Domain Shuffling and the Evolution of Vertebrates

Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Domain shuffling and the evolution of vertebrates Takeshi Kawashima,1,2,3,9 Shuichi Kawashima,4 Chisaki Tanaka,5 Miho Murai,6 Masahiko Yoneda,6 Nicholas H. Putnam,2,7 Daniel S. Rokhsar,2,7 Minoru Kanehisa,4,8 Nori Satoh,1 and Hiroshi Wada5,9 1Okinawa Institute of Science and Technology, Uruma, Okinawa 904-2234, Japan; 2Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; 3Japanese Society for Promotion of Sciences, Tokyo 102-8471, Japan; 4Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; 5Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; 6Department of Nursing & Health, School of Nursing & Health, Aichi Prefectural University, Nagoya 463-8502, Japan; 7Center for Integrative Genomics, University of California, Berkeley, Berkeley, California 94720, USA; 8Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan The evolution of vertebrates has included a number of important events: the development of cartilage, the immune system, and complicated craniofacial structures. Here, we examine domain shuffling as one of the mechanisms that contributes novel genetic material required for vertebrate evolution. We mapped domain-shuffling events during the evolution of deuterostomes with a focus on how domain shuffling contributed to the evolution of vertebrate- and chordate-specific characteristics. We identified ;1000 new domain pairs in the vertebrate lineage, including ;100 that were shared by all seven of the vertebrate species examined. Some of these pairs occur in the protein components of vertebrate-specific structures, such as cartilage and the inner ear, suggesting that domain shuffling made a marked contribution to the evolution of vertebrate-specific characteristics. The evolutionary history of the domain pairs is traceable; for example, the Xlink domain of aggrecan, one of the major components of cartilage, was originally utilized as a functional domain of a surface molecule of blood cells in protochordate ancestors, and it was recruited by the protein of the matrix component of cartilage in the vertebrate ancestor. We also identified genes that were created as a result of domain shuffling in ancestral chordates. Some of these are involved in the functions of chordate structures, such as the endostyle, Reissner’s fiber of the neural tube, and the notochord. Our analyses shed new light on the role of domain shuffling, especially in the evolution of vertebrates and chordates. [Supplemental material is available online at www.genome.org.] The question of how novel structures are created by changing mechanisms might have been involved in domain shuffling, such genetic information is one of the most challenging issues in evo- as the simple fusion of genes and recruitment of mobile elements lutionary biology. It is generally accepted that the morphological (Babushok et al. 2007; Ekman et al. 2007). features of various multicellular animals are built on a common set In contrast to thorough investigation of the mechanistic of genes. Carroll et al. (2001) and Davidson (2006) proposed that aspects of domain shuffling, the contribution of the new genes the novel features emerged as a result of altered gene expression created by domain shuffling to the evolution of phenotype has patterns. Novel genetic material has also contributed to the evo- not been sufficiently explored. Because domain shuffling occurs lution of novel structures. Much attention has been focused on more frequently in metazoan lineages than in unicellular organ- gene duplications as a mechanism for the evolution of novel ge- isms, suggesting that domain shuffling played an important role netic material. Particularly in the case of vertebrate evolution, in the evolution of multicellularity (Patthy 2003; Ekman et al. whole genome duplications that occurred twice in ancestral ver- 2007), we reasoned that domain shuffling also contributed to the tebrates have been regarded as the main force driving the evolu- elaboration of metazoan body plans. In this study, we compre- tion of novel structures (Holland et al. 1994). As an additional hensively investigated the domain shuffling events during deu- mechanism, we focus here on domain shuffling (Chothia et al. terostome evolution. The complete amphioxus genome sequence 2003; Babushok et al. 2007). Several different molecular mecha- provides sufficient deuterostome genomic sequences (Dehal et al. nisms for domain shuffling have been proposed. Since the 2002; Sea Urchin Genome Sequencing Consortium 2006; Putnam domains are often correlated with exon boundaries, exon shuf- et al. 2008) to map the domain shuffling events accurately. We fling is believed to be one of the major forces driving domain listed gene models that were created by domain shuffling in the shuffling (Liu and Grigoriev 2004). In addition, the introns at the ancestors of vertebrates, and