De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

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A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab052 ◽

2021 ◽

Author(s):

Guangtu Gao ◽

Susana Magadan ◽

Geoffrey C Waldbieser ◽

Ramey C Youngblood ◽

Paul A Wheeler ◽

...

Keyword(s):

Rainbow Trout ◽

Chromosome Number ◽

Genome Assembly ◽

De Novo Assembly ◽

De Novo ◽

Sequence Data ◽

Structural Variations ◽

High Coverage ◽

Haploid Chromosome Number ◽

Long Reads

Abstract Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

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Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽

10.3390/genes12091359 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1359

Author(s):

Esther Camacho ◽

Sandra González-de la Fuente ◽

Jose C. Solana ◽

Alberto Rastrojo ◽

Fernando Carrasco-Ramiro ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Leishmania Major ◽

De Novo ◽

Gene Annotation ◽

Leishmania Species ◽

De Novo Genome Assembly ◽

Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

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The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus

Genome Biology and Evolution ◽

10.1093/gbe/evz141 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1965-1970 ◽

Cited By ~ 7

Author(s):

Nikola Palevich ◽

Paul H Maclean ◽

Abdul Baten ◽

Richard W Scott ◽

David M Leathwick

Keyword(s):

Genome Sequence ◽

Molecular Mechanisms ◽

De Novo ◽

Sequence Data ◽

Animal Health ◽

Draft Genome ◽

Whole Genome Sequence ◽

Parasitic Nematodes ◽

Hybrid Assembly ◽

Genetic Structures

Abstract Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda.

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A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae

Genome Biology and Evolution ◽

10.1093/gbe/evz269 ◽

2019 ◽

Vol 12 (1) ◽

pp. 3635-3646 ◽

Cited By ~ 3

Author(s):

Arnab Ghosh ◽

Matthew G Johnson ◽

Austin B Osmanski ◽

Swarnali Louha ◽

Natalia J Bayona-Vásquez ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Genome Structure ◽

Protein Domain ◽

Alligator Mississippiensis ◽

Structure Evolution ◽

Functional Protein ◽

High Quality ◽

Saltwater Crocodile ◽

Crocodylus Porosus

Abstract Crocodilians are an economically, culturally, and biologically important group. To improve researchers’ ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple noncoding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, 10 in C. porosus and 6 in Alligator mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological, and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.

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Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome

GigaScience ◽

10.1093/gigascience/giaa114 ◽

2020 ◽

Vol 9 (10) ◽

Cited By ~ 1

Author(s):

Yan Li ◽

Guangliang Gao ◽

Yu Lin ◽

Silu Hu ◽

Yi Luo ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Spatial Organization ◽

De Novo ◽

Single Copy ◽

Interaction Patterns ◽

Anser Anser ◽

Pacific Biosciences ◽

Eukaryotic Genes ◽

Chromosome Level

ABSTRACT Background The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing. Findings We generated a 1.11-Gb goose genome with contig and scaffold N50 values of 1.85 and 33.12 Mb, respectively. The assembly contains 39 pseudo-chromosomes (2n = 78) accounting for ∼88.36% of the goose genome. Compared with previous goose assemblies, our assembly has more continuity, completeness, and accuracy; the annotation of core eukaryotic genes and universal single-copy orthologs has also been improved. We have identified 17,568 protein-coding genes and a repeat content of 8.67% (96.57 Mb) in this genome assembly. We also explored the spatial organization of chromatin and gene expression in the goose liver tissues, in terms of inter-pseudo-chromosomal interaction patterns, compartments, topologically associating domains, and promoter-enhancer interactions. Conclusions We present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese.

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NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

GigaScience ◽

10.1093/gigascience/giaa105 ◽

2020 ◽

Vol 9 (10) ◽

Cited By ~ 1

Author(s):

Willem de Koning ◽

Milad Miladi ◽

Saskia Hiltemann ◽

Astrid Heikema ◽

John P Hays ◽

...

Keyword(s):

Genome Assembly ◽

Bioinformatics Analysis ◽

De Novo ◽

Sequence Data ◽

Ease Of Use ◽

Easy Access ◽

Complex Data ◽

Sequencing Data ◽

Long Read ◽

Sequencing Platforms

Abstract Background Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies–based long-read sequencing “nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers. Results The Galaxy platform provides a user-friendly interface to computational command line–based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed “NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads. Conclusions A range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.

