Noncoding and Repetitive DNA
It is well established that conifer genomes are comprised largely of noncoding and repetitive DNA (Chaps. 2 and 3). However, the much smaller fraction of the genome comprised of protein-coding genes has been the focus of most research (see Chaps. 5, 6, and 7) because these genes ultimately lead to phenotypes and the genetic differences among species and individuals within species (Sects. “Ribosomal DNA” and “Tandem Repeats: Satellite, Minisatellite, and Microsatellite DNA”). Nevertheless, some attention has been paid to characterizing the nature of noncoding and repetitive DNA and what functional significance, if any, this DNA might have. In this chapter, we will introduce the types of noncoding and repetitive DNA that have been discovered in conifers and what is known about how and when in evolutionary time this DNA was amplified and became so abundant. We will also point to how variability in this DNA has been used in population genetic studies (Chap. 9) and evolutionary and phylogenetic studies (Chaps. 15 and 16). There are four general classes of noncoding and repetitive DNA that will be discussed: (1) ribosomal DNA, (2) tandemly duplicated DNA, (3) transposons and retrotransposons, and (4) pseudogenes.
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