Whole-genome survey information revealed the genome characteristics, mitochondrial genome diversity and evolutionary patterns of Stomatopoda species.

BACKGROUND: Stomatopoda possess extremely unique biological characteristics and evolutionary process; however, their phylogenetic relationships remain controversial. To avoid gene tree conflicts caused by a small number of genetic markers in previous phylogenetic studies of Stomatopoda, this study provides the first whole-genome survey sequencing data for three Stomatopoda species (Odontodactylus japonicus, Odontodactylus scyllarus, and Lysiosquillina maculata). RESULTS: Genome size assessment indicates that the genomes of the three species are extraordinarily large (O. japonicus: 8,942 Mb; O. scyllarus: 11,068 Mb; L. maculata: 12,743 Mb), and characterized by high heterozygosity (1.25%-1.51%) and extensive repeats (83.26%-86.22%). We further assembled and annotated the mitochondrial genomes of three Stomatopoda species, and results showed that the total length of the O. japonicus mitochondrial genome was 16,237 bp and contained 37 genes, while O. scyllarus and L. maculata have an ATP8 deletion and their lengths were 16,110 bp and 16,204 bp, respectively. In addition, mitochondrial coding sequences exhibited strong A/T bias and species-specific codon preferences, and structural modeling of tRNAs confirmed conserved cloverleaf conformations with lineage-specific deviations. Furthermore, we have found that the phylogenetic relationships within Stomatopoda remain inconsistent when inferred from different genetic markers. The further phylogenetic tree that incorporates multiple genetic markers (including mitochondrial genome, coding DNA sequences and amino acids) suggests that L. maculata occupies a more basal position. Additionally, the divergence time between Stomatopoda and other three orders (Decapoda, Amphipoda, and Isopoda) was approximately 385.00 Mya. CONCLUSIONS: Overall, our whole-genome survey sequencing and integrative phylogenomic analyses provide new insights into resolving the controversies on the phylogenetic relationships within Stomatopoda. These results can improve our understanding of the evolutionary process of Stomatopoda genome and provide valuable resources for future phylogenetic studies of Stomatopoda.