BUSCADOR RECOLECTA

Instituto de Salud Carlos III Ministerio de Ciencia e Innovación (España) Agencia Estatal de Investigación (España) Fundación Científica Asociación Española Contra el Cáncer European Commission, Peer reviewed

The genome browser screenshots of the Hox-located chromosomes of BFL (a) and PFL (b). Histograms of all TEs (red), DNA transposons (DNA, yellow), long terminal repeats (LTR, green), long interspersed nuclear elements (LINE, blue), and short interspersed nuclear elements (SINE, purple) are shown. The bin size for each histogram of TEs is 50,000 bp or 10,000 bp (indicated on the left). Red boxes denote the genomic regions of the Hox clusters., Peer reviewed

GO enrichment analyses of genes located on the specific chromosomes of the hemichordate PFL. The enriched GO terms (adjusted p-value <0.05) are clustered and divided into different modules. Descriptions of the most enriched GO terms of biological process (BP) within each module for genes located on PFL 9 (a), PFL18 (c), and PFL23 (e). The full list of enriched GO terms is provided in S4 Data. Results of the GO enrichment network analysis of genes located on PFL9 (b), PFL18 (d), and PFL23 (f). All labels are consistent with S17 Fig. The data underlying this figure can be found in S4 Data., Peer reviewed

GO enrichment analyses of genes located on the specific chromosomes of the sea star POC. The enriched GO terms (adjusted p-value <0.05) are clustered and divided into different modules. Descriptions of the most enriched GO terms of biological process (BP) within each module for genes located on POC12 (a), POC6 (c), and POC9 (e). The bars indicate -log10 adjusted p-values for the corresponding GO terms. The full list of enriched GO terms, including BP (biological process), CC (cellular component), and MF (molecular function), is provided in S2 Data. Results of the GO enrichment network analysis of genes located on POC12 (b), POC6 (d), and POC9 (f). Each individual node of the network denotes a specific enriched GO term. Different colors represent different modules of GO terms. Unclassified GO terms are labeled in gray color. Sizes of the circles indicate numbers of genes in each GO term. Manually selected GO terms are indicated with asterisks (*).The data underlying this figure can be found in S2 Data., Peer reviewed

The identified chromosomal rearrangement events in bilaterians are not found in the jellyfish genome. SPU3 was derived from DALG R, which dispersed into other chromosomes in chordates. Since SPU3 corresponds to RES19, the chordate dispersal event did not occur in the jellyfish (a). BFL3 and BFL16 correspond to different RES chromosomes, while their ALGs (DALGs B2 and C2) fused into ambulacraria AALG B2⊗C2. Thus, the ambulacrarian fusion event was not found in the jellyfish (b). Similarly, PYE1 and PYE17 both correspond to ambulacraria AALG B2⊗C2 and match to different RES chromosomes (c). The 4 shared fusion events in spiralians were not found in the jellyfish genome, as sea urchin chromosomes corresponding to fused spiralian chromosomes match to different jellyfish chromosomes (indicated by columns of the same color) (d). The data underlying this figure can be found in S1 Data., Peer reviewed

Pairwise genome comparisons between ecdysozoans and sea urchin SPU showing complex chromosomal rearrangement events in ecdysozoan species, including nematode (a), prawn (b), and horseshoe crabs (c and d). The butterfly genome seems more conserved than the other examined ecdysozoans (e and f). The 4 spiralian fusion events were not found in butterflies, as sea urchin chromosomes corresponding to fused spiralian chromosomes match to different butterfly chromosomes (indicated by columns of the same color). The data underlying this figure can be found in S1 Data., Peer reviewed

(a) Syntenic analysis of sea urchin LVA and LPI shows remarkable microsynteny conservation (i.e., linear relationships between chromosome pairs). Sea urchin LVA2 corresponds to SPU6 and SPU18, indicating LVA2 was fused from 2 ancestral chromosomes (b). Similarly, sea urchin LPI2 also corresponds to SPU6 and SPU18 (c), suggesting that this fusion event is a common trait in the Lytechnus genus. Furthermore, LVA1 corresponds to SPU8 and SPU19 (b), and LPI5 corresponds to SPU13 and SPU19 (c), indicating additional lineage-specific fusion events in sea urchin LVA and LPI. The data underlying this figure can be found in S1 Data., Peer reviewed

