Comparative Genomics

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 {\texttimes} environment interaction, and likely epigenetic factors and it becomes easy to account for the large amount of variation in form and function among conifers.