Abstract
This well-known quote from Dobzhansky, made long before the development of genomic sciences, is the overriding theme of this chapter. We have tried to summarize the study of conifer genetics and genomics in three sections of this volume; Genomes, Variation, and Evolution. In this chapter, we attempt to bring all these sections together to develop a deeper understanding of genomes and variation in the context of the evolution of species of Coniferales. The earliest form of comparative genomics in conifers was the work in comparing chromosome number, genome size, and karyotypes across taxa (Chap. 2). We saw that the 1N chromosome number in conifers varies little; from 11 to 13 with just a few exceptions (Table 2.1). Polyploidy is extremely rare, with just the tetraploids Fitzroya cupressoides (Alerce) and Juniperus chinensis “Pfitzeriana” and the hexaploid Sequoia sempervirens (coast redwood). Genome size in conifers, however, varies over nearly an order of magnitude with the smallest genome being 4067 Mb (Microcachrys tetragona) and the largest being 35,084 Mb (Pinus gerardiana) (Table 2.1). The variation in genome size can be accounted for by differences in noncoding DNA (Chap. 4); the number of protein coding loci appears to be quite similar among species (Chap. 3). Karyotype analysis using various chromosome banding techniques showed great similarity among chromosomes not only across species but even among chromosomes within species. It was not until FISH techniques were developed and used that karyotype differences among chromosomes were observed and homoeologous chromosomes among species could be determined (Chap. 2). The classical era of genomics (pre-2000) established the conservative aspect of conifer chromosome evolution and that the large phenotypic differences among conifers would be due to the allelic differences among species for a similar set of protein-coding loci (Chap. 10) and differences in the expression of these alleles at these loci (Chap. 5). Add to these differences epistatic variation, genotype × environment interaction, and likely epigenetic factors and it becomes easy to account for the large amount of variation in form and function among conifers.
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References
Ahuja, M. R., Devey, M. E., Groover, A. T., Jermstad, K. D., & Neale, D. B. (1994). Mapped DNA probes from loblolly pine can be used for restriction fragment length polymorphism mapping in other conifers. Theoretical and Applied Genetics, 88(3–4), 279–282.
Baker, E. A., Wegrzyn, J. L., Sezen, U. U., Falk, T., Maloney, P. E., Vogler, D. R., et al. (2018). Comparative transcriptomics among four white pine species. G3: Genes, Genomes Genetics, 8(5), 1461–1474.
Brown, G. R., Kadel, E. E., Bassoni, D. L., Kiehne, K. L., Temesgen, B., Van Buijtenen, J. P., et al. (2001). Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics, 159(2), 799–809.
Chagné, D., Brown, G., Lalanne, C., Madur, D., Pot, D., Neale, D., & Plomion, C. (2003). Comparative genome and QTL mapping between maritime and loblolly pines. Molecular Breeding, 12(3), 185–195.
Chancerel, E., Lepoittevin, C., Le Provost, G., Lin, Y. C., Jaramillo-Correa, J. P., Eckert, A. J., et al. (2011). Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics, 12(1), 368.
Clark, A. G., et al. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450(7167), 203–218.
Conkle, M. T. (1981, April). Isozyme variation and linkage in six conifer species. In Conkle MT, technical coordinator. Proc. Symp. Isozymes North Am. Forest Trees and Forest Inspects. Gen. Tech. REP. PSW-48. Berkeley, California: Pacific SW Forest and Range Exp. Sta (pp. 11–17).
De La Torre, A. R., Birol, I., Bousquet, J., Ingvarsson, P. K., Jansson, S., Jones, S. J., et al. (2014b). Insights into conifer giga-genomes. Plant Physiology, 166(4), 1724–1732.
Devey, M. E., Sewell, M. M., Uren, T. L., & Neale, D. B. (1999). Comparative mapping in loblolly and radiata pine using RFLP and microsatellite markers. Theoretical and Applied Genetics, 99(3–4), 656–662.
Harry, D. E., Temesgen, B., & Neale, D. B. (1998). Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones. Theoretical and Applied Genetics, 97(3), 327–336.
Ingvarsson, P. K., Hvidsten, T. R., & Street, N. R. (2016). Towards integration of population and comparative genomics in forest trees. New Phytologist, 212(2), 338–344.
Jermstad, K. D., Eckert, A. J., Wegrzyn, J. L., Delfino-Mix, A., Davis, D. A., Burton, D. C., & Neale, D. B. (2011). Comparative mapping in Pinus: sugar pine (Pinus lambertiana Dougl.) and loblolly pine (Pinus taeda L.). Tree Genetics & Genomes, 7(3), 457–468.
Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., et al. (2015). Genomic signatures of evolutionary transitions from solitary to group living. Science. https://doi.org/10.1126/science.aaa4788.
Kole, C. (Ed.). (2007). Forest trees (Vol. 7). Berlin, Germany: Springer Science & Business Media.
Komulainen, P., Brown, G. R., Mikkonen, M., Karhu, A., Garcia-Gil, M. R., O’malley, D., et al. (2003). Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theoretical and Applied Genetics, 107(4), 667–678.
Krutovsky, K. V., Troggio, M., Brown, G. R., Jermstad, K. D., & Neale, D. B. (2004). Comparative mapping in the Pinaceae. Genetics, 168(1), 447–461.
Pavy, N., Pelgas, B., Laroche, J., Rigault, P., Isabel, N., & Bousquet, J. (2012b). A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biology, 10(1), 84.
Pelgas, B., Beauseigle, S., Acheré, V., Jeandroz, S., Bousquet, J., & Isabel, N. (2006). Comparative genome mapping among Picea glauca, P. mariana× P. rubens and P. abies, and correspondence with other Pinaceae. Theoretical and Applied Genetics, 113(8), 1371.
Swenson, N. G., Iida, Y., Howe, R., Wolf, A., Umaña, M. N., Petprakob, K., et al. (2017). Tree co-occurrence and transcriptomic response to drought. Nature Communications, 8(1), 1996.
Temesgen, B., Brown, G. R., Harry, D. E., Kinlaw, C. S., Sewell, M. M., & Neale, D. B. (2001). Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theoretical and Applied Genetics, 102(5), 664–675.
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., et al. (2014b). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320.
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Neale, D.B., Wheeler, N.C. (2019). Comparative Genomics. In: The Conifers: Genomes, Variation and Evolution. Springer, Cham. https://doi.org/10.1007/978-3-319-46807-5_17
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