Abstract: 【Aim】 This study aims to reconstruct the phylogenetic relationships among the higher-level taxa (families and subfamilies) of Termitoidae using transcriptome and low-coverage whole-genome sequencing data, providing a phylogenomic approach for studing the systematic evolution of termites. 【Methods】 By downloading the existing transcriptome (70) and low-coverage whole-genome (5) sequencing data of 67 species of termites and 8 related species of Blattodea, we used BUSCO to evaluate these sequence data and screen the singlecopy nuclear genes. MAFFT was used to align the nucleotide and amino acid sequences of the obtained single-copy nuclear genes, and trimAl was used to trim the alignments. Phykit was used to generate nucleotide and amino acid sequence data supermatrices with different completeness (including 50% and 25% missing data, respectively) to investigate the effect of missing data on the phylogenetic reconstruction. IQ-TREE was used to construct the maximum likelihood (ML) trees based on each matrix. In addition, ASTRAL was utilized to summarize the ML trees constructed on each marker included in the amino acid dataset faa_all, and obtain the species tree. Finally, FcLM analysis implemented in IQ-TREE was used to test the topology structure of different trees and obtain support for possible phylogenetic relationships inferred from different datasets. 【Results】 A total of 1 325 single-copy nuclear genes from the existing transcriptome and low-coverage whole-genome sequencing data of termites were obtained. Based on these single-copy nuclear genes, we constructed genomescale supermatrices of nucleotide and amino acid sequence data, with nucleotide sequence datasets ranging from 144 294 to 1 839 525 sites and amino acid datasets ranging from 48 098 to 613 175 sites. Different types of data matrices generated similar phylogenetic relationships in Termitoidae and three nucleotide data matrices produced the same inter-family phylogenetic relationships. For the amino acid data, two out of the three concatenated gene datasets produced inter-family phylogenetic relationships that were largely consistent with the nucleotide sequence datasets. This study supports the monophyly of Termitoidae and suggests that Mastotermitidae is the sister group to all other termite families. In most analyses, Archotermopsidae and Stolotermitidae were sister groups, forming the 2nd diverging branch within Termitoidae. The family Kalotermitidae is also a relatively ancient lineage within the termites, positioned after the Archotermopsidae and Stolotermitidae. The family Kalotermitidae forms a sister group relationship with the Neoisoptera. All analyses strongly support the monophyly of Neoisoptera. Within Neoisoptera, the family Stylotermitidae is the sister group to the remaining termite lineages. The family Serritermitidae is also a relatively basal lineage within Neoisoptera. The family Rhinotermitidae is a non-monophyletic group. The family Termitidae is a monophyletic group, with four out of the six concatenated gene datasets and species trees supporting the subfamily Macrotermitinae as the sister group to all other subfamilies within Termitidae. Most analyses support the subfamily Apicotermitinae as the 2nd branch within Termitidae. The concatenated gene data matrix supports the non-monophyly of Termitinae, but the species tree recovered Termitinae as a monophyletic group. 【Conclusion】 This study demonstrates the utility of transcriptome and low-coverage whole-genome sequencing data in reconstructing the phylogenetic relationships within Termitoidae, yielding results consistent with the previous studies. However, further data sampling, including specimens and molecular markers, is needed to elucidate the inter-subfamily relationships within this insect group.

Key words:  Termite, transcriptome, whole-genome, single-copy nuclear gene, phylogeny, monophyletic group