Chromosome-level genome assembly and population genomic analysis provide
novel insights into the immunity and evolution of Sogatella
furcifera
Abstract
Sogatella furcifera is an agricultural pest of great concern in
China and Southeast Asian countries. However, the lack of accurate and
complete reference genome resources has hindered the understanding of
immunity and evolution of S. furcifera. Here, we utilized
Nanopore sequencing to generate a chromosome-level assembly and
annotation of the S. furcifera genome (0.64 Gb), with a GC
content of 34.25%. This genome comprised 15 chromosomes covering
95.04% of the estimated genome size, together with an additional 624
small scaffolds making up the remaining 4.96% of the genome of S.
furcifera. A total of 24,669 protein-coding genes as well as 1211 long
noncoding RNA and 7595 circular RNA transcripts were well annotated and
predicted. Comparative genomic analysis revealed the rapidly evolved
genes associated with multiple immune-related pathways in S.
furcifera, which may be responsible for its rapid evolutionary
adaptation. In addition, 14 immune genes in the classic immune pathways
were selected for functional validation through RNA interference
experiments, demonstrating the antiviral effects of Dorsal and Dif genes
in S. furcifera. Genome resequencing of 44 individuals from 12
geographic populations revealed an absence of population structures and
frequent gene flow among all populations. Sweep analysis indicated that
2926 genes were under natural selection and significantly enriched in
several biological processes of morphogenesis and immunity. The first
systematic identification of immune genes and noncoding RNAs from
chromosome-level genome assembly plus the comparative and population
genomic analysis will provide more insights into the understanding of
the immunity and evolutionary adaptation of S. furcifera.