Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab031 ◽

2021 ◽

Author(s):

Wayne Xu ◽

James R Tucker ◽

Wubishet A Bekele ◽

Frank M You ◽

Yong-Bi Fu ◽

...

Keyword(s):

Reference Genome ◽

Single Copy ◽

Barley Cultivar ◽

Malting Barley ◽

Orthologous Genes ◽

Hordeum Vulgare L ◽

Chromosome Conformation ◽

Mate Pair ◽

Genome Assemblies ◽

First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.401010 ◽

2020 ◽

Vol 10 (6) ◽

pp. 1823-1827 ◽

Cited By ~ 6

Author(s):

Miriam Schreiber ◽

Martin Mascher ◽

Jonathan Wright ◽

Sudharasan Padmarasu ◽

Axel Himmelbach ◽

...

Keyword(s):

Genome Assembly ◽

Single Copy ◽

Golden Promise ◽

Orthologous Genes ◽

Chromosome Conformation ◽

Reference Assembly ◽

Proximity Ligation ◽

Mate Pair ◽

A Genome

Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv. Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv. Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. A high-quality Golden Promise reference assembly will be useful and utilized by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.

A genome assembly of the barley ‘transformation reference’ cultivar Golden Promise

10.1101/2020.02.12.945550 ◽

2020 ◽

Author(s):

Miriam Schreiber ◽

Martin Mascher ◽

Jonathan Wright ◽

Sudharasan Padmarasu ◽

Axel Himmelbach ◽

...

Keyword(s):

Genome Assembly ◽

Single Copy ◽

Golden Promise ◽

Orthologous Genes ◽

Chromosome Conformation ◽

Reference Assembly ◽

Proximity Ligation ◽

Mate Pair ◽

A Genome

AbstractBackgroundBarley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv. Golden Promise, the most efficient genotype for genetic transformation.FindingsWe have developed a barley cv. Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database.ConclusionsA high-quality Golden Promise reference assembly will be useful and utilised by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.

Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

Frontiers in Plant Science ◽

10.3389/fpls.2021.625416 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nataliya V. Melnikova ◽

Elena N. Pushkova ◽

Ekaterina M. Dvorianinova ◽

Artemy D. Beniaminov ◽

Roman O. Novakovskiy ◽

...

Keyword(s):

Genome Assembly ◽

Single Copy ◽

Dioecious Species ◽

Male And Female ◽

Male Genome ◽

Oxford Nanopore ◽

Genome Assemblies ◽

First Time ◽

High Quality Genome ◽

Y Haplotype

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

Practical guide for obtaining and validating chromosome-scale genome assemblies with Hi-C scaffolding

10.22541/au.160968142.22103947/v1 ◽

2021 ◽

Author(s):

Kazuaki Yamaguchi ◽

Mitsutaka Kadota ◽

Osamu Nishimura ◽

Yuta Ohishi ◽

Yuki Naito ◽

...

Keyword(s):

Single Copy ◽

Test Case ◽

Range Interaction ◽

Chromosome Conformation ◽

Genome Sequence Assembly ◽

Genome Wide ◽

Reptile Species ◽

Genome Assemblies ◽

Massive Information ◽

Completeness Assessment

Recent development of ecological studies has been fueled by the introduction of massive information based on chromosome-scale genome sequences, even for species whose genetic linkage was previously not accessible. This was enabled mainly by the application of Hi-C, a method for genome-wide chromosome conformation capture which was originally developed for investigating long-range interaction of chromatins. Performing genomic scaffolding using Hi-C data is highly resource-demanding in elaborate laboratory steps for sequencing sample preparation, building primary genome sequence assembly as an input, and computation for genome scaffolding using Hi-C data, followed by careful validation. This article summarizes existing solutions for these steps and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among frequently exerted metrics for evaluating scaffolding results, we investigate the validity of completeness assessment using single-copy reference orthologs and report problems with the widely used program pipeline BUSCO.

Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

F1000Research ◽

10.12688/f1000research.12867.2 ◽

2018 ◽

Vol 6 ◽

pp. 1972 ◽

Cited By ~ 1

Author(s):

Amy L. Longmuir ◽

Peter L. Beech ◽

Mark F. Richardson

Keyword(s):

Plant Pathogen ◽

Reference Genome ◽

Phytophthora Cinnamomi ◽

Gene Prediction ◽

Single Copy ◽

Draft Assembly ◽

Protein Encoding ◽

Pathogen Control ◽

Genome Assemblies ◽

Encoding Genes

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings: Some 308 million raw reads were generated for the two strains, DU054 and WA94.26. Independent genome assembly produced final genome sequences of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 94.4% and 91.5% of the stramenopile single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analyses and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

Parasitology ◽

10.1017/s0031182017000348 ◽

2017 ◽

Vol 144 (10) ◽

pp. 1302-1315 ◽

Cited By ~ 2

Author(s):

PETER C. THOMPSON ◽

DANTE S. ZARLENGA ◽

MING-YUAN LIU ◽

BENJAMIN M. ROSENTHAL

Keyword(s):

Reference Genome ◽

Trichinella Spiralis ◽

Evolutionary Genetics ◽

Invasion Biology ◽

Phenotypic Traits ◽

Draft Assembly ◽

Long Read ◽

Genome Assemblies ◽

First Time ◽

Insight Into

SUMMARYGenome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.

Chromosome-level assembly of the common vetch reference genome (Vicia sativa)

10.1101/2021.10.11.464017 ◽

2021 ◽

Author(s):

Hangwei Xi ◽

Vy nguyen ◽

Christopher M Ward ◽

Iain R Searle

Keyword(s):

Reference Genome ◽

Cropping Systems ◽

Single Copy ◽

Vicia Sativa ◽

Arid Environments ◽

Common Vetch ◽

Chromosome Conformation ◽

Protein Coding ◽

The Usa ◽

Chromosome Level

Background: Vicia sativa L. (Common Vetch, n = 6) is an annual, herbaceous, climbing legume that is distributed in tropical, sub-tropical and temperate climates. Originating in the Fertile Crescent of the Middle East, V. sativa is now widespread and grows in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we here present a chromosome-level reference genome sequence for V. sativa. Results: We applied a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis to construct a chromosome-level genome of V. sativa. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.9 gigabases (Gb) with a median contig length of 684 kb. Benchmarking Universal Single-Copy Orthologs (BUSCO) of the assembly demonstrated a very high completeness of 98 % of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 58,415 protein-coding genes. Conclusions: The high-quality chromosome-level genome assembly of V. sativa will provide novel insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.

Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola

10.1101/164574 ◽

2017 ◽

Cited By ~ 1

Author(s):

Kirill Grigorev ◽

Sergey Kliver ◽

Pavel Dobrynin ◽

Aleksey Komissarov ◽

Walter Wolfsberger ◽

...

Keyword(s):

Reference Genome ◽

Single Copy ◽

Selection Signatures ◽

Caribbean Islands ◽

Assembly Strategy ◽

Genome Data ◽

String Graph ◽

Additional Sequence ◽

The Caribbean ◽

Genome Assemblies

AbstractSolenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly for solenodons has never been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation has likely resulted in extreme homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies for performance with genetically impoverished species’ genomes. The string-graph based assembly strategy seems a better choice compared to the conventional de Brujn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (S. p. woodi). In addition, we obtained one additional sequence of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on the venomous genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. Patterns of SNP variation allowed us to infer population demography, which indicated a subspecies split within the Hispaniolan solenodon at least 300 Kya.

Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies

10.22541/au.162183528.83085003/v1 ◽

2021 ◽

Author(s):

Kazuaki Yamaguchi ◽

Mitsutaka Kadota ◽

Osamu Nishimura ◽

Yuta Ohishi ◽

Yuki Naito ◽

...

Keyword(s):

Single Copy ◽

Test Case ◽

Range Interaction ◽

Chromosome Conformation ◽

Genome Sequence Assembly ◽

Genome Wide ◽

Reptile Species ◽

Genome Assemblies ◽

Massive Information ◽

Technical Considerations

The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome-scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi-C, a method for genome-wide chromosome conformation capture that was originally developed for investigating the long-range interaction of chromatins. Performing genomic scaffolding using Hi-C data is highly resource-demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi-C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi-C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome-scale genome assemblies using single-copy reference orthologs, and report problems of the widely used program pipeline BUSCO.

Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway

Horticulture Research ◽

10.1038/s41438-021-00627-7 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Hong-Lei Li ◽

Lin Wu ◽

Zhaoming Dong ◽

Yusong Jiang ◽

Sanjie Jiang ◽

...

Keyword(s):

Biosynthetic Pathway ◽

Southwest China ◽

Reference Genome ◽

Zingiber Officinale ◽

Gene Families ◽

Chromosome Conformation ◽

Long Reads ◽

Transcription Factor Networks ◽

Species Specific ◽

Haplotype 1

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.