Additional file 2 of Parallel evolution of amphioxus and vertebrate small-scale gene duplications
Creators: name: Brasó-Vives, Marina
name: Marlétaz, Ferdinand
name: Echchiki, Amina
name: Mantica, Federica
name: Acemel, Rafael D.
name: Gómez-Skarmeta, José L.
name: Hartasánchez, Diego A.
name: Le Targa, Lorlane
name: Pontarotti, Pierre
name: Tena, Juan J.
name: Maeso, Ignacio
name: Escriva, Hector
name: Irimia, Manuel
name: Robinson-Rechavi, Marc
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology

description: Additional file 2: Figure S1. BraLan3 genome assembly and annotation quality comparison. Drer, Ggal, Mmus, Hsap, Bflo and Bbel correspond to the latest available genome assemblies for zebrafish, chicken, mouse, human, Florida amphioxus (B. floridae) and an Asian amphioxus (B. belcheri), respectively (see Methods). Blan2 corresponds to the latest genome reference for the European amphioxus previous to this publication [8] and Blan3 corresponds to BraLan3, the genome reference for the European amphioxus presented in this study. Percentage of the genome assembly sequence in scaffolds (sequences) of length greater than 1 million (M) nucleotides (size of chromosomal magnitude) versus the number of existing sequence gaps in these chromosomal-size sequences. Figure S2. A. Venn diagram representing the number of amphioxus specific orthologous groups (black) and amphioxus species-specific genes (gray). B. Percentage of small-scale gene duplications that are either multichromosomal, distant monochromosomal and tandem gene duplications in B. lanceolatum, chicken, mouse and human (Blan, Ggal, Mmus and Hsap respectively). Zebrafish is excluded from this comparison because of the effect that the 3R WGD in the teleost lineage could have had in the chromosomal localization of small-scale duplications. C. Similar to Fig. 5 for amphioxus inter-chromosomal, intra-chromosomal distant and tandemly duplicated small-scale duplicates that have single-copy orthologs in zebrafish. For B and C, Tandem gene duplications are defined as consecutive genes along the chromosomal sequence. Figure S3. Embryonic gene expression in single-copy and duplicated genes in B. lanceolatum. A. Box plots showing the distribution of the mean gene expression in transcripts per million (TPM) units across embryonic developmental stages for B. lanceolatum single-copy and small-scale duplicated genes. B. Same as A but dividing B. lanceolatum genes according to their vertebrate ortholog (single-copy, ohnolog, small-scale duplicate or B. lanceolatum specific). C-D. Box plots showing the distribution of developmental stage specificity of B. lanceolatum gene expression (Tau statistic) for the same gene groups as A and B. Tau values range from 0 (ubiquitous expression) to 1 (expression only in 1 tissue). Figure S4. Lower level of expression of duplicated genes compared to single copy genes within functional categories. Each point corresponds to a Gene Ontology (GO) term and its size refers to its number of human genes. A and B show molecular function categories, while C and D show biological processes categories. A and C show average expression in adult tissues, while B and D show average expression in embryonic stages. All points are filled with the same semi-transparent black color, thus opaque regions imply a high point density. Figure S5. Gene synteny comparison of B. lanceolatum and B. floridae with B. belcheri. One-to-one orthologs' synteny conservation between B. lanceolatum, B. floridae and B. belcheri. Black lines across plots correspond to the fusion/fission points of chromosome 1 in B. lanceolatum and chromosome 3 in B. floridae. Different colors depict different B. lanceolatum chromosomes on the left plots and different B. floridae chromosomes on the right plot. Figure S6. B. lanceolatum gene synteny comparison with B. floridae and G. gallus. A. Duplicated genes (many-to-many, many-to-one and one-to-many orthologs) synteny conservation between B. lanceolatum and B. floridae. B. B. lanceolatum within species duplicated genes (many-to-many, many-to-one and one-to-many orthologs) synteny conservation. C. One-to-one orthologs synteny conservation between B. lanceolatum and chicken (G. gallus). D. Same as in A for B. lanceolatum and chicken (G. gallus). In all cases (A-C) every gene is represented by its mid-point coordinates in the genome. Different colors depict different B. lanceolatum chromosomes.