Chromosome evolution of deuterostome ALGs E, B2, C2, and Q. [Dataset]

(a) Reconstruction of deuterostome ALGs E, B2, C2, and Q based on pairwise comparisons. The sea star POC2 and POC9 correspond to sea urchin SPU1 (b). POC2 corresponds to a single hemichordate chromosome PFL6, and POC9 corresponds to PFL18 and PFL23 (c). These 3 PFL chromosomes (PFL6, PFL18, and PFL23) also correspond to SPU1 (d). This observation suggests that the chromosomes in the sea star (POC2, POC9, and POC20) correspond to those in the LCA of the 2 echinoderm species, while SPU1 resulted from fusion of the 2 echinoderm ancestral chromosomes (echinoderm ALGs E and B2⊗C2). To infer the ambulacrarian ancestral condition, the amphioxus BFL genome was compared to the ambulacrarian genomes. POC2 and PFL6 correspond to a single amphioxus chromosome BFL5, supporting the conclusion that echinoderm ALG E has a deeper root in the ambulacrarian LCA and deuterostome LCA (ambulacraria/deuterostome ALG E). On the other hand, POC9 and both PFL18 and PFL23 correspond to 2 amphioxus chromosomes, BFL16 and BFL3 (e–g). Based on this observation, it may be inferred that POC9 could represent the ambulacraria ancestral chromosome (ambulacraria ALG B2⊗C2), and hemichordate PFL18 and PFL23 resulted from a split of ambulacraria ALG B2⊗C2. Notably, in addition to POC9, amphioxus BFL3 also corresponds to POC20 (e). POC20 shows one-to-one correspondence with SPU21 and PFL22 (b–d), suggesting that an ancestral chromosome was present at least in the LCA of ambulacrarians (ambulacraria ALG Q) and remained intact in the echinoderm lineage (echinoderm ALG Q). To infer the deuterostome ancestral condition and the evolutionary history of BFL3, the scallop PYE genome was compared to those of the deuterostome genomes (h–k). The observation that BFL16 corresponds to a single PYE chromosome (PYE1) supports the idea that the deuterostome LCA possessed this chromosome (deuterostome ALG B2). Additionally, BFL3 corresponds to PYE17 and PYE2. PYE2 also corresponds to BFL13 and 2 one-to-one corresponding chromosomes in ambulacrarian species (POC20/SPU21/PFL22 and POC3/SPU9/PFL15). Therefore, the deuterostome LCA likely possessed ALGs C2 and Q. In the lineage leading to ambulacrarians, deuterostome ALGs B2 and C2 fused and became ambulacraria ALG B2⊗C2. Furthermore, BFL3 also corresponds to 2 vertebrate chromosomes [19,20], so the chordate LCA likely inherited deuterostome ALGs C2 and Q, and these 2 chromosomes then fused specifically in amphioxus to become BFL3. The data underlying this figure c