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

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.

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The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies

Scientific Data ◽

10.1038/s41597-019-0194-3 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 8

Author(s):

Baohua Chen ◽

Zhixiong Zhou ◽

Qiaozhen Ke ◽

Yidi Wu ◽

Huaqiang Bai ◽

...

Keyword(s):

Marine Fish ◽

Single Molecule ◽

Large Scale ◽

Reference Genome ◽

De Novo ◽

Larimichthys Crocea ◽

Chromosome Conformation ◽

Protein Coding ◽

Total Length ◽

Chromosome Level

Abstract Larimichthys crocea is an endemic marine fish in East Asia that belongs to Sciaenidae in Perciformes. L. crocea has now been recognized as an “iconic” marine fish species in China because not only is it a popular food fish in China, it is a representative victim of overfishing and still provides high value fish products supported by the modern large-scale mariculture industry. Here, we report a chromosome-level reference genome of L. crocea generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The genome sequences were assembled into 1,591 contigs with a total length of 723.86 Mb and a contig N50 length of 2.83 Mb. After chromosome-level scaffolding, 24 scaffolds were constructed with a total length of 668.67 Mb (92.48% of the total length). Genome annotation identified 23,657 protein-coding genes and 7262 ncRNAs. This highly accurate, chromosome-level reference genome of L. crocea provides an essential genome resource to support the development of genome-scale selective breeding and restocking strategies of L. crocea.

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The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies

Scientific Data ◽

10.1038/s41597-019-0195-2 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 7

Author(s):

Zhixiong Zhou ◽

Bo Liu ◽

Baohua Chen ◽

Yue Shi ◽

Fei Pu ◽

...

Keyword(s):

Single Molecule ◽

Reference Genome ◽

De Novo ◽

Breeding Programs ◽

Chromosome Conformation ◽

Protein Coding ◽

Single Molecule Sequencing ◽

Total Length ◽

Genome Scale ◽

Chromosome Level

Abstract Takifugu bimaculatus is a native teleost species of the southeast coast of China where it has been cultivated as an important edible fish in the last decade. Genetic breeding programs, which have been recently initiated for improving the aquaculture performance of T. bimaculatus, urgently require a high-quality reference genome to facilitate genome selection and related genetic studies. To address this need, we produced a chromosome-level reference genome of T. bimaculatus using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 2,193 contigs with a total length of 404.21 Mb and a contig N50 length of 1.31 Mb. After chromosome-level scaffolding, 22 chromosomes with a total length of 371.68 Mb were constructed. Moreover, a total of 21,117 protein-coding genes and 3,471 ncRNAs were annotated in the reference genome. The highly accurate, chromosome-level reference genome of T. bimaculatus provides an essential genome resource for not only the genome-scale selective breeding of T. bimaculatus but also the exploration of the evolutionary basis of the speciation and local adaptation of the Takifugu genus.

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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.

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An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)

Genome Biology and Evolution ◽

10.1093/gbe/evaa063 ◽

2020 ◽

Vol 12 (4) ◽

pp. 456-462 ◽

Cited By ~ 5

Author(s):

Warren Brian Simison ◽

James F Parham ◽

Theodore J Papenfuss ◽

Athena W Lam ◽

James B Henderson

Keyword(s):

Reference Genome ◽

Single Copy ◽

Trachemys Scripta ◽

Future Research ◽

Chromosome Counts ◽

Trachemys Scripta Elegans ◽

Chromosome Fusion ◽

Slider Turtle ◽

Tetrapod Evolution ◽

Chromosome Level

Abstract Among vertebrates, turtles have many unique characteristics providing biologists with opportunities to study novel evolutionary innovations and processes. We present here a high-quality, partially phased, and chromosome-level Red-Eared Slider (Trachemys scripta elegans, TSE) genome as a reference for future research on turtle and tetrapod evolution. This TSE assembly is 2.269 Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50 = 129.68 Mb and N90 = 19 Mb), and has a total of 28,415 annotated genes. We introduce synteny analyses using BUSCO single-copy orthologs, which reveal two chromosome fusion events accounting for differences in chromosome counts between emydids and other cryptodire turtles and reveal many fission/fusion events for birds, crocodiles, and snakes relative to TSE. This annotated chromosome-level genome will provide an important reference genome for future studies on turtle, vertebrate, and chromosome evolution.