A stepwise process of sea urchin chromosomal evolution. We divided the process into 4 time points: t0, t1, t2, and ts (bottom right panel). At “t0,” individual chromosomes have not fused. At “t1,” 2 chromosomes are fused by either end-end translocation or centric insertion. At “t2,” intra-chromosomal translocations occur, although long stretches of chromosomal regions are still maintained. At “ts,” extensive intra-chromosomal rearrangements have occurred, and the fused chromosome becomes scrambled (fusion-with-mixing). We deduced 5 major fusion events that occurred during sea urchin chromosomal evolution, as follows. (1) Echinoderm EALGs E and B2⊗C2 fused and mixed to become sea urchin SALG E⊗(B2⊗C2) (t0 to ts in green). (2) EALGs B3 and J1 fused via centric insertion, followed by translocation to become SALG J1↘B3(t0 to t2 in maroon). (3) A Lytechinus-specific fusion event resulted from end-end fusion of SALGs G and D without obvious translocation (t0 to t1 in gray). (4) An LVA-specific fusion event involved Lytechinus LALGs F and J1⊗B3 without obvious translocation (t0 to t1 in Navajo white). (5) An LPI-specific fusion resulted from end-end fusion of Lytechinus LALGs F1 and C1, followed by an intrachromosomal translocation event (t0 to t2 in blue). Box sizes do not reflect the actual sizes of chromosomes., Peer reviewed

(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 can be found in S1 Data., Peer reviewed

(a) Reconstruction of deuterostome ALGs O2, B3, and J1 based on pairwise comparisons. The sea star POC6 corresponds to sea urchin SPU20 and SPU8 (b) and hemichordate PFL2 and PFL11 (c); SPU20 and SPU8 also correspond to these 2 PFL chromosomes (d), indicating that these 2 chromosomes were present at least in the ambulacrarian and echinoderm LCAs, and POC6 resulted from fusion of the 2 ancestral chromosomes (ALGs O2 and B3). Intriguingly, in addition to POC6, SPU8 also corresponds to POC14, while POC14 corresponds to a single hemichordate chromosome PFL17. Consistently, SPU8 corresponds to PFL11 and PFL17 (d), indicating that a single chromosome corresponding to POC14/PFL17 is an ancestral trait (ALG J1), while SPU8 resulted from chromosomal fusion (ALGs B3 and J1). Therefore, it can be inferred that the LCAs of ambulacrarians and echinoderms possessed these 3 ALGs (O2, B3, and J1), which remained as individual chromosomes in hemichordates but underwent different fusion events in different echinoderm lineages. Fusion of ALGs O2 and B3 led to sea star POC6, while fusion of ALGs B3 and J1 resulted in sea urchin SPU8. Consistent with this hypothesis, 3 distinct amphioxus chromosomes BFL19, BFL18, and BFL17 correspond to POC6 and POC14 (e); SPU20 and SPU8 (f); and PFL2, PFL11, and PFL17 (g). This correspondence supports the idea that the presence of the 3 ALGs can be traced back to the LCA of deuterostomes and remained in the chordate LCA. This conclusion is further reinforced by the observation that the scallop genome contains 3 distinct chromosomes (PYE3, PYE19, and PYE18) corresponding to POC6 and POC14 (h); SPU20 and SPU8 (i); PFL2, PFL11, and PFL17 (j); and BFL19, BFL18, and BFL17 (k). Additionally, the 3 amphioxus chromosomes BFL19, BFL18, and BFL17 have been shown to correspond to 3 distinct vertebrate chromosomes [19,20], supporting the conclusion that the chordate LCA possessed these 3 chromosomes. The data underlying this figure can be found in S1 Data., Peer reviewed