Fig 1.
Millipede phylogenetic position and life cycle.
(A) Schematic diagram showing the phylogeny of myriapods, crustaceans, and insects; (B) life cycle of the orange rosary millipede, Helicorthomorpha holstii (based on [3] and our observations); (C) life cycle of the rusty millipede, Trigoniulus corallinus (based on [4]).
Table 1.
Comparison of myriapod genome assembly quality.
Fig 2.
TE content, genomic locality, and estimates of accumulation history for sequenced members of the Myriapoda.
Phylogenetic relationships among taxa are indicated on the left-hand side of the figure, alongside schematics of each myriapod species. From left to right: (i) pie charts scaled in proportion to assembled genome size, illustrating the relative contribution to myriapod genomes from each major repeat class; (ii) stacked bar charts illustrating the proportion of each repeat class found in genic (≤2 kb from an annotated gene) versus intergenic regions (>2 kb from an annotated gene) for each myriapod species, expressed as a percentage of the total assembled genome; (iii) repeat landscape plots illustrating TE accumulation history for each myriapod genome, based on Kimura distance-based copy divergence analyses, with sequence divergence (CpG adjusted Kimura substitution level) illustrated on the x-axis, percentage of the genome represented by each TE type on the y-axis, and transposon type indicated by the colour chart on the right-hand side. The underlying data of this figure can be found in S8 Data. CpG, region of DNA where a cytosine nucleotide is followed by a guanine nucleotide; LINE, long interspersed nuclear element; LTR, long terminal repeat; SINE, short interspersed nuclear element; TE, transposable element; tRNA, transfer RNA.
Fig 3.
(A) Hox and ParaHox gene cluster genomic organisations in millipedes and other arthropods. (B) Synteny comparisons between Hox gene scaffolds. Mindots = Minimum number of genes required to define a syntenic block.
Fig 4.
(A) Genomic organisation of miR-100/let-7/miR-125 clusters in various animals; (B) luciferase assays showing the repression activities of Hox genes by miR-iab-8 in both millipedes. The underlying data of this figure can be found in S8 Data.
Fig 5.
Argonaute duplication in millipedes.
(A) Schematic diagram showing the biogenesis pathway of microRNAs (upper) and a table summarising the number of gene copies contained in each millipede genome (lower); (B) schematic diagram showing the duplicates of the Ago gene in the 2 genomes. Conserved domains of AGO—ArgoN (red), ArgoL (blue), PAZ (green), and PIWI (orange). Inverted triangles, in TcoAGO2, indicate the position of multiple stop codons found in the corresponding gene sequence. Scale bar = 500 nucleotides. (C) Confirmation of the TcoAGO2 pseudogene. PCR and Sanger sequencing were carried out on gDNA collected from 3 Trigoniulus corallinus individuals that were not used for genome sequencing. Ago, Argonaute; gDNA, genomic DNA; miRNA, microRNA; UTR, untranslated region.
Fig 6.
Chemical defence in millipedes.
Schematic diagram of the metabolic pathways of (A) HCN and benzaldehyde and (B) quinone in millipedes. The pathways are drawn based on previous studies [38–41]. (C) The ozadene defensive gland of the millipede T. corallinus. HCN, hydrogen cyanide.
Fig 7.
Synteny comparisons of myriapod (millipedes Helicorthomorpha and Trigoniulus and centipede Strigamia) and deuterostome genomes.
Note that different degrees of syntenic regions could be detected between millipede genomes and deuterostome genomes, and between the centipede genome to deuterostome genomes.