Variation and Evolution of Genome Size in Gymnosperms

Ahuja MR (2005) Polyploidy in gymnosperms revisited. Silvae Genetica 54: 59-69. https://doi.org/10.1515/sg-2005-001010.1515/sg-2005-0010 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

Hizume M, Shibata F, Matsusakii Y, Kondo T (2000) Chromosomal localization of telomere sequence repeats in five gymnosperm species. Chromosome Science 4: 39-42 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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. Search in Google Scholar

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. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

Ohri D (2021b) Karyotype evolution in conifers. Feddes Repertorium. https://doi.org/10.1002/fedr.20210001410.1002/fedr.202100014 Search in Google Scholar

Ohri D, Khoshoo TN (1986) Genome size in gymnosperms. Plant Systematics and Evolution 153: 119-132. https://doi.org/10.1007/bf0098942110.1007/BF00989421 Search in Google Scholar

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 Search in Google Scholar

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. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

Soranzo N, Provan J, Powell W (1998) Characterisation of microsatellite loci in Pinus sylvestris L. Mol. Ecol. 7:1260-1261 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

The Plant List (2010) Version 1 Published on the Internet; http://www.theplantlist.org/ Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar