High-quality genome assembly and high-density genetic map of asparagus bean

AbstractAsparagus bean (Vigna. unguiculata ssp. sesquipedialis), known for its very long and tender green pods, is an important vegetable crop broadly grown in the developing countries. Despite its agricultural and economic values, asparagus bean does not have a high-quality genome assembly for breeding novel agronomic traits. In this study, we reported a high-quality 632.8 Mb assembly of asparagus bean based on the whole genome shotgun sequencing strategy. We also generated a high-density linkage map for asparagus bean, which helped anchor 94.42% of the scaffolds into 11 pseudo-chromosomes. A total of 42,609 protein-coding genes and 3,579 non-protein-coding genes were predicted from the assembly. Taken together, these genomic resources of asparagus bean will facilitate the investigation of economically valuable traits in a variety of legume species, so that the cultivation of these plants would help combat the protein and energy malnutrition in the developing world.

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Complete Genome Sequence of Pseudomonas sp. Strain SGAir0191, Isolated from Tropical Air Collected in Singapore

Microbiology Resource Announcements ◽

10.1128/mra.00617-19 ◽

2019 ◽

Vol 8 (34) ◽

Author(s):

Anthony Wong ◽

Ana Carolina M. Junqueira ◽

Ankur Chaturvedi ◽

Akira Uchida ◽

Rikky W. Purbojati ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Complete Genome Sequence ◽

Complete Genome ◽

Pseudomonas Sp ◽

High Quality ◽

Protein Coding ◽

Protein Coding Genes ◽

Air Sample ◽

High Quality Genome

Pseudomonas sp. strain SGAir0191 was isolated from an air sample collected in Singapore, and its genome was sequenced using a combination of long and short reads to generate a high-quality genome assembly. The complete genome is approximately 5.07 Mb with 4,370 protein-coding genes, 19 rRNAs, and 73 tRNAs.

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Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

Toxins ◽

10.3390/toxins10120488 ◽

2018 ◽

Vol 10 (12) ◽

pp. 488 ◽

Cited By ~ 5

Author(s):

Shiyong Zhang ◽

Jia Li ◽

Qin Qin ◽

Wei Liu ◽

Chao Bian ◽

...

Keyword(s):

High Throughput ◽

Genome Assembly ◽

Raw Materials ◽

Pelteobagrus Fulvidraco ◽

Yellow Catfish ◽

High Quality ◽

Protein Coding ◽

Toxin Genes ◽

Sequencing Platforms ◽

High Quality Genome

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

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

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-20-0060-a ◽

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.

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Genome sequence of the model rice variety KitaakeX

10.1101/653089 ◽

2019 ◽

Author(s):

Rashmi Jain ◽

Jerry Jenkins ◽

Shengqiang Shu ◽

Mawsheng Chern ◽

Joel A. Martin ◽

...

Keyword(s):

Oryza Sativa ◽

Rice Plant ◽

De Novo ◽

Rice Variety ◽

High Quality ◽

Protein Coding ◽

Genomic Variations ◽

Protein Coding Genes ◽

Gene Annotations ◽

High Quality Genome

AbstractHere, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics.

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High-Quality Genome Assembly and Annotation of the California Harvester Ant Pogonomyrmex californicus (Buckley, 1867)

10.1101/2020.09.01.277236 ◽

2020 ◽

Author(s):

Jonas Bohn ◽

Reza Halabian ◽

Lukas Schrader ◽

Victoria Shabardina ◽

Raphael Steffen ◽

...

Keyword(s):

Genome Assembly ◽

High Quality ◽

Protein Coding ◽

Primary Polygyny ◽

Pogonomyrmex Californicus ◽

The North ◽

Harvester Ant ◽

Mating Flights ◽

North And South America ◽

High Quality Genome

ABSTRACTThe harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America and California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in the North America. P. californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present high quality genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in good agreement with previously estimated genome size and we were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO completeness at the 95% level. This high quality genome will pave the way for investigations of the genomic underpinnings of social polymorphism in queen number, regulation of aggression, and the evolution of adaptations to dry habitats in P. californicus.

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

Horticulture Research ◽

10.1038/s41438-020-00391-0 ◽

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.

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A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

GigaScience ◽

10.1093/gigascience/giz098 ◽

2019 ◽

Vol 8 (8) ◽

Cited By ~ 5

Author(s):

Lu Wang ◽

Jinwei Wu ◽

Xiaomei Liu ◽

Dandan Di ◽

Yuhong Liang ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Gene Families ◽

Rhinopithecus Roxellana ◽

High Quality ◽

Chromosome Conformation ◽

Protein Coding ◽

A Genome ◽

Close Relationship ◽

High Quality Genome

Abstract Background The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered colobine species endemic to China, which has several distinct traits including a unique social structure. Although a genome assembly for R. roxellana is available, it is incomplete and fragmented because it was constructed using short-read sequencing technology. Thus, important information such as genome structural variation and repeat sequences may be absent. Findings To obtain a high-quality chromosomal assembly for R. roxellana qinlingensis, we used 5 methods: Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, BioNano optical maps, 10X Genomics link-reads, and high-throughput chromosome conformation capture. The assembled genome was ∼3.04 Gb, with a contig N50 of 5.72 Mb and a scaffold N50 of 144.56 Mb. This represented a 100-fold improvement over the previously published genome. In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated. Gene family analysis showed that 993 and 2,745 gene families were expanded and contracted, respectively. The reconstructed phylogeny recovered a close relationship between R. rollexana and Macaca mulatta, and these 2 species diverged ∼13.4 million years ago. Conclusion We constructed a high-quality genome assembly of the Qinling golden snub-nosed monkey; it had superior continuity and accuracy, which might be useful for future genetic studies in this species and as a new standard reference genome for colobine primates. In addition, the updated genome assembly might improve our understanding of this species and could assist conservation efforts.

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Genome assembly and annotation of Macadamia tetraphylla

10.1101/2020.03.11.987057 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ying-Feng Niu ◽

Guo-Hua Li ◽

Shu-Bang Ni ◽

Xi-Yong He ◽

Cheng Zheng ◽

...

Keyword(s):

Genome Sequence ◽

Agronomic Traits ◽

Average Length ◽

Biological Research ◽

High Quality ◽

Protein Coding ◽

Macadamia Integrifolia ◽

Oxford Nanopore ◽

High Quality Genome ◽

Oxford Nanopore Technologies

AbstractMacadamia is a kind of evergreen nut trees which belong to the Proteaceae family. The two commercial macadamia species, Macadamia integrifolia and M. tetraphylla, are highly prized for their edible kernels. Catherine et al. reported M. integrifolia genome using NGS sequencing technology. However, the lack of a high-quality assembly for M. tetraphylla hinders the progress in biological research and breeding program. In this study, we report a high-quality genome sequence of M. tetraphylla using the Oxford Nanopore Technologies (ONT) technology. We generated an assembly of 750.54 Mb with a contig N50 length of 1.18 Mb, which is close to the size estimated by flow cytometry and k-mer analysis. Repetitive sequence represent 58.57% of the genome sequence, which is strikingly higher compared with M. integrifolia. A total of 31,571 protein-coding genes were annotated with an average length of 6,055 bp, of which 92.59% were functionally annotated. The genome sequence of M. tetraphylla will provide novel insights into the breeding of novel strains and genetic improvement of agronomic traits.

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