Less is more: compact genomes pay dividends.

In 1993, Sydney Brenner, like many others, recognized that vertebrates are distinct in their morphology and development and that access to the complete sequence of a vertebrate genome would yield valuable insights into the biology of higher species not obtainable from genome studies of yeast, fly, or even the nematode. Moreover, at that time it was not possible, through sequencing technology, to rapidly generate the huge volumes of accurate, inexpensive sequence data necessary for sequencing the human genome to succeed in a costeffective manner. The good news was that evolution likely dictated that vertebrates would be distinguished from each other at the genomic level more by the ways in which their genes were regulated rather than by profound differences in gene repertoire (Elgar 1996a). Thus, the goal was to find a vertebrate genome of intermediate size that would be both (1) representative of higher organisms and (2) small enough and gene-dense enough for large-scale genomic studies. Brenner’s organism of choice was the pufferfish (a.k.a. blowfish) Fugu rubripes (Brenner et al. 1993). The era of compact vertebrate genomics was born. But why Fugu, an exotic Japanese delicacy, known more for its bloated appearance and potent neurotoxin (potentially lethal to diners if not prepared by a knowledgeable chef) than for its utility as a model organism? In a survey of the haploid DNA content of nearly 300 teleostean fishes, Ralph Hinegardner (1968) observed that members of the Tetraodontidae family in particular tend to have very small genomes—on the order of 400 Mb, some 7.5-fold smaller than the 3000-Mb human genome (0.4–0.5 pg/cell vs. 3 pg in the human). Whereas its size suggested that it would be more manageable than a mammalian genome, what was more telling was the discovery that <8% of Fugu DNA is repetitive, as compared to ∼60% of human DNA. In their review, Koop and Nadeau (1996) summarized transcript quantity data in Fugu versus man and concluded that whereas five times more of the pufferfish genome is transcribed, its absolute gene number appears to be comparable to mammals. How is this possible? Beyond an overall paucity of repetitive DNA in Fugu, the pufferfish also exhibits substantial compaction of both introns and intergenic distances. Undoubtedly, such compaction is directly related to the intronic expansion that has taken place in the last ∼430 million years, that is, the span of time separating teleosts from mammals, making them our most distant extant vertebrate ancestors (Powers 1991). In addition to Koop and Nadeau (1996), at least two reviews by Greg Elgar, Sydney Brenner, and colleagues encapsulate the promise of Fugu as a model organism and provide a survey of comparative pufferfish genomics efforts through 1996 (Elgar 1996b; Elgar et al. 1996). A cursory survey of Medline from the last 5 years reveals that representatives of >30 distinct gene families have been cloned and genomically characterized in Fugu. In addition, comparative mapping studies have now examined physical distance, genetic distance, and/ or, at a minimum, conserved synteny relationships between Fugu genes and their mammalian orthologs. Although it is difficult to synthesize these data concisely, the general tendency of Fugu genes to be significantly smaller than their human counterparts has been borne out. Of genes where both human and Fugu genomic sequences are available, to my knowledge only one—the neural cell adhesion molecule L1—is actually larger in Fugu than in man (by a factor of 1.1; Coutelle et al. 1998). For most other individual genes, the extent of compaction in pufferfish ranges from 2.5-fold for the tuberous sclerosis gene TSC2 (Maheshwar et al. 1996) to >30fold for complement component C9 and the amyloid precursor protein gene APP (Yeo et al. 1997; Villard et al. 1998). As stated, substantially smaller introns appear to be the rule in pufferfish and, along with reductions in intergenic distances, the primary source of Fugu’s reduction in genomic size. Although intron–exon boundaries, exon size, exon number, and even alternative splice site usage have been more or less conserved for >400 million years in a number of genes (e.g., Gardiner 1997; Coutelle et al. 1998; Llevadot et al. 1998; Villard et al. 1998), intron size does not appear to be under the same selective constraints. In some cases, intronic compaction may approach 50-fold (McNaughton et al. 1997; Villard et al. 1998). Similarly, studies of intergenic distances in Fugu also prove reduction to be the order of the day. How et al. (1996) and Schofield et al. (1997) have both examined tandemly arrayed genes that span large chromosomal regions in human and found substantial compaction in pufferfish. Aparicio et al. (1997) showed that Fugu Hox gene clusters are compact by virtue of a combination of gene loss and reduction in intergenic distances. To date, perhaps the most dramatic example of reduction of intergenic distance comes from Trower et al. (1996), who showed that a three-gene cluster occupied >600 kb on human chromosome 14q24.3 but only 12.4 kb in Fugu. Why vertebrate genome expansion has taken place over the course of evolution—the explosion of repeat families in mammals is one obvious reason—is a fascinating subject but, unfortunately, also beyond the scope of this commentary. E-MAIL [email protected]; FAX (216) 368-5857. Insight/Outlook