The genome of Phlebotomus chinensis, the primary vector of visceral leishmaniasis in China: insights from chromosome-level assembly and comparative analysis.

backgroundPhlebotomus chinensis is the primary vector of visceral leishmaniasis (VL) in China. However, the lack of a high-quality genome assembly for this species has limited research on its biology, vector-pathogen interactions, and evolutionary adaptations. To address this critical gap, the first chromosome-level genome assembly of Ph. chinensis was constructed.

methodsNanopore long-read sequencing served as the primary method, complemented by Illumina short-read sequencing for base-level error correction and Hi-C mapping for chromosomal anchoring and chromosome-level scaffolding. Genome annotation integrated transcriptome data from adult, larvae and pupae, homologous protein predictions from closely related sand fly species, and ab initio gene prediction. Comparative genomic analyses were further performed to explore evolutionary relationships and genomic differences between Ph. chinensis, Ph. papatasi, and Lutzomyia longipalpis.

resultsA total of 127.05 Gb of Nanopore data, 10.57 Gb of Illumina clean data, 52.95 Gb of Hi-C clean data, and 14.95 Gb of RNA-seq data were obtained. The final assembled genome size was 195.21 Mb with a scaffold N50 of 49.30 Mb, and 97.24% of the sequences were successfully anchored to 4 chromosomes. Annotation identified 10,909 protein-coding genes (91.48% of which were functionally annotatable), along with 73 rRNAs, 92 small RNAs, 82 regulatory RNAs, 374 tRNAs, 11,870 simple sequence repeats, 6053 tandem repeats, and 478,622 transposable elements. Phylogenetic analysis revealed that Ph. chinensis is phylogenetically closest to Ph. papatasi, with an estimated divergence time of approximately 27.1 million years ago. Gene family evolution was dominated by contraction, with 229 expanded and 575 contracted gene families identified in the Ph. chinensis branch. Additionally, 209 positively selected genes were detected, which are crucial for immune response regulation and metabolic processes related to its vectorial capacity. Furthermore, 95 P450 genes were identified, classified into four subfamilies: CYP2, CYP3, mitochondrial CYP (mito), and CYP4.

conclusionsA high-quality chromosome-level genome assembly of Ph. chinensis is reported here for the first time. This assembly serves as a critical genomic resource to advance research into the vector biology, insecticide resistance mechanisms, and evolutionary history, and lays a solid foundation for the development of precision VL control strategies in China.