Pinus banksiana has at least seven expressed alcohol dehydrogenase genes in two linked groups

Abstract

The alcohol dehydrogenase (Adh) gene family is much more complex in Pinus banksiana than in angiosperms, with at least seven expressed genes organized as two tightly linked clusters. Intron number and position are highly conserved between P. banksiana and angiosperms. Unlike angiosperm Adh genes, numerous duplications, as large as 217 bp, were observed within the noncoding regions of P. banksiana Adh genes and may be a common feature of conifer genes. A high frequency of duplication over a wide range of scales may contribute to the large genome size of conifers.It is well-established that nuclear genomes are much larger in conifers than in angiosperms. In conifers, 2C values (where C is the total amount of DNA in a haploid nucleus) typically range from 20 to 50 pg (1), whereas the corresponding values in angiosperms are typically less than 10 pg and often less than 2 pg (2). However, relatively little is known about the organization of these large conifer genomes. While the proportion of repeated DNA is higher than in angiosperms, there is little relationship between total genomic and repetitive DNA (3). Nuclear rDNA repeat units are much longer in conifers (4-6) and Southern blot analyses of pine DNA with cDNA probes often reveal complex band patterns, suggesting larger gene families and͞or larger genes than in angiosperms (7-10).One of the best characterized plant gene families codes for alcohol dehydrogenases (ADH; EC 1.1.1.1), enzymes that play a central role in anaerobic metabolism (11,12). Most angiosperms express two or three ADH isozymes (13) and Southern blots generally display a corresponding level of complexity (14,15). Sequence data are available for Adh genes of a number of angiosperm species, but relatively little is known about this gene family in conifers, with the only published sequences being three partial Pinus radiata Adh cDNAs, likely representing two loci (7). Typically, two to four ADH isozymes are observed in pines (16), but P. radiata Adh cDNA clones hybridize to many fragments of P. radiata and Pinus taeda DNA (7) and many diverse genomic Adh clones were recovered from these species (17). These observations suggest that the Adh gene family is larger in pines than in angiosperms and͞or that pine Adh genes are larger. We characterized Adh genes in Pinus banksiana Lamb. (jack pine) to examine these hypotheses. Also, due to the successful development of segregating PCR-based gene-specific markers, we were able to examine linkage relationships among Adh loci. METHODSIsozyme Analysis. P. banksiana seeds were germinated on distilled (d) H 2 O-moistened filter paper in Petri dishes at room temperature for 8 days, yielding seedling root lengths of 1-2 cm. The germinating seeds were then given either anaerobic treatment (immersed for 20 hr in dH 2 O under filter paper) or aerobic treatment (seeds remained on moist filter paper).Starch gel electrophoresis (18) was used to examine ADH enzyme activity in the haploid megagametophytes and diploid roots of these seedlings.cDNA Cloning and Char...

Phylogeny, Duplication, and Intraspecific Variation of Adh Sequences in New World Diploid Cottons (Gossypium L., Malvaceae)

“…Typically, plant Adh sequences contain 10 exons and 9 introns (e.g., Dennis et al, 1984Dennis et al, , 1985Perry and Furnier, 1996;Sang et al, 1997;Trick et al, 1988), although there are exceptions, such as Arabidopsis thaliana, with only 7 exons and 6 introns (Chang and Meyerowitz, 1986). The Gossypium AdhA sequences reported here (which span the coding region from exon 2 to exon 8) are lacking introns 4 and 7, which appear to have been precisely removed (Small et al, 1999;Fig.…”

“…Alcohol dehydrogenase genes have been characterized from many angiosperms, and with few exceptions, the number and placement of introns is highly conserved (e.g., Dennis et al, 1985Dennis et al, , 1986Perry and Furnier, 1996;Sang et al, 1997;Trick et al, 1988). The exceptions all appear to fall into the category of intron loss.…”

“…The mechanism(s) responsible for intron loss are not well characterized, although recombination or gene conversion between a cDNA or processed pseudogene and a functional copy is one potential process (Häger et al, 1996;Charlesworth et al, 1998;Drouin and Moniz de Sá, 1997;Loguercio and Wilkins, 1998). The fact that pine Adh sequences share the 10 exon/9 intron structure (Perry and Furnier, 1996) with angiosperms suggests that this configuration is ancestral and that the absence of introns in some sequences represents intron loss.…”

Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda

“…Gene families are thought to be abundant in conifers (Perry and Furnier 1996;Kinlaw and Neale 1997). EST projects suggest that the number of expressed gene family members may not be very high, but the number of related nonexpressed pseudogenes is higher than in many other plant groups.…”

“…Gene families are common in pines (Perry and Furnier 1996;Kinlaw and Neale 1997). The orthologous members must be identified in the different species.…”