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Chromosome-scale assembly of wild barley accession ‘OUH602’

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab244 ◽

2021 ◽

Author(s):

Kazuhiro Sato ◽

Martin Mascher ◽

Axel Himmelbach ◽

Georg Haberer ◽

Manuel Spannagl ◽

...

Keyword(s):

Reference Genome ◽

Wild Barley ◽

Artificial Chromosome ◽

Gene Identification ◽

Barley Accession ◽

Genomic Information ◽

Protein Coding ◽

Fertile Crescent ◽

Tropical Areas ◽

Chromosome Level

Abstract Barley (Hordeum vulgare) was domesticated from its wild ancestral form ca. 10,000 years ago in the Fertile Crescent and is widely cultivated throughout the world, except for in tropical areas. The genome size of both cultivated barley and its conspecific wild ancestor is approximately 5 Gb. High-quality chromosome-level assemblies of 19 cultivated and one wild barley genotype were recently established by pan-genome analysis. Here, we release another equivalent short-read assembly of the wild barley accession ‘OUH602’. A series of genetic and genomic resources were developed for this genotype in prior studies. Our assembly contains more than 4.4 Gb of sequence, with a scaffold N50 value of over 10 Mb. The haplotype shows high collinearity with the most recently updated barley reference genome, ‘Morex’ V3, with some inversions. Gene projections based on ‘Morex’ gene models revealed 46,807 protein-coding sequences and 43,375 protein coding genes. Alignments to publicly available sequences of bacterial artificial chromosome (BAC) clones of ‘OUH602’ confirm the high accuracy of the assembly. Since more loci of interest have been identified in ‘OUH602’, the release of this assembly, with detailed genomic information, should accelerate gene identification and the utilization of this key wild barley accession.

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A Reference Genome Sequence for Giant Sequoia

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401612 ◽

2020 ◽

Vol 10 (11) ◽

pp. 3907-3919

Author(s):

Alison D. Scott ◽

Aleksey V. Zimin ◽

Daniela Puiu ◽

Rachael Workman ◽

Monica Britton ◽

...

Keyword(s):

Sierra Nevada ◽

Genome Sequence ◽

Reference Genome ◽

Chromosome Conformation ◽

Protein Coding ◽

Reference Genome Sequence ◽

Oxford Nanopore ◽

Sierra Nevada Mountains ◽

Genomic Tools ◽

Giant Sequoia

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, were used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

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Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

GigaScience ◽

10.1093/gigascience/giaa013 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 1

Author(s):

Xupo Ding ◽

Wenli Mei ◽

Qiang Lin ◽

Hao Wang ◽

Jun Wang ◽

...

Keyword(s):

Genome Assembly ◽

Gene Annotation ◽

Draft Genome ◽

Single Copy ◽

Aquilaria Sinensis ◽

Final Size ◽

Plant Resources ◽

Protein Coding ◽

High Level ◽

Chromosome Level

Abstract Backgroud Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information. Findings We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18–84.37 million years ago. Conclusions Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.

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Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia

GigaScience ◽

10.1093/gigascience/giab024 ◽

2021 ◽

Vol 10 (4) ◽

Cited By ~ 1

Author(s):

Jin-Long Yang ◽

Dan-Dan Feng ◽

Jie Liu ◽

Jia-Kang Xu ◽

Ke Chen ◽

...

