GSA Journals
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Genome Assembly and Annotation for Eaton et al., 2023

posted on 2024-05-09, 14:46 authored by Katherine EatonKatherine Eaton, Trevor Krabbenhoft, Nathan J. C. Backenstose, Moises BernalMoises Bernal

This is the complete genome assembly of the pinfish (Lagodon rhomboides). We used long-read nanopore sequencing to generate an initial assembly with Flye. This draft assembly was polished with short-read Illumina sequences (using the program Pilon). Finally, this assembly was scaffolded into a chromosome-scale genome using HiC chromatin conformation capture technology, yielding the final assembly shown here. The assembly is contained in the file titled: Final_Genome_TO_NCBI.fa

The complete genome annotation of this genome is contained in the file: Lrhomboides_rnd.2.1.all.maker.krakencontamremoved.gff.gz. This contains the predicted genes and transcripts from MAKER. 

Proteins predicted from the MAKER genome annotation were annotated based on BLAST similarity to proteins from the Sparus aurata, Larimichthys crocea, and Danio rerio genomes. The results of these BLAST annotations are available in the file: all_annotations.csv.


Article title

The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history

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