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

2020 ◽  
Author(s):  
Chao Wang ◽  
Ola Wallerman ◽  
Maja-Louise Arendt ◽  
Elisabeth Sundström ◽  
Åsa Karlsson ◽  
...  
Keyword(s):  
Reference Genome ◽  
Cancer Genes ◽  
Rna Seq ◽  
Structural Variants ◽  
Functional Elements ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Genomic Regions

AbstractHere we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.

scholarly journals A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Chao Wang ◽  
Ola Wallerman ◽  
Maja-Louise Arendt ◽  
Elisabeth Sundström ◽  
Åsa Karlsson ◽  
...  
Keyword(s):  
Reference Genome ◽  
Cell Receptor ◽  
Chromosome Length ◽  
Domestic Dog ◽  
Gene Products ◽  
Cancer Genes ◽  
Rna Seq ◽  
Structural Variants ◽  
Protein Coding ◽  
Genomic Regions

AbstractWe present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

GSD_1.0 (canFam4): A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

2020 ◽  
Author(s):  
Chao Wang ◽  
Ola Wallerman ◽  
Maja-Louise Arendt ◽  
Elisabeth Sundström ◽  
Åsa Karlsson ◽  
...  
Keyword(s):  
Reference Genome ◽  
Cell Receptor ◽  
Chromosome Length ◽  
Domestic Dog ◽  
Gene Products ◽  
Cancer Genes ◽  
Rna Seq ◽  
Protein Coding ◽  
Leukocyte Antigen ◽  
Genomic Regions

Abstract We present GSD_1.0, a novel high-quality domestic dog reference genome with chromosome length scaffolds and gap number reduced 41-fold, from 23,836 to 585. Annotation with novel and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of closed gaps harboured previously hidden functional elements, including promoters, genes and miRNAs. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leukocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. The sequencing of 27 dogs from 19 breeds with linked read technology uncovered 22.1 million SNPs, indels and larger structural variants. Intersection with protein coding genes showed that 1.4% could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

scholarly journals High quality, phased genomes of Phytophthora ramorum clonal lineages NA1 and EU1

2021 ◽  
Author(s):  
Nicholas C Carleson ◽  
Caroline M Press ◽  
Niklaus J Grunwald
Keyword(s):  
Reference Genome ◽  
Phytophthora Ramorum ◽  
Sudden Oak Death ◽  
Valuable Resource ◽  
High Quality ◽  
Total Size ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Live Oak ◽  
Long Read

Phytophthora ramorum is the causal agent of sudden oak death in West Coast forests and currently two clonal lineages, NA1 and EU1, cause epidemics in Oregon forests. Here, we report on two high-quality genomes of individuals belonging to the NA1 and EU1 clonal lineages respectively, using PacBio long-read sequencing. The NA1 strain Pr102, originally isolated from coast live oak in California, is the current reference genome and was previously sequenced independently using either Sanger (P. ramorum v1) or PacBio (P. ramorum v2) technology. The EU1 strain PR-15-019 was obtained from tanoak in Oregon. These new genomes have a total size of 57.5 Mb, with a contig N50 length of ~3.5-3.6 Mb and encode ~15,300 predicted protein-coding genes. Genomes were assembled into 27 and 28 scaffolds with 95% BUSCO scores and are considerably improved relative to the current JGI reference genome with 2,575 or the PacBio genomes with 1,512 scaffolds. These high-quality genomes provide a valuable resource for studying the genetics, evolution, and adaptation of these two clonal lineages.

scholarly journals A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

2020 ◽  
Vol 33 (7) ◽  
pp. 880-883
Author(s):  
Stefan Kusch ◽  
Heba M. M. Ibrahim ◽  
Catherine Zanchetta ◽  
Celine Lopez-Roques ◽  
Cecile Donnadieu ◽  
...  
Keyword(s):  
Host Range ◽  
Sclerotinia Sclerotiorum ◽  
Genome Assembly ◽  
Plant Pathogens ◽  
Reference Genome ◽  
Close Relative ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Reference Genome Assembly

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

scholarly journals A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Qingzhen Wei ◽  
Jinglei Wang ◽  
Wuhong Wang ◽  
Tianhua Hu ◽  
Haijiao Hu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Specific Gene ◽  
High Quality ◽  
Total Size ◽  
Protein Coding ◽  
Fruit Length ◽  
Protein Coding Genes

Abstract Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.

scholarly journals Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus

2021 ◽  
Author(s):  
R. Alan Harris ◽  
Muthuswamy Raveendran ◽  
Dustin T Lyfoung ◽  
Fritz J Sedlazeck ◽  
Medhat Mahmoud ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Syrian Hamster ◽  
Reference Genome ◽  
Sequence Data ◽  
Mesocricetus Auratus ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Sequencing Technologies ◽  
Long Read ◽  
Short Read Sequence

Background The Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was published in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and higher continuity. Findings Here, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gbp, similar to the 2.50 Gbp length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein coding genes and 10,459 noncoding genes were annotated in BCM_Maur_2.0 compared to 20,495 protein coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where approximately 17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0 in which the number of unresolved bases is reduced to 3.00%. Conclusions Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.

scholarly journals Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

ABSTRACTThe Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

scholarly journals De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation

2019 ◽  
Vol 7 (2) ◽  
pp. 391-402 ◽  
Author(s):  
Yaoxi He ◽  
Haiyi Lou ◽  
Chaoying Cui ◽  
Lian Deng ◽  
Yang Gao ◽  
...  
Keyword(s):  
High Altitude ◽  
De Novo Assembly ◽  
De Novo ◽  
Population Analysis ◽  
Extreme Environments ◽  
Structural Variants ◽  
Base Pairs ◽  
High Quality ◽  
Long Read ◽  
Altitude Adaptation

Abstract Structural variants (SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%–1.53%) compared to other East Asian genomes (0.70%–0.98%), reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence—a 662-bp intronic insertion in the SCUBE2 gene—is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.

scholarly journals Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mikhail Pomaznoy ◽  
Ashu Sethi ◽  
Jason Greenbaum ◽  
Bjoern Peters
Keyword(s):  
Gene Expression ◽  
Differential Expression Analysis ◽  
Cell Types ◽  
Library Preparation ◽  
Rna Seq ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Machine Learning Model ◽  
Specific Manner ◽  
Library Preparation Protocol

Abstract RNA-seq methods are widely utilized for transcriptomic profiling of biological samples. However, there are known caveats of this technology which can skew the gene expression estimates. Specifically, if the library preparation protocol does not retain RNA strand information then some genes can be erroneously quantitated. Although strand-specific protocols have been established, a significant portion of RNA-seq data is generated in non-strand-specific manner. We used a comprehensive stranded RNA-seq dataset of 15 blood cell types to identify genes for which expression would be erroneously estimated if strand information was not available. We found that about 10% of all genes and 2.5% of protein coding genes have a two-fold or higher difference in estimated expression when strand information of the reads was ignored. We used parameters of read alignments of these genes to construct a machine learning model that can identify which genes in an unstranded dataset might have incorrect expression estimates and which ones do not. We also show that differential expression analysis of genes with biased expression estimates in unstranded read data can be recovered by limiting the reads considered to those which span exonic boundaries. The resulting approach is implemented as a package available at https://github.com/mikpom/uslcount.

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