D (2021b) Karyotype evolution in conifers. Feddes Repertorium. https://doi.org/10.1002/fedr.20210001410.1002/fedr.202100014
- Ohri D, Khoshoo TN (1986) Genome size in gymnosperms. Plant Systematics and Evolution 153: 119-132. https://doi.org/10.1007/bf0098942110.1007/BF00989421
- Oliveira EJ, Pádua JG, Zucchi MI, Vencovsky R, Vieira MLC (2006) Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology 29: 294-297. https://doi.org/10.1590/s1415-4757200600020001810.1590/S1415-47572006000200018
- Paton AJ, Brummitt N, Govaerts R, Harman K, Hinchcliffe S, Allkin B, Lughadha EN (2008) Towards target 1 of the global strategy for plant conservation: A working list of all known plant species—progress and prospects. Taxon 57: 602–611.
- Pellicer J, Leitch IJ (2019) The Plant C-value data base (Release 7.1): an updated repository of plant genome size data for comparative studies. New Pytolo-gist 226: 301-305. https://doi.org/10.1111/nph.1626110.1111/nph.1626131608445
- Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ (2018) Genome Size Diversity and Its Impact on the Evolution of Land Plants. Genes 9: 88. https://doi.org/10.3390/genes902008810.3390/genes9020088585258429443885
- Perera D, Magbanua ZV, Thummasuwan S, Mukherjee D, IIa MA, Chouvarinee P, Nairn CJ, Schmutzh J, Grimwood J, Deang JFD, Peterson DG (2018) Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis. Gene 663: 165–177. https://doi.org/10.1016/j.gene.2018.04.02410.1016/j.gene.2018.04.02429655895
- Perry DL, Furnier GR (1996) Pinus banksiana has at least seven expressed alcohol dehydrogenase genes in two linked groups. Proceedings National Academy of Sciences USA 93: 13020–13023. https://doi.org/10.1073/pnas.93.23.1302010.1073/pnas.93.23.13020240398917537
- Pfeiffer A, Olivieri AM, Morgante M (1997) Identification and characterization of icrosatellites in Norway spruce (Picea abies K.). Genome 40:411–419. https://doi.org/10.1139/g97-05510.1139/g97-0559276931
- Puttick MN, Clark J, Donoghue PCJ (2015) Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms. Proc. R. Soc. B 282: 20152289. http://dx.doi.org/10.1098/rspb.2015.2289.10.1098/rspb.2015.2289468578526631568
- Rake AV, Miksche JP, Hall RB, Hansen KM (1980) DNA reassocitation kinetics of four conifers. Canadian Journal of Genetics and Cytology 22: 69–79. https://doi.org/10.1139/g80-01010.1139/g80-010
- Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil M del R (2014) Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC Plant Biology 14:220. https://doi.org/10.1186/s12870-014-0220-810.1186/s12870-014-0220-8416055325143005
- Rastogi S, Ohri D (2020a) Chromosome numbers in gymnosperms-An update. Silvae Genetica 69: 13-19. https://doi.org/10.2478/sg-2020-000310.2478/sg-2020-0003
- Rastogi S, Ohri D (2020b) Karyotype evolution in cycads. Nucleus 63: 131-141. https://doi.org/10.1007/s13237-019-00302-210.1007/s13237-019-00302-2
- Romo A, Hidalgo O, Boratynski A, Sobierajska K, Jasinka A, Vallès J, Garnatje T (2013) Genome size and ploidy levels in highly fragmented habitats: the case of western Mediterranean Juniperus (Cupressaceae) with special emphasis on J. thurifera L. Tree Genetics and Genomes 9: 587-599. https://doi.org/10.1007/s11295-012-0581-910.1007/s11295-012-0581-9
- Rueda M, Godoy O, Hawkins BA (2017) Spatial and evolutionary parallelism between shade and drought tolerance explains the distributions of conifers in the conterminous United States. Global Ecology and Biogeography 26: 31–42. https://doi.org/10.1111/geb.1251110.1111/geb.12511
