Connexins during 500 Million Years-From Cyclostomes to Mammals

Abstract

It was previously shown that the connexin gene family had relatively similar subfamily structures in several vertebrate groups. Still, many details were left unclear. There are essentially no data between tunicates, which have connexins that cannot be divided into the classic subfamilies, and teleosts, where the subfamilies are easily recognized. There are also relatively few data for the groups that diverged between the teleosts and mammals. As many of the previously analyzed genomes have been improved, and many more genomes are available, we reanalyzed the connexin gene family and included species from all major vertebrate groups. The major results can be summarized as follows: (i) The same connexin subfamily structures are found in all Gnathostomata (jawed vertebrates), with some variations due to genome duplications, gene duplications and gene losses. (ii) In contrast to previous findings, birds do not have a lower number of connexins than other tetrapods. (iii) The cyclostomes (lampreys and hagfishes) possess genes in the alpha, beta, gamma and delta subfamilies, but only some of the genes show a phylogenetic affinity to specific genes in jawed vertebrates. Thus, two major evolutionary transformations have occurred in this gene family, from tunicates to cyclostomes and from cyclostomes to jawed vertebrates.

Keywords: cartilaginous fishes; connexins; evolution; gap junctions; lamprey; phylogeny; vertebrates.

Figure 1

Simplified overview of the relationships between the involved species. The abbreviations given in parentheses (rightmost) refer to the species abbreviations used in the present work. The groups outlined in green and blue font belong to the paraphyletic groups Chondrostei and Reptilia, respectively. Note that, formally, Aves also belongs to the Reptilia group. The tree itself is loosely based on https://en.wikipedia.org/wiki/Chordate, https://en.wikipedia.org/wiki/Vertebrate and https://en.wikipedia.org/wiki/Tetrapod, from which many of the animal illustrations are taken. The main species from which we tried to collect all their connexins sequences are indicated without square brackets, while the supplementary sequences were collected from the species in square brackets.

Figure 2

Compressed phylogenetic tree for connexins, except GJE1, in jawed vertebrates. The orthologous gene groups are indicated by their Greek nomenclature, using upper case letters if mammalian sequences are included in the orthogroup and lower-case letters if mammalian sequences are not included in the group. Sequences belonging to the gje1/GJE1 group are not included in this tree (see text). The letters at each branch signify the vertebrate groups as follows: A, Placental mammals, B, Marsupials, C, Monotremata (platypus), D, Aves (birds), E, Crocodylia, F, Testudines (turtles), G, Squamata (lizards and snakes), H, Amphibia, I, Lobe-finned fish (Latimeria), J, Chondrostei—Polypteriformes (reedfish), K, Chondrostei—Acipenseriformes (sturgeons), L, Holostei (spotted gar), M, Teleostei and N, Chondrichthyes (cartilaginous fishes). A space is left in the sequence of the letters to make it more evident that one or more groups are lacking that particular gene. The tree was constructed on the basis of the amino acid sequence (205 positions and 559 sequences) of the conserved domains by the Neighbor-Joining method using the Jones–Taylor–Thornton (JTT) substitution matrix and with the rate variations among the sites corresponding to a gamma value = 1.1. Bootstrap statistics are shown at the branching points (500 iterations). Bootstrap values below 30 are not shown. The compressed branches are shown in expanded form in Supplementary Figures S44–S68.

Figure 3

Compressed phylogenetic tree for connexins, except GJE1, in cyclostomes and gnathostomes. The annotation for the vertebrates is as described in the legend of Figure 2. The cyclostome sequences are indicated with their preliminary gene name (defined as described in the text) followed by the abbreviation describing the cyclostome species: Pm, Petromyzon marinus, sea lamprey; Et, Entosphenus tridentatus, Pacific lamprey; LcAL, Lethentheron camtschaticum, Arctic lamprey and Eb, Eptatretus burgeri, inshore hagfish. The cyclostome branches are indicated in red. The tree was constructed on the basis of the amino acid sequence (205 positions and 635 sequences) of the conserved domains by the Neighbor-Joining method using the JTT substitution matrix and with the rate variations among sites corresponding to a gamma value = 1.1 (same as in Figure 2) and with bootstrap statistics (500 iterations). Bootstrap values below 30 are not shown. Some of the orthogroups were united to save space and for giving a better overview. A Neighbor-Joining tree including GJE1, using the same JTT substitution matrix but with a gamma parameter = 0.8, is shown in Supplementary Figure S71.