Long read sequencing of retinal RNA improves killifish transcriptome annotation
Rebba, S.; van Schalkwyk, L.; Krzywanska, A. M.; MacDonald, R. B.; Clark, B. B.; Ruzycki, P. A. · genomics · 2026-09-07 · 原文
DOI：10.64898/2026.09.02.748420作者：6 位
Purpose The African Turquoise Killifish has recently emerged as a powerful model for aging and age-related disease research studies. However, molecular based investigations have been limited by preliminary genome and transcriptome builds with incomplete reference genome sequence, fragmented chromosome assembly, and missing gene annotations. These issues make primary (alignment and quantification) and secondary (Gene Ontology, Gene Set Enrichment Analysis, cross-species comparisons) analyses difficult to reliably implement and interpret. This study seeks to generate a complete retinal reference transcriptome to facilitate future killifish transcriptomic, epigenetic, and proteomic studies of the visual system. Methods We generated an enhanced retina transcriptome using long-read PacBio RNAseq data that was processed using a robust computational pipeline to merge reads, classify genes, and annotate with nearest orthologous gene names from other species. This new annotation was compared to available references and validated using bulk and single cell RNAseq datasets. Results Comparison of the widely used Nfu_20140520 and the newly released NfurGRZ-RIMD1 genome builds identified NfurGRZ
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1. 人话版
Purpose The African Turquoise Killifish has recently emerged as a powerful model for aging and age-related disease research studies.
However, molecular based investigations have been limited by preliminary genome and transcriptome builds with incomplete reference genome sequence, fragmented chromosome assembly, and missing gene annotations.
2. 领域脉络
本文类目：genomics，属于其所在研究脉络的最新进展。
3. 机制拆解
These issues make primary (alignment and quantification) and secondary (Gene Ontology, Gene Set Enrichment Analysis, cross-species comparisons) analyses difficult to reliably implement and interpret.
This study seeks to generate a complete retinal reference transcriptome to facilitate future killifish transcriptomic, epigenetic, and proteomic studies of the visual system.
Methods We generated an enhanced retina transcriptome using long-read PacBio RNAseq data that was processed using a robust computational pipeline to merge reads, classify genes, and annotate with nearest orthologous gene names from other species.
4. 证据与数字
Results Comparison of the widely used Nfu_20140520 and the newly released NfurGRZ-RIMD1 genome builds identified NfurGRZ
5. 反例与边界
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