- Rungis D, Berube Y, Zhang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J, Ritland K (2004) Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theoretical and Applied Genetics 109:1283–1294. https://doi.org/10.1007/s00122-004-1742-510.1007/s00122-004-1742-515351929
- Salazar-Tortosa D, Castro J, Saladin B, Zimmermann NE, De Casas RR (2020) Arid environments select for larger seeds in pines (Pinus spp.). Evolutionary Ecology 34:11–26. https://doi.org/10.1007/s10682-019-10016-110.1007/s10682-019-10016-1
- Schmidt A, Doudrick RL, Heslop-Harrison JS, Schmidt T (2000) The contribution of short repeats of low sequence complexity to large conifer genomes. Theoretical and Applied Genetics 101: 7–14. https://doi.org/10.1007/s00122005144210.1007/s001220051442
- Schubert I, Vu GTH (2016) Genome stability and evolution attempting a holistic view. Trends in Plant Science 21: 749-757. https://doi.org/10.1016/j.tplants.2016.06.00310.1016/j.tplants.2016.06.00327427334
- Seoane-Zonjic P, Cañas RA, Bautista R, Gómez-Maldonado J, Arrillaga I, Fernández-Pozo N, Claros MG, Cánovas FM, Ávila C (2016) Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing. BMC Genomics 17:148. https://doi.org/10.1186/s12864-016-2490-z10.1186/s12864-016-2490-z476984326922242
- Shibata F, Hizume M (2008) Comparative FISH karyotype analysis of 11 Picea species. Cytologia 73: 203-211. https://doi.org/10.1508/cytologia.73.20310.1508/cytologia.73.203
- Shibata F, Matsusaki Y, Hizume M (2005) AT-rich sequence containing Arabidopsis type telomere sequence and the chromosomal distribution in Pinus densiflora. Theoretical and Applied Genetics 110: 1253-1258. https://doi.org/10.1007/s00122-005-1960-510.1007/s00122-005-1960-515791450
- Skinner JS, Timko MP (1998) Loblolly pine (Pinus taeda L.) contains multiple expressed genes encoding light-dependent NADPH: protochlorophyllide oxidoreductase (POR). Plant Cell Physiol. 39: 795–806. https://doi.org/10.1093/oxfordjournals.pcp.a02943710.1093/oxfordjournals.pcp.a0294379787456
- Smarda P, Horova L, Knapek O, Dieck H, Dieck M, Razna K, Hrubik P, Orloci L, Papp L, Vesela K, Vesely P, Bures P (2018) Multiple haploids triploids and tetraploids found in modern day `living fossil’ Ginkgo biloba. Horticulture Research 5:55. https://doi.org/10.1038/s41438-018-0055-910.1038/s41438-018-0055-9616584530302259
- Smith DN, Devey ME (1994) Occurrence and inheritance of microsatellite loci in Pinus radiata. Genome 37: 977–983. https://doi.org/10.1139/g94-13810.1139/g94-1387828844
- Soranzo N, Provan J, Powell W (1998) Characterisation of microsatellite loci in Pinus sylvestris L. Mol. Ecol. 7:1260-1261
- Stevens KA et al. (2016) Sequence of the sugar pine megagenome. Genetics 204,1613–1626. https://doi.org/10.1534/genetics.116.19322710.1534/genetics.116.193227516128927794028
- Stival Sena J, Giguère I, Boyle B, Rigault P, Birol I, Zuccolo A, Ritland K, Ritland C, Bohlmann J, Jones S, Bousquet J, Mackay J (2014) Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC Plant Biology 14:95. http://www.biomedcentral.com/1471-2229/14/95.10.1186/1471-2229-14-95410804724734980
- Stuart-Rogers C, Flavell AJ (2001) The evolution of Ty1-copia group retrotransposons in gymnosperms. Mol. Biol. Evol. 18: 155–163. https://doi.org/10.1093/oxfordjournals.molbev.a00378910.1093/oxfordjournals.molbev.a00378911158374
- The Plant List (2010) Version 1 Published on the Internet; http://www.theplantlist.org/
- Victoria FC, da Maia LC, de Oliveira AC (2011) In silico comparative analysis of SSR markers in plants. BMC Plant Biology 11:15.10.1186/1471-2229-11-15303730421247422
- Vinogradov AE (1999) Intron-genome size relationship on a large evolutionary scale. J. Mol. Evol. 49: 376–384. https://doi.org/10.1007/pl0000656110.1007/PL00006561
