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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.
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This content will become publicly available on April 6, 2026
A new chromosome-level genome assembly for western painted turtle Chrysemys picta belli, a model for extreme physiological adaptations
The western painted turtle, Chrysemys picta bellii, has the greatest tolerance to anoxia of any tetrapod studied to date. These turtles reside in the northern United States and southern Canada, and survive months of anoxia while submerged in ice-locked ponds and bogs. Reference genomes provide an important resource for elucidating the molecular bases for such unique physiological traits. An initial reference genome for this species was published in 2013, but the assembly is highly fragmented which poses several limitations for downstream analyses and biological interpretation. In this study, we created a new and improved assembly by combining PacBio HiFi, 10x Genomics Chromium, Hi-C sequence data and BioNano optical mapping derived from a single individual to generate a new haplotype-resolved chromosome-level assembly for C. picta bellii, called SLU_Cpb5.0. The genome size of the primary assembly is 2.372 Gb with a scaffold N50 of 133.6 Mb, which is a 6.5-fold improvement over the existing assembly. Genome annotation of SLU_Cpb5.0 revealed 12,242 novel genes compared to previous assemblies. Our PacBio Iso-Seq RNA sequencing data for twelve tissues unraveled over 100,000 novel transcript isoforms and 4,325 novel genes that were not annotated by standard NCBI pipeline. We also observed distinct patterns of tissue-specific isoform expression, creating a robust foundation for future characterization of the functions of these genes. The improved genome assembly and annotation will facilitate comparative genomics studies to better understand the genetic basis of C.picta bellii's extreme physiological adaptations and other aspects of its biology.
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- Award ID(s):
- 1951332
- PAR ID:
- 10596872
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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