Keyword(s):

East Asia ◽

Marine Biology ◽

Chromosome Conformation ◽

Protein Coding ◽

Catecholamine Biosynthesis ◽

Mytilus Coruscus ◽

Non Coding Rna ◽

Oxford Nanopore ◽

Genome Information ◽

Chromosome Level

Abstract Background The hard-shelled mussel (Mytilus coruscus) is widely distributed in the temperate seas of East Asia and is an important commercial bivalve in China. Chromosome-level genome information of this species will contribute not only to the development of hard-shelled mussel genetic breeding but also to studies on larval ecology, climate change biology, marine biology, aquaculture, biofouling, and antifouling. Findings We applied a combination of Illumina sequencing, Oxford Nanopore Technologies sequencing, and high-throughput chromosome conformation capture technologies to construct a chromosome-level genome of the hard-shelled mussel, with a total length of 1.57 Gb and a median contig length of 1.49 Mb. Approximately 90.9% of the assemblies were anchored to 14 linkage groups. We assayed the genome completeness using BUSCO. In the metazoan dataset, the present assemblies have 89.4% complete, 1.9% incomplete, and 8.7% missing BUSCOs. Gene modeling enabled the annotation of 37,478 protein-coding genes and 26,917 non-coding RNA loci. Phylogenetic analysis showed that M. coruscus is the sister taxon to the clade including Modiolus philippinarum and Bathymodiolus platifrons. Conserved chromosome synteny was observed between hard-shelled mussel and king scallop, suggesting that this is shared ancestrally. Transcriptomic profiling indicated that the pathways of catecholamine biosynthesis and adrenergic signaling in cardiomyocytes might be involved in metamorphosis. Conclusions The chromosome-level assembly of the hard-shelled mussel genome will provide novel insights into mussel genome evolution and serve as a fundamental platform for studies regarding the planktonic-sessile transition, genetic diversity, and genomic breeding of this bivalve.

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A chromosome-level genome assembly and annotation of the humpback grouper Cromileptes altivelas

10.1101/2020.06.22.164277 ◽

2020 ◽

Author(s):

Yun Sun ◽

Dongdong Zhang ◽

Jianzhi Shi ◽

Guisen Chen ◽

Ying Wu ◽

...

Keyword(s):

Genome Assembly ◽

Chromosome Conformation ◽

Protein Coding ◽

Market Values ◽

Final Assembly ◽

Long Reads ◽

High Gene ◽

Food Fish ◽

High Quality Genome ◽

Chromosome Level

AbstractCromileptes altivelas that belongs to Serranidae in the order Perciformes, is widely distributed throughout the tropical waters of the Indo-West Pacific regions. Due to their excellent food quality and abundant nutrients, it has become a popular marine food fish with high market values. Here, we reported a chromosome-level genome assembly and annotation of the humpback grouper genome using more than 103X PacBio long-reads and high-throughput chromosome conformation capture (Hi-C) technologies. The N50 contig length of the assembly is as large as 4.14 Mbp, the final assembly is 1.07 Gb with N50 of scaffold 44.78 Mb, and 99.24% of the scaffold sequences were anchored into 24 chromosomes. The high-quality genome assembly also showed high gene completeness with 27,067 protein coding genes and 3,710 ncRNAs. This high accurate genome assembly and annotation will not only provide an essential genome resource for C. altivelas breeding and restocking, but will also serve as a key resource for studying fish genomics and genetics.

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Chromosome-level reference genome of the jellyfish Rhopilema esculentum

GigaScience ◽

10.1093/gigascience/giaa036 ◽

2020 ◽

Vol 9 (4) ◽

Cited By ~ 3

Author(s):

Yunfeng Li ◽

Lei Gao ◽

Yongjia Pan ◽

Meilin Tian ◽

Yulong Li ◽

...

Keyword(s):

Genome Assembly ◽

Evolutionary History ◽

Reference Genome ◽

Protein Coding ◽

Fishery Resource ◽

Rhopilema Esculentum ◽

Sequencing Technologies ◽

Genome Wide ◽

History Of ◽

Chromosome Level

Abstract Background Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. Findings In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. Conclusions We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.

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