UMMS Affiliation
RNA Therapeutics Institute; Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology
Publication Date
2018-01-29
Document Type
Article Postprint
Disciplines
Biology | Computational Biology | Ecology and Evolutionary Biology | Genetics | Genomics
Abstract
We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and > 393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2 -O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo.
Keywords
chromosomes, evolutionary biology, genes, genomics, genome assembly, piRNA, siRNA, miRNA, sex determination, cultured cell, 41 High Five, CRISPR, cabbage looper, Trichoplusia ni, Lepidoptera
Rights and Permissions
© 2018, Fu et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
DOI of Published Version
10.7554/eLife.31628
Source
Elife. 2018 Jan 29;7. pii: 31628. doi: 10.7554/eLife.31628. Link to article on publisher's site
Journal/Book/Conference Title
eLife
Related Resources
PubMed ID
29376823
Repository Citation
Fu, Yu; Yang, Yujing; Zhang, Han; Farley, Gwen; Wang, Junling; Quarles, Kaycee A.; Weng, Zhiping; and Zamore, Phillip D., "The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology" (2018). Open Access Articles. 3274.
https://escholarship.umassmed.edu/oapubs/3274
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Biology Commons, Computational Biology Commons, Ecology and Evolutionary Biology Commons, Genetics Commons, Genomics Commons