AUTHOR=Fu Chun , Long WenCong , Luo ChaoBing , Nong Xiong , Xiao XiMeng , Liao Hong , Li YuanQiu , Chen Ying , Yu JiaXin , Cheng SiXuan , Baloch Saira , Yang YaoJun 

TITLE=Chromosome-Level Genome Assembly of Cyrtotrachelus buqueti and Mining of Its Specific Genes

JOURNAL=Frontiers in Ecology and Evolution

VOLUME=9

YEAR=2021

URL=https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2021.729100

DOI=10.3389/fevo.2021.729100

ISSN=2296-701X

ABSTRACT=<p><bold>Background:</bold> The most severe insect damage to bamboo shoots is the bamboo-snout beetle (<italic>Cyrtotrachelus buqueti</italic>). Bamboo is a perennial plant that has significant economic value. <italic>C. buqueti</italic> also plays a vital role in the degradation of bamboo lignocellulose and causing damage. The genome sequencing and functional gene annotation of <italic>C. buqueti</italic> are of great significance to reveal the molecular mechanism of its efficient degradation of bamboo fiber and the development of the bamboo industry.</p><p><bold>Results:</bold> The size of <italic>C. buqueti</italic> genome was close to 600.92 Mb by building a one paired-end (PE) library and k-mer analysis. Then, we developed nine 20-kb SMRTbell libraries for genome sequencing and got a total of 51.12 Gb of the original PacBio sequel reads. Furthermore, after filtering with a coverage depth of 85.06×, clean reads with 48.71 Gb were obtained. The final size of <italic>C. buqueti</italic> genome is 633.85 Mb after being assembled and measured, and the contig N50 of <italic>C. buqueti</italic> genome is 27.93 Mb. The value of contig N50 shows that the assembly quality of <italic>C. buqueti</italic> genome exceeds that of most published insect genomes. The size of the gene sequence located on chromosomes reaches 630.86 Mb, accounting for 99.53% of the genome sequence. A 1,063 conserved genes were collected at this assembled genome, comprising 99.72% of the overall genes with 1,066 using the Benchmark Uniform Single-Copy Orthology (BUSCO). Moreover, 63.78% of the <italic>C. buqueti</italic> genome is repetitive, and 57.15% is redundant with long-term elements. A 12,569 protein-coding genes distributed on 12 chromosomes were acquired after function annotation, of which 96.18% were functional genes. The comparative genomic analysis results revealed that <italic>C. buqueti</italic> was similar to <italic>D. ponderosae.</italic> Moreover, the comparative analysis of specific genes in <italic>C. buqueti</italic> genome showed that it had 244 unique lignocellulose degradation genes and 240 genes related to energy production and conversion. At the same time, 73 <italic>P450</italic> genes and 30 <italic>GST</italic> genes were identified, respectively, in the <italic>C. buqueti</italic> genome.</p><p><bold>Conclusion:</bold> The high-quality <italic>C. buqueti</italic> genome has been obtained in the present study. The assembly level of this insect’s genome is higher than that of other most reported insects’ genomes. The phylogenetic analysis of <italic>P450</italic> and <italic>GST</italic> gene family showed that <italic>C. buqueti</italic> had a vital detoxification function to plant chemical components.</p>