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Improvements to the Gulf pipefish Syngnathus scovelli genome.


ABSTRACT: The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first S. scovelli genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation. Here, using PacBio long-read high-fidelity sequences and a proximity ligation library, we generate an improved assembly to obtain 22 chromosome-level scaffolds. Compared to the first assembly, the gaps in the improved assembly are smaller, the N75 is larger, and our genome is ~95% BUSCO complete. Using a large body of RNA-Seq reads from different tissue types and NCBI's Eukaryotic Annotation Pipeline, we discovered 28,162 genes, of which 8,061 are non-coding genes. Our new genome assembly and annotation are tagged as a RefSeq genome by NCBI and provide enhanced resources for research work involving S. scovelli..

SUBMITTER: Ramesh B 

PROVIDER: S-EPMC10038202 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Improvements to the Gulf pipefish <i>Syngnathus scovelli</i> genome.

Ramesh Balan B   Small Clay M CM   Healey Hope H   Johnson Bernadette B   Barker Elyse E   Currey Mark M   Bassham Susan S   Myers Megean M   Cresko William A WA   Jones Adam Gregory AG  

GigaByte (Hong Kong, China) 20230220


The Gulf pipefish <i>Syngnathus scovelli</i> has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first <i>S. scovelli</i> genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation. Here, using PacBio long-read high-fidelity  ...[more]

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