Intron turnover of slc26a1 and slc26a2 and convergence of intron insertion sites

Abstract

Intron gain and loss are rare events in vertebrates; however, comparative genome analysis of elephant sharks, tetrapods, and teleosts revealed a higher level of intron turnover in teleosts. slc26a1 and slc26a2 are members of the anion-exchanger gene family. Human, zebrafish, and Japanese pufferfish slc26a1 consist of two, two, and seven exons, respectively, and slc26a2, two, three, and four exons, respectively. To better understand intron turnover in teleosts, we analyzed the exon-intron organization of slc26a1 and slc26a2 in 81 vertebrates, including 62 ray-finned fish. In most Eurypterygii, which comprise the majority of the Neoteleostei and include Acanthomorpha, Aulopiformes, and Myctophiformes, slc26a1 and slc26a2 have seven and four exons, respectively, whereas those of most other ray-finned fishes consist of two and three exons, respectively, suggesting that intron gain occurred in both slc26a1 and slc26a2 of the Eurypterygii ancestor. In addition, notothenioid slc26a2 has six exons, suggesting that two introns were inserted into the notothenioid ancestor. The two newly acquired introns in the notothenioid consist of transposon-like sequences, suggesting that they were generated via transposon insertion. The positions of some of the newly acquired introns of slc26a1 and slc26a2 in Eurypterygii are identical or very close to those of other slc26 members. These results demonstrate the lineage-specific intron gains of slc26a1 and slc26a2 in ray-finned fish and convergence at the insertion sites of some of the newly acquired introns.

Keywords: Convergent evolution; Intron gain; Intron turnover; Ray-finned fish; Transposable element.

Fig. 1

Exon–intron organization of slc26a1, slc26a2, and slc26a12 in vertebrates. Results for 28 species are shown. Exons are indicated by filled-in colored boxes and numbers, and introns are indicated by white vertical bars (right). Divergence times of species were retrieved from the TimeTree database (http://www.timetree.org/) and shown on the left. The accession number of each sequence is summarized in Table 1.

Fig. 2

Comparison of intron positions among jawed vertebrate slc26a1, slc26a2, and slc26a12, related genes of lamprey had hagfish, and human slc26a3. (A) Schematic representation of the domain structure of human Slc26a1 protein. Transmembrane domains and the STAS (Sulfate Transporter and Anti-Sigma factor antagonist) domain are indicated by black and gray boxes, respectively. (B) Position of intron insertion sites in comparison with Slc26a1 domain structure shown in (A). Horizontal bars indicate polypeptide of each protein. Boxes indicate the site of intron insertion. The numbers indicate the position of intron insertion within each codon.

Fig. 3

Phylogenetic analysis of Slc26a1, Slc26a2, and Slc26a12 in vertebrates. The amino acid sequences of Slc26a1, Slc26a2, and Slc26a12 in jawed vertebrates were aligned with Slc26a2-like and Slc26a12-like in jawless fishes using ClustalW software and a phylogenetic tree was constructed by the maximum-likelihood method using IQ-TREE. Numbers indicate bootstrap values. The accession numbers of the amino-acid sequences used in this study are listed in Table 1.

Fig. 4

Exon–intron organization of slc26a1 and slc26a2 in spotted gar and teleosts. Results from 59 teleost species from 47 orders/suborders/families are presented and compared with those of the spotted gar, a basal ray-finned fish that is not a teleost. Exons are indicated by filled colored boxes and numbered, and introns are indicated by white vertical bars (right). Divergence times of species were retrieved from the TimeTree database (http://www.timetree.org/) and shown on the left. The tree topology between Osteoglossiformes (Asian bonytongue), Elopiformes (tarpon), Albuliformes (West African bonefish), and Anguilliformes (European eel and European conger) was drawn based on the recent study by Parey et al.. The tree topology between Galaxiiformes (peladilla) and Eurypterygii was drawn based on the recent study by Lavoué et al. and Near et al.. The accession number of each sequence is summarized in Table 1.

Fig. 5

Timing of recent intron turnovers of slc26a2 in Syngnathiformes and Notothenioidei and two scenarios for the intron turnovers of slc26a1 and slc26a2 in Euteleostei. (A) Timing of recent intron loss of slc26a2 in Syngnathiformes. (B) Timing of recent intron gain of slc26a2 in Notothenioidei. In (A) and (B), arrows indicate timing of recent intron turnovers of slc26a in each lineage. Divergence times of species were retrieved from the TimeTree database (http://www.timetree.org/) and shown on the left. (C) Two scenarios for the intron turnovers of slc26a1 and slc26a2 in Euteleostei. Upper panel indicates a scenario for the intron turnovers based on the evolutionary analyses by Lavoué et al. and Near et al., and lower panel indicates that based on the study by Betancur-R et al..

Fig. 6

Schematic representation of the primary structure of recently acquired introns in notothenioid slc26a2 and transposable element-like sequence. (A) Length and exon–intron organization of slc26a2 in a notothenioid emerald rockcod. Exons and introns are indicated by black boxes and horizontal bars, respectively. (B) Schematic representation of the sequence of the newly acquired intron 3 in notothenioid. (C) Schematic representation of the sequence of the newly acquired intron 5 in notothenioid. NTE, notothenioid putative transposable element. (D–K) Insertions of notothenioid putative transposable elements NTE-1 s to multiple loci of the notothenioid genomes. Insertion of NTE-1 to slc26a2 (D) and other loci (E–K) is shown. Accession numbers and the regions of indicated sequences are listed at the beginning of each line. Double slash indicates shortening sequence. Gaps are indicated by dashes in the sequences. Putative direct and inverted repeats are shown in red and blue, respectively. Protein coding and noncoding sequences are indicated by upper- and lower-case letters, respectively. gt-ag of intron 3 in slc26a2 are shown by gray boxes. Tbe Trematomus bernacchii, Nro Notothenia rossii, Cac Chaenocephalus aceratus, Han Harpagifer antarcticus, Pal Pogonophryne albipinna, Ema Eleginops maclovinus, Bdi Bovichtus diacanthus.