Abstract
The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.
Highlights
Bradysia odoriphaga is a notorious pest that impacts the production of Liliaceae family vegetables, especially the Chinese chive (Allium tuberosum), which is one of the main ingredients in Chinese dumplings [1]
Reads were classified by whether the 5’ primer, 3’ primer, or poly A tail were detected, with reads containing 5’ primer, 3’ primer, and poly A tail considered as full-length; those with the 5’ primer and 3’ primer, 3’ primer and poly A tail, or 5’ primer and poly A tail classified as non-full-length; and all other reads classified as short reads
We identified two isoforms of the acetylcholinesterase gene (Figure S1)
Summary
Bradysia odoriphaga is a notorious pest that impacts the production of Liliaceae family vegetables, especially the Chinese chive (Allium tuberosum), which is one of the main ingredients in Chinese dumplings [1]. This pest can cause more than 50% loss of the Chinese chive production or even total destruction in the absence of a chemical control [2]. B. odoriphaga is that most of its lifecycle is underground, and people only realize the damage when the chives stunt or even die Another reason for difficulties controlling the pest is that its rapid life-cycle results in high resistance to commonly used insecticides [3,4]. The short-read length is limited in that complex regions with repetitive or heterozygous sequences may be misassembled [12], and PCR amplification bias during
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
