RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

Abstract

Grassland butterflies are considered representative indicators of biodiversity and ecosystem health. Their dramatic decline caused by habitat destruction, intensifying agriculture and global warming has prompted concern for conservation. While ecological indices of butterflies have been documented, there is a lack of genomic resources relative to the biological importance of this group. Here, we report, first whole-transcriptomic resource for Fabriciana nerippe, a brush-footed butterfly member that is endangered in Korea. Approximately, 241.3 million clean reads were obtained from paired-end Illumina sequencing of adult whole-body RNA. The de novo assembly resulted in 114 405 unigenes with length ranging from 133 to 33 218 bp. We found 41 868 assembled unigenes homologous to sequences in locally curated PANM-DB (Protostome DB). We assigned gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology terms to 18 085 and 5779 unigenes, respectively. InterProScan predicted 6691 protein domains for the assembled unigene sequences, with the reverse transcriptase and zinc finger domains found to be the most predominant. A total of 315 282 simple sequence repeats (SSRs) were identified from the assembled unigenes, when considering dinucleotide to octanucleotide repeats with a minimum of three repeat units. AT/AT, AAT/ATT, and AAAT/ATTT represented the most prominent SSR repeat types in the transcriptome. The unigene annotation profile and microsatellites generated in the study can serve as a reference resource for closely related species and gene functional analysis studies. Our data can be utilized to study ecological drift and loss of the species, consequently leading to better protection of the population.

Expression differences inAphidius ervi(Hymenoptera: Braconidae) females reared on different aphid host species

“…3 ). This GO term distribution is congruent with other insect transcriptomes already sequenced ( Hwang et al., 2016 ).…”

Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery

“…The locally curated PANM-DB was an addition to the Molluscs database, and covers the available sequences of the Protostomia group in a multi-FASTA format [53]. Furthermore, our results showed that more than 90% of unigenes with a sequence length >2000 bp matched with a homologous protein in the databases, which is possible because the protein-coding genes generally give rise to longer full-length transcripts [54]. The BLASTX top-hit species distribution showed putative homology of the annotated unigene sequences across species in the PANM-DB.…”

Transcriptome studies of the floodwater mosquito, Aedes vexans (Diptera: Culicidae) with potential as secondary vectors using Illumina HiSeq 4,000 sequencing

“…PANM‐DB is the database of choice for sequence annotation of insect and molluscan non‐model species (Hwang et al . 2016; Kang et al . 2018; Patnaik et al .…”

“…The result obtained confirms that annotation using PANM-DB is more efficient with greater number of valuable annotations compared to other public databases. PANM-DB is the database of choice for sequence annotation of insect and molluscan non-model species (Hwang et al 2016;Kang et al 2018;Patnaik et al 2016aPatnaik et al , 2016bPatnaik et al 2019). In the annotated results, the highest number of unigenes (6,875 sequences) found homologous sequences exclusively in PANM-DB, whereas about 10,983 unigenes were found annotated to all the four databases.…”