examined how domain shuffling boundaries of domains show a marked excess of symmetrical contributed to the evolution of new genes for vertebrate-specific phase combinations, and, consequently, these domains may be characteristics. The contribution of domain shuffling was also inserted without changing the reading frame of ancestral genes examined in the evolution of chordates. (Kaessmann et al. 2002; Vibranovski et al. 2005). Some other Results and Discussion 9Corresponding authors. E-mail [email protected]; fax 81-29-853-4671. Detection of domain shuffling in deuterostome evolution E-mail [email protected]; fax 81-98-934-5622. Article published online before print. Article and publication date are at We identified pairs of protein domains found in single-gene mod- http://www.genome.org/cgi/doi/10.1101/gr.087072.108. els, including the human, mouse, rat, chicken, frog, pufferfish, 19:000–000 Ó 2009 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/09; www.genome.org Genome Research 1 www.genome.org Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Kawashima et al. zebrafish, ascidian, and amphioxus genomes. We took the order of Based on the table of shared domain pairs (Table 1), we the domains into account, so that the domain pair A and B (in mapped the gained and lost domain pairs on a phylogenetic tree order from the N terminus) was treated as a distinct pair from that had been previously deduced by using concatenated amino domains in the order B and A. This is because these domain pairs acid sequences (Fig. 1A; Putnam et al. 2008). If more than two taxa with different orders are more likely to have been gained by dis- shared domain pairs, we regarded the pairs as having been ac- tinct domain shuffling events than by divergence from a common quired in the last common ancestor. If pairs were shared in only ancestral pair. We surveyed domain pairs found in all splicing some of the descendent taxa, we assumed that those pairs were variants in order to detect all domain pairs transcribed in the lost in the rest of the descendent taxa. This method to reconstruct genomes. As outgroups, domain pairs from the proteomes of a sea the gain/loss of domain pairs does not follow the maximum par- urchin, fly, mosquito, gastropod snail, two species of nematode, simony principle. Rather, to filter domain pairs that are more sea anemone, choanoflagellate, slime mold, yeast, and plant likely to have been achieved by independent domain shuffling (Arabidopsis) were obtained (Supplemental Table 1). In the 20 events, we examined the overall domain structures of the gene proteomes, profile-HMM (HMMER) searches of the Pfam database models and defined a convergent index (CI) (see Methods). Al- (E-value cutoff of 10À3; see Methods) recognized 4649 protein though these independent acquisitions were thought to be rare domains. Of these, 2727 were found paired with other domains. (Gough 2005), we detected several domain pairs that are likely to Approximately 2000–5500 domain pairs were found in the gene have been achieved independently. By filtering domain pairs of models of each species. For example, 4057 domain pairs were CI $ 0.5, we found that 15 pairs that were shared by the sea urchin found in the human gene models, with 2251 found in ascidian and some chordates had rather different domain architectures and 5387 in amphioxus. From these datasets, we surveyed domain (Supplemental Fig. 1). Therefore, these domain pairs were more pairs shared by the major deuterostome taxa (Table 1). By this likely to have been acquired by convergence. Among 269 domain method, triplets of domains were detected as two or three domain pairs that were assumed to have been gained in the ancestors of pairs in one gene model (e.g., SNF2 histone linker PHD RING chordates, 13 pairs showed a CI $ 0.5, and thus were suggested to helicase or attractin in Table 2). have evolved convergently. No domain pairs shared by ascidians and vertebrates, and new pairs acquired in the vertebrate lineage, showed a CI $ 0.5. After filtering domain pairs of CI < 0.5, 209 pairs were as- Table 1. Shared domain combinations and unique domains sumed to have been acquired in the common ancestors of deuterostomes, 256 pairs in the common ancestors of chordates, and Class I Class II Unique combinationsa combinationsb domainsc 35 in the common ancestors of ascidian and vertebrates. Re- garding the gained and lost pairs in each deuterostome taxon, it is VCBSO 0 1326 1532 notable that many of the new pairs (1965 pairs) were acquired in VCBS_ 0 20 2 the amphioxus lineage, which exceeded the number observed in VCB_O 0 355 116 the vertebrate lineage. Because some ambiguity remains in the VC_SO 0 129 25 V_BSO 0 458 161 gene models predicted from the genome sequences and EST se- _CBSO 0 15 0 quences, some of the predicted gene models may combine two VCB__ 0 43 5 distinct transcripts.

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