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Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads

10.1101/660605 ◽

2019 ◽

Cited By ~ 1

Author(s):

Xin Zhou ◽

Lu Zhang ◽

Ziming Weng ◽

David L. Dill ◽

Arend Sidow

Keyword(s):

Genetic Variation ◽

Genome Sequence ◽

Genome Assembly ◽

Sequence Data ◽

Association Studies ◽

Cost Effective ◽

Whole Genome Sequence ◽

Personal Genome ◽

Whole Genome ◽

Nucleotide Polymorphisms

AbstractVariant discovery in personal, whole genome sequence data is critical for uncovering the genetic contributions to health and disease. We introduce a new approach, Aquila, that uses linked-read data for generating a high quality diploid genome assembly, from which it then comprehensively detects and phases personal genetic variation. Assemblies cover >95% of the human reference genome, with over 98% in a diploid state. Thus, the assemblies support detection and accurate genotyping of the most prevalent types of human genetic variation, including single nucleotide polymorphisms (SNPs), small insertions and deletions (small indels), and structural variants (SVs), in all but the most difficult regions. All heterozygous variants are phased in blocks that can approach arm-level length. The final output of Aquila is a diploid and phased personal genome sequence, and a phased VCF file that also contains homozygous and a few unphased heterozygous variants. Aquila represents a cost-effective evolution of whole-genome reconstruction that can be applied to cohorts for variation discovery or association studies, or to single individuals with rare phenotypes that could be caused by SVs or compound heterozygosity.

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Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection

10.1101/521138 ◽

2019 ◽

Author(s):

Antonis Kioukis ◽

Vassiliki A. Michalopoulou ◽

Laura Briers ◽

Stergios Pirintsos ◽

David J. Studholme ◽

...

Keyword(s):

Genome Sequence ◽

De Novo ◽

Sequence Data ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Draft Genome ◽

Illumina Miseq ◽

Crop Wild Relatives ◽

Demographic Model ◽

Sequencing Data

AbstractCrop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security.The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape.Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica.De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins.Furthermore, our demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.

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An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion

Wellcome Open Research ◽

10.12688/wellcomeopenres.11864.1 ◽

2017 ◽

Vol 2 ◽

pp. 42 ◽

Cited By ~ 22

Author(s):

Erica M Pasini ◽

Ulrike Böhme ◽

Gavin G. Rutledge ◽

Annemarie Voorberg-Van der Wel ◽

Mandy Sanders ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Malaria Parasite ◽

Reference Genome ◽

Sequence Data ◽

Single Copy ◽

Chromosome 9 ◽

Reference Genome Sequence ◽

Plasmodium Cynomolgi ◽

Average Gene

Background: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres. Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated a new reference genome sequence, PcyM, sourced from an Indian rhesus monkey. We compare the newly assembled genome sequence with those of several other Plasmodium species, including a re-annotated P. coatneyi assembly. Results: The new PcyM genome assembly is of significantly higher quality than the existing reference, comprising only 56 pieces, no gaps and an improved average gene length. Detailed manual curation has ensured a comprehensive annotation of the genome with 6,632 genes, nearly 1,000 more than previously attributed to P. cynomolgi. The new assembly also has an improved representation of the subtelomeric regions, which account for nearly 40% of the sequence. Within the subtelomeres, we identified more than 1300 Plasmodium interspersed repeat (pir) genes, as well as a striking expansion of 36 methyltransferase pseudogenes that originated from a single copy on chromosome 9. Conclusions: The manually curated PcyM reference genome sequence is an important new resource for the malaria research community. The high quality and contiguity of the data have enabled the discovery of a novel expansion of methyltransferase in the subtelomeres, and illustrates the new comparative genomics capabilities that are being unlocked by complete reference genomes.

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BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

10.1101/464420 ◽

2018 ◽

Author(s):

Giulia Guidi ◽

Marquita Ellis ◽

Daniel Rokhsar ◽

Katherine Yelick ◽

Aydın Buluç

Keyword(s):

Genome Assembly ◽

Probabilistic Model ◽

De Novo ◽

Sparse Matrix ◽

Genome Structure ◽

Matrix Multiplication ◽

Synthetic Data ◽

Error Rates ◽

Species Variation ◽

Long Read

AbstractRecent advances in long-read sequencing enable the characterization of genome structure and its intra- and inter-species variation at a resolution that was previously impossible. Detecting overlaps between reads is integral to many long-read genomics pipelines, such as de novo genome assembly. While longer reads simplify genome assembly and improve the contiguity of the reconstruction, current long-read technologies come with high error rates. We present Berkeley Long-Read to Long-Read Aligner and Overlapper (BELLA), a novel algorithm for computing overlaps and alignments via sparse matrix-matrix multiplication that balances the goals of recall and precision, performing well on both.We present a probabilistic model that demonstrates the feasibility of using short k-mers for detecting candidate overlaps. We then introduce a notion of reliable k-mers based on our probabilistic model. Combining reliable k-mers with our binning mechanism eliminates both the k-mer set explosion that would otherwise occur with highly erroneous reads and the spurious overlaps from k-mers originating in repetitive regions. Finally, we present a new method based on Chernoff bounds for separating true overlaps from false positives using a combination of alignment techniques and probabilistic modeling. Our methodologies aim at maximizing the balance between precision and recall. On both real and synthetic data, BELLA performs amongst the best in terms of F1 score, showing performance stability which is often missing for competitor software. BELLA’s F1 score is consistently within 1.7% of the top entry. Notably, we show improved de novo assembly results on synthetic data when coupling BELLA with the Miniasm assembler.

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