Draft genome of the cotton aphid Aphis gossypii

Qingmei Quan; Xiao Hu; Bohu Pan; Baosheng Zeng; Ningning Wu; Gangqi Fang; Yanghui Cao; Xiaoya Chen; Xuan Li; Yongping Huang; Shuai Zhan

doi:10.1016/j.ibmb.2018.12.007

Draft genome of the cotton aphid Aphis gossypii

Insect Biochem Mol Biol. 2019 Feb:105:25-32. doi: 10.1016/j.ibmb.2018.12.007. Epub 2018 Dec 24.

Authors

Qingmei Quan¹, Xiao Hu¹, Bohu Pan², Baosheng Zeng³, Ningning Wu³, Gangqi Fang³, Yanghui Cao¹, Xiaoya Chen⁴, Xuan Li⁵, Yongping Huang⁶, Shuai Zhan⁷

Affiliations

¹ Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
² Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
³ Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; Plant Science Research Center, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
⁵ Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
⁶ Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. Electronic address: yphuang@sibs.ac.cn.
⁷ Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. Electronic address: szhan@sibs.ac.cn.

PMID: 30590189
DOI: 10.1016/j.ibmb.2018.12.007

Abstract

The cotton aphid Aphis gossypii Glover is a worldwide agricultural pest that feeds on cotton, melon, and other landscape plants, causing a high level of economic loss. In addition to the common characteristics shared with other aphids, Ap. gossypii has evolved multiple biotypes that present substantial differences in host adaption. These intriguing biological features are of interest from both a fundamental and applied perspective. However, the molecular studies of Ap. gossypii have been restrained by the lack of a reference genome. Furthermore, in order to establish a platform for the development of novel and sustainable control methods, it is necessary to generate genomic resources for Ap. gossypii. Here, we present a 294 Mb draft genome sequence of Ap. gossypii, which consists of 4,724 scaffolds with an N50 size of 438 kb. Compared to other aphid species with published genomes, Ap. gossypii presents the most compact genome size. A total of 14,694 protein-coding genes were predicted and annotated in the consensus gene set, 98.03% of CEGMA genes and 93.5% of BUSCO genes were captured respectively. Genome-wide selection analyses revealed that significantly evolving pathways in the genus Aphis are related to biological processes of detoxification, steroid biosynthesis, and ethylbenzene degradation. The acquisition of the genome of Ap. gossypii makes it possible to understand the molecular mechanism of intricate biological traits of this species, and will further facilitate the study of aphid evolution.

Keywords: Aphis gossypii; Comparative genomic analysis; Genome annotation; Genome assembly; Genome evolution.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adaptation, Biological
Animals
Aphids / genetics*
Biological Evolution*
Female
Genome, Insect*
Multigene Family