A dynamic history of gene duplications and losses characterizes the evolution of the SPARC family in eumetazoans

Abstract

The vertebrates share the ability to produce a skeleton made of mineralized extracellular matrix. However, our understanding of the molecular changes that accompanied their emergence remains scarce. Here, we describe the evolutionary history of the SPARC (secreted protein acidic and rich in cysteine) family, because its vertebrate orthologues are expressed in cartilage, bones and teeth where they have been proposed to bind calcium and act as extracellular collagen chaperones, and because further duplications of specific SPARC members produced the small calcium-binding phosphoproteins (SCPP) family that is crucial for skeletal mineralization to occur. Both phylogeny and synteny conservation analyses reveal that, in the eumetazoan ancestor, a unique ancestral gene duplicated to give rise to SPARC and SPARCB described here for the first time. Independent losses have eliminated one of the two paralogues in cnidarians, protostomes and tetrapods. Hence, only non-tetrapod deuterostomes have conserved both genes. Remarkably, SPARC and SPARCB paralogues are still linked in the amphioxus genome. To shed light on the evolution of the SPARC family members in chordates, we performed a comprehensive analysis of their embryonic expression patterns in amphioxus, tunicates, teleosts, amphibians and mammals. Our results show that in the chordate lineage SPARC and SPARCB family members were recurrently recruited in a variety of unrelated tissues expressing collagen genes. We propose that one of the earliest steps of skeletal evolution involved the co-expression of SPARC paralogues with collagenous proteins.

Figure 1.

Paralogy and orthology relationships of the SPARC gene family members in eumetazoans. (a) Bayesian inference phylogenetic tree of the SPARC family. SPOCK family was used as outgroup. Posterior probabilities are shown on each node. Scale bar indicates the number of substitutions per site. See the electronic supplementary material, table S1 for accession numbers and name abbreviations. (b) Synteny conservation among vertebrate and amphioxus SPARC chromosomal regions. The amphioxus SPARCB and SPARC/SPARCL1 genes are located on three overlapping genomic contigs numbered 329, 562 and 131 (i). This amphioxus region is co-orthologous to regions of the human (ii) chromosomes 4 (containing SPARCL1), 5 (containing SPARC) and 10, as well as regions of the zebrafish (iii) chromosomes 1 (containing SPARCL1), 7, 14 (containing SPARC), 17 (containing SPARCB) and 12.

Figure 2.

Comparative analysis of gene expression patterns of chordate SPARC homologues. (a–f) SPARC/SPARCL1 in situ hybridizations, amphioxus embryos are at (a) the early neurula, (b) mid–late neurula and (c) larvae stages. (d) Ascidian embryos are at the late neurula, (e) tadpole and (f) larvae stages. (g–r) SPARC in situ hybridizations, zebrafish embryos are at stages (g) 18 hpf, (h) 24 hpf, and (i,j) 72 hpf. Amphibian embryos are at stages (k) 21, (l) 27 and (m) 31. Mouse embryos are at stages (n) E7.5, (o) E8.5, (p) E11.5, (q,r) E10.5. (s–z) SPARCL1 in situ hybridizations, zebrafish embryos are at stages (s) 24 hpf, (t) 48 hpf and (u) 72 hpf. Mouse embryos are at stages (v) E7.5, (w) E8.5, (x) E9.5, (y) E10.5 and (z) E11.5. (a′–h′) SPARCB in situ hybridizations, amphioxus embryos are at the (a′) mid–late neurula, late (b′) neurula and (c′) larvae stages. Ascidian embryos are at the early (d′) gastrula, (e′) neurula, (f′) early tailbud and (g′,h′) late tailbud stages. Embryos are oriented with their anterior and dorsal sides leftward and upward, respectively, except for (a,d,k,e′) (dorsal view); (n–r,v–z) (anterior upward, dorsal towards the left); and (d′) (vegetal pole view), (h′) (ventral views). For mouse embryos, the images were inverted and the right side of the embryos is shown. A summary of the phylogenetic relationships of these genes is indicated on the right. Description of the different expression patterns can be found in the main text.

Figure 3.

Evolutionary scenario of the SPARC gene family in eumetazoans. The diagram depicts a phylogenetic tree of metazoan species whose SPARC homologues were analysed in this study. Whole-genome duplications are indicated at the base of each branch in which they were inferred to have occurred. We have considered here a scenario with no gene loss before these duplications and we have indicated the gene losses that probably occurred between these duplications and the ancestor of osteichtyans or teleosts. On the right the presence of SPARC family members with their syntenic relationships in different eumetazoan species is shown.