Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae)

Abstract The sugarcane aphid, Melanaphis sacchari, is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. In this study, we used nanopore long reads and a high-throughput chromosome conformation capture chromatin interaction maps to g...

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Bibliographic Details
Published in:G3 : genes - genomes - genetics 2024-11, Vol.14 (11)
Main Authors: Zhao, Jinshuai, Xie, Liqiang, Zhao, Xinrui, Li, Luhua, Cui, Jianghui, Chen, Jinfeng
Format: Article
Language:English
Subjects:
Animals
Aphids - genetics
Chromosome Mapping
Genome Report
Genome, Insect
Genomics - methods
Molecular Sequence Annotation
Phylogeny
Repetitive Sequences, Nucleic Acid
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Summary:Abstract The sugarcane aphid, Melanaphis sacchari, is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. In this study, we used nanopore long reads and a high-throughput chromosome conformation capture chromatin interaction maps to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the 3 autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes, and a total of 12,530 protein-coding genes were annotated, achieving 95.8% Benchmarking Universal Single-Copy Ortholog gene completeness. This offered a substantial improvement compared with previous low-quality genomic resources. A phylogenomic analysis by comparing M. sacchari with 24 published aphid genomes representing 3 aphid tribes revealed that M. sacchari belonged to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study are useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.
ISSN:2160-1836
2160-1836
DOI:10.1093/g3journal/jkae223