- Von Stackelberg M, Rensing SA, Reski R (2006) Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. BMC Plant Biology 6:9. https://doi.org/10.1186/1471-2229-6-910.1186/1471-2229-6-9152643416734891
- Voronova A, Belevich V, Korica A, Rungis D (2017) Retrotransposon distribution and copy number variation in gymnosperm genomes. Tree Genetics & Genomes 13:88. https://doi.org/10.1007/s11295-017-1165-510.1007/s11295-017-1165-5
- Voytas DF, Cummings MP, Konieczny A, Ausubel FM, Rodermel SR (1992) Copia-like retrotransposons are ubiquitous among plants. Proceedings National Academy of Sciences USA 89:7124–7128. https://doi.org/10.1073/pnas.89.15.712410.1073/pnas.89.15.7124496581379734
- Wakamiya I, Newton RJ, Johnston JS, Price HJ (1993) Genome size and environmental factors in the genus Pinus. American Journal of Botany. 80: 1235–1241. https://doi.org/10.1002/j.1537-2197.1993.tb15360.x10.1002/j.1537-2197.1993.tb15360.x
- Wakamiya I, Price HJ, Messina MG, Newton RJ (1996) Pine genome diversity and water relations. Physiologia Plantarum 96: 13–20. https://doi.org/10.1034/j.1399-3054.1996.960103.x10.1034/j.1399-3054.1996.960103.x
- Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ et al. (2018) A genome for gnetophytes and early evolution of seed plants. Nature Plants 4: 82–89. https://doi.org/10.1038/s41477-017-0097-210.1038/s41477-017-0097-229379155
- Wang SQ, Ran JH (2014) Evolution and biogeography of gymnosperms. Molecular Phylogenetics and Evolution 75: 24-40. https://doi.org/10.1016/j.ympev.2014.02.00510.1016/j.ympev.2014.02.00524565948
- Warren RL, Keeling CI, Yuen MMS, Raymond A, Taylor GA et al. (2015) Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. The Plant Journal 83: 189–212.10.1111/tpj.1288626017574
- Wegrzyn J, Lin B, Zieve J, Dougherty W, Martinez-Garcia P, Koriabine M, Holtz-Morris A, de Jong P, Crepeau M, Langley C et al. (2013) Insights into the loblolly pine genome: Characterization of BAC and fosmid sequences. PLoS ONE 8: e72439. https://doi.org/10.1371/journal.pone.007243910.1371/journal.pone.0072439376281224023741
- Wegrzyn JL, Liechty JD, Stevens KA et al. (2014) Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196: 891–909. https://doi.org/10.1534/genetics.113.15999610.1534/genetics.113.159996394881424653211
- Wendel JF, Cronn RC, Alvarez I, Liu B, Small RL, Senchina DS (2002) Intron size and genome size in plants. Mol. Biol. Evol. 19: 2346–2352F https://doi.org/10.1093/oxfordjournals.molbev.a00406210.1093/oxfordjournals.molbev.a00406212446829
- Won H, Renner SS (2005) The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Molecular Phylogenetics and Evolution 36 : 581–597. https://doi.org/10.1016/j.ympev.2005.03.01110.1016/j.ympev.2005.03.01116099382
- Yagi E, Akita T, Kawahara T (2011) A novel Au SINEsequence found in a gymnosperm, Genes Genet. Syst. 86: 19-25. https://doi.org/10.1266/ggs.86.1910.1266/ggs.86.1921498919
- Yazdani R, Scott I, Jansson G, Plomion C, Mathur G (2003) Inheritance and diversity of simple sequence repeat (SSR) microsatellite markers in various families of Picea abies. Hereditas 138: 219–227. https://doi.org/10.1034/j.1601-5223.2003.01524.x10.1034/j.1601-5223.2003.01524.x14641487
- Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16. https://doi.org/10.1046/j.0962-1083.2001.01418.x10.1046/j.0962-1083.2001.01418.x11903900
- Zonneveld BJM, Lindstrom AJ (2016) Genome sizes for 71 species of Zamia (Cycadales: Zamiaceae) correspond with three different biogeographic regions. Nordic J. Bot. 34: 744-751. https://doi.org/10.1111/njb.0109410.1111/njb.01094