A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

Wang, Chao; Wallerman, Ola; Arendt, Maja L.; Sundström, Elisabeth; Karlsson, Åsa; Nordin, Jessika; Mäkeläinen, Suvi; Pielberg, Gerli; Hanson, Jeanette; Ohlsson, Åsa; Saellström, Sara; Rönnberg, Henrik; Ljungvall, Ingrid; Häggström, Jens; Bergström, Tomas F.; Hedhammar, Åke; Meadows, Jennifer R. S.; Lindblad‐Toh, Kerstin

doi:10.1101/2020.07.02.185108

Cited by 5 publications

(3 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Comparison of our Great Dane genome to the CanFam3.1 reference revealed several key findings important to canine genome biology. Several other long-read assemblies of canines are planned or have been recently released (63,64). The availability of these resources, along with other long-read canine that assembles that are planned or have been recently released (63,64), will provide significant benefits to the canine genomics community.…”

Section: Discussionmentioning

confidence: 99%

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Halo

Pendleton

Shen

et al. 2020

Preprint

View full text Add to dashboard Cite

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long non-coding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3’ end of LINE-1_Cfs (i.e., LINE-1_Cf 3’-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.SignificanceAdvancements in long-read DNA sequencing technologies provide more comprehensive views of genomes. We used long-read sequences to assemble a Great Dane dog genome that provides several improvements over the existing reference derived from a Boxer dog. Assembly comparisons revealed that gaps in the Boxer assembly often occur at the beginning of protein-coding genes and have a high-GC content, which likely reflects limitations of previous technologies in resolving GC-rich sequences. Dimorphic LINE-1 and SINEC retrotransposon sequences represent the predominant differences between the Great Dane and Boxer assemblies. Proof-of-principle experiments demonstrated that expression of a canine LINE-1 could promote the retrotransposition of itself and a SINEC_Cf consensus sequence in cultured human cells. Thus, ongoing retrotransposon activity may contribute to canine genetic diversity.

show abstract

Section: Discussionmentioning

confidence: 99%

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Halo

Pendleton

Shen

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…We explored three popularly used software applications for merging transcriptome assemblies -StringTie-merge [76,[126][127][128][129][130][131][132], TACO [133][134][135][136][137][138] and Cuffmerge [139][140][141][142][143][144] to combine 116 A. thaliana assemblies constructed by StringTie [59], Scallop [61] and Strawberry [60] (Please check section 3 of Additional file 9 for more details). The best assembly was reported by StringTie-merge and was hence used for all other organisms.…”

Section: Psiclass Meta-assembly Work Better Than Other Approachesmentioning

confidence: 99%

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Banerjee

Bhandary

Woodhouse

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative. Results: We present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species. Conclusions: FINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision - ideal for bench researchers with limited experience in handling computational tools.

show abstract

“…This process allows for a rapid filtering of millions of variants to hundreds or tens of variants that can then be prioritized rapidly based upon the currently understood function of a particular gene. Next-generation reference genomes built using long-range sequencing technology [ 6 , 7 ], along with ever-improving genome annotations, are also rapidly improving the feasibility of using whole-genome resequencing to identify variants of interest for a particular trait or condition.…”

mentioning

confidence: 99%

Special Issue “Molecular Basis of Inherited Diseases in Companion Animals”

Friedenberg

Bannasch

2021

Genes

View full text Add to dashboard Cite

show abstract

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

Cited by 5 publications

References 60 publications

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Special Issue “Molecular Basis of Inherited Diseases in Companion Animals”

Contact Info

Product

Resources

About