ArticleGigaScience2017
De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads.
Article in GigaScience, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
156 citing papers in PubMed, 1 synthesis or guideline pooled it, 263 citations in OpenAlex.
- Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives.Plant communications · 2022Pooled it
- Identification of carnivory in the flowering plant Saxifraga via multidisciplinary evidence.Nature communications · 2026Article
- A genome assembly of the North American golden eagle, Aquila chrysaetos canadensis.The Journal of heredity · 2026Article
- Genome assembly for the Sierra Nevada Parnassian (Parnassius behrii) and a brief review of butterfly genome sizes.The Journal of heredity · 2026Review
- Chromosome-level reference genome of a foundational California native legume, Acmispon strigosus.The Journal of heredity · 2026Article
- The genome assemblies of the Tui chub, Siphateles bicolor, and Arroyo chub, Gila orcuttii.The Journal of heredity · 2026Article
- A chromosome-level genome assembly for the beach-spawning California grunion, Leuresthes tenuis.The Journal of heredity · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- A genome assembly for mule deer, Odocoileus hemionus, from Southern California.The Journal of heredity · 2026Article
- A high-quality reference genome for the ornate shrew (Sorex ornatus).The Journal of heredity · 2026Article
- "A genome assembly of the California flannelbush, Fremontodendron californicum".The Journal of heredity · 2026Article
- A genome assembly of Douglas' meadowfoam, Limnanthes douglasii R. BR.The Journal of heredity · 2026Article
- A chromosome level genome assembly of the marine flowering plant, Torrey's surfgrass (Phyllospadix Torreyi) reveals an exceptionally large Y-chromosome.The Journal of heredity · 2026Article
- Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal (Mirounga angustirostris).The Journal of heredity · 2026Article
- A genome assembly of Greene's tuctoria, Tuctoria greenei, an amphibious endemic and endangered California vernal pool grass.The Journal of heredity · 2026Article
- A reference genome for Colusa grass, Neostapfia colusana, a threatened and endangered California vernal pool plant.The Journal of heredity · 2026Article
- Genome assemblies of two bumble bee species: Bombus sonorus and Bombus vosnesenskii.The Journal of heredity · 2026Article
- A reference genome for the rough limpet Lottia Scabra, an intertidal species from the northeastern Pacific.The Journal of heredity · 2026Article
- A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles.The Journal of heredity · 2026Article
- The reference genome of a Sierra Nevada endemic, the cut-leaved monkeyflower, Mimulus laciniatus (syn. Erythranthe lacinata).The Journal of heredity · 2026Article
96 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be numerous misassemblies in the references, including missing sequences in gaps, erroneous sequences flanking gaps, base call errors in difficult-to-sequence regions, complex repeat structure errors, and allelic differences between the 2 haplotypes. These improvements were validated by single long-genome and transcriptome reads and resulted for the first time in completely resolved protein-coding genes widely studied in neuroscience and specialized in vocal learning species. These findings demonstrate the impact of long reads, sequencing of previously difficult-to-sequence regions, and phasing of haplotypes on generating the high-quality assemblies necessary for understanding gene structure, function, and evolution.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.