Biodiversity Genomes
We present the complete genome sequences of 5 species of Sardinella. Illumina sequencing was performed on genetic material from wild-caught specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
Introduction
Sardinella species are found in the Atlantic, Indian and Pacific Ocean. They are abundant in warmer waters of the tropical and subtropical oceans. All 5 species presented here occur in the Indo-Pacific region (Willette et al. 2011; Thomas et al. 2014). Adults are generally coastal, schooling, marine fish but juveniles are often found in lagoons and estuaries. Sardinella tawilis is a unique freshwater member among this group, inhabiting the volcanic Taal Lake in the Philippines (Willette, Carpenter, and Santos 2014). Fish of the genus have seven to 14 striped markings along the scales of the top of the head. The paddle-shaped supramaxilla bones are characteristic; they separate Sardinella from other genera and their shapes help distinguish species. They have paired predorsal scales and enlarged fin rays.
Methods
DNA extraction was performed using the Qiagen DNAeasy genomic extraction kit using the standard protocol. A paired-end sequencing library was constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150 bp format. The resulting fastq files were trimmed of adapter/primer sequence and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v2.5 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Results and Data Availability
All data, including raw reads and assembled genome sequence, is available via Genbank.
| TaxName | Raw_reads | Genome |
|---|---|---|
| Sardinella gibbosa | SRR24062822 | JASCIP000000000 |
| Sardinella lemuru | SRR24061572 | JASCQZ000000000 |
| Sardinella tawilis | SRR24061547 | JASCQY000000000 |
| Sardinella fimbriata | SRR24061541 | JASCQX000000000 |
| Sardinella hualiensis | SRR24060895 | JAUCNH000000000 |
Funding
Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.
REFERENCES
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