Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity

Abstract

It has been speculated that before vertebrates evolved somatic diversity-based adaptive immunity, the germline-encoded diversity of innate immunity may have been more developed. Amphioxus occupies the basal position of the chordate phylum and hence is an important reference to the evolution of vertebrate immunity. Here we report the first comprehensive genomic survey of the immune gene repertoire of the amphioxus Branchiostoma floridae. It has been reported that the purple sea urchin has a vastly expanded innate receptor repertoire not previously seen in other species, which includes 222 toll-like receptors (TLRs), 203 NOD/NALP-like receptors (NLRs), and 218 scavenger receptors (SRs). We discovered that the amphioxus genome contains comparable expansion with 71 TLR gene models, 118 NLR models, and 270 SR models. Amphioxus also expands other receptor-like families, including 1215 C-type lectin models, 240 LRR and IGcam-containing models, 1363 other LRR-containing models, 75 C1q-like models, 98 ficolin-like models, and hundreds of models containing complement-related domains. The expansion is not restricted to receptors but is likely to extend to intermediate signal transducers because there are 58 TIR adapter-like models, 36 TRAF models, 44 initiator caspase models, and 541 death-fold domain-containing models in the genome. Amphioxus also has a sophisticated TNF system and a complicated complement system not previously seen in other invertebrates. Besides the increase of gene number, domain combinations of immune proteins are also increased. Altogether, this survey suggests that the amphioxus, a species without vertebrate-type adaptive immunity, holds extraordinary innate complexity and diversity.

Box 1.

Most used abbreviations

Figure 1.

The ME tree of the TIR domain of insect TLRs, 48 amphioxus TLRs and vertebrate TLRs. The gene ID in gray represents alleles. The vertebrate TLR3, TLR5, and TLR7 families are too diverged to include in this tree. (Dashed lines) The possible position of those divergent sequences not used in the tree construction; (dots) the truncated P-TLRs. Another tree of more reliable statistical significance is shown in Supplemental Figure S3. (m) Mouse; (f) Fugu; (tet) tetraodon; (ch) chicken; (xt) Xenopus; (hal) halibut; (md) Musca domestica; (ag) Anopheles gambiae; (d) Drosophila.

Figure 2.

A schematic comparison of TLR, NLR, RLH, and TNF pathways between vertebrates and amphioxus. Dashed lines indicate that the pathway has no functional evidence as yet. The colors used for different domains have no special meaning.

Figure 3.

The ME tree of CTLD of amphioxus CTLs, including 879 amphioxus CTLDs. Subfamilies are colored. Five large amphioxus-specific CTL families are labeled A, B, C, D, and E.

Figure 4.

A schematic of the evolution of the complement system. (Solid line) The pathway has experimental evidence; (dashed lines) no experimental support; (?) the existence of the item or pathway is not verified; (*) amphiMASP1/3 gene can produce two proteins, MASP1 and MASP3; (**) amphioxus contains the most abundant CCP domains, see Supplemental Table S1; (***) the human C1q proteins recognize antibody, while the lamprey C1q serves as a lectin.

Figure 5.

(A) The ME tree of the amphioxus TNF family. Both alleles are included in the analysis. (Bf) B. floridae. (B) The configuration of the TNF cluster on Scaffold_7. Gray ovals indicate genes with expression data (Supplemental Fig. S9).