scholarly journals Genome Assembly and Population Resequencing Reveal the Geographical Divergence of 'Shanmei'(Rubus corchorifolius)

2021 ◽  
Author(s):  
Yinqing Yang ◽  
Kang Zhang ◽  
Ya Xiao ◽  
Lingkui Zhang ◽  
Yile Huang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Ancestral Population ◽  
Effective Population ◽  
High Quality ◽  
Local Environments ◽  
Rubus Species ◽  
Rubus Chingii ◽  
Rubus Chingii Hu ◽  
Genomic Regions ◽  
High Quality Genome

Rubus corchorifolius (Shanmei or mountain berry, 2n =14) is widely distributed in China, and its fruit has high nutritional and medicinal values. Here, we report a high-quality chromosome-scale genome assembly of Shanmei, with a size of 215.69 Mb and encompassing 26696 genes. Genome comparisons among Rosaceae species show that Shanmei and Fupenzi(Rubus chingii Hu) are most closely related, and then is blackberry (Rubus occidentalis). Further resequencing of 101 samples of Shanmei collected from four regions in provinces of Yunnan, Hunan, Jiangxi and Sichuan in South China reveals that the Hunan population of Shanmei possesses the highest diversity and may represent the relatively more ancestral population. Moreover, the Yunnan population undergoes strong selection based on nucleotide diversity, linkage disequilibrium and the historical effective population size analyses. Furthermore, genes from candidate genomic regions that show strong divergence are significantly enriched in flavonoid biosynthesis and plant hormone signal transduction, indicating the genetic basis of adaptation of Shanmei to the local environments. The high-quality genome sequences and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

2021 ◽  
Author(s):  
Hui Zhang ◽  
Yuexing Wang ◽  
Ce Deng ◽  
Sheng Zhao ◽  
Peng Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Quality ◽  
Rice Hybrid ◽  
High Quality Genome

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

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 488 ◽  
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.

scholarly journals Genome Sequence Resource of Magnaporthe oryzae Laboratory Strain 2539

2020 ◽  
Vol 33 (8) ◽  
pp. 1029-1031
Author(s):  
Meilian Chen ◽  
Baohua Wang ◽  
Guodong Lu ◽  
Zhenhui Zhong ◽  
Zonghua Wang
Keyword(s):  
Genome Sequence ◽  
Magnaporthe Oryzae ◽  
Genome Assembly ◽  
Laboratory Strain ◽  
Model System ◽  
Blast Disease ◽  
High Quality ◽  
Host Pathogen Interaction ◽  
Host Pathogen ◽  
High Quality Genome

Magnaporthe oryzae causes blast disease on more than 50 species of monocot plants, including important crops such as rice, millet, and most recently wheat. Additionally, it is an important model system for studying host-pathogen interaction. Here, we report a high-quality genome assembly and annotation of a laboratory strain 2539 of M. oryzae, which is a widely used progeny of a rice-infecting isolate and a grass-infecting isolate. The genome sequence of strain 2539 will be useful for studying the evolution, host adaption, and pathogenicity of M. oryzae, which will be beneficial for a better understanding of the mechanisms of host-pathogen interaction.

scholarly journals High-quality genome assembly of channel catfish, Ictalurus punctatus

GigaScience ◽  
2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Xiaohui Chen ◽  
Liqiang Zhong ◽  
Chao Bian ◽  
Pao Xu ◽  
Ying Qiu ◽  
...  
Keyword(s):  
Ictalurus Punctatus ◽  
Genome Assembly ◽  
Channel Catfish ◽  
High Quality ◽  
High Quality Genome

scholarly journals A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

GigaScience ◽  
2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Sarah B Kingan ◽  
Julie Urban ◽  
Christine C Lambert ◽  
Primo Baybayan ◽  
Anna K Childers ◽  
...  
Keyword(s):  
Invasive Species ◽  
Genome Assembly ◽  
De Novo ◽  
Fragment Size ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Lycorma Delicatula ◽  
Long Read ◽  
Genome Assemblies ◽  
High Quality Genome

ABSTRACT Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. Results The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. Conclusions We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

scholarly journals A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

GigaScience ◽  
2021 ◽  
Vol 10 (12) ◽  
Author(s):  
Ralf C Mueller ◽  
Patrik Ellström ◽  
Kerstin Howe ◽  
Marcela Uliano-Silva ◽  
Richard I Kuo ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Genome Assembly ◽  
Host Response ◽  
Influenza Viruses ◽  
Avian Influenza Viruses ◽  
High Quality ◽  
Pathogenic Avian Influenza ◽  
Tufted Duck ◽  
Long Read ◽  
High Quality Genome

Abstract Background The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.

scholarly journals LRez: C ++ API and toolkit for analyzing and managing Linked-Reads data

2021 ◽  
Author(s):  
Pierre Morisse ◽  
Claire Lemaitre ◽  
Fabrice Legeai
Keyword(s):  
Genome Assembly ◽  
Low Cost ◽  
Variant Calling ◽  
Supplementary Information ◽  
Supplementary Data ◽  
High Quality ◽  
Dna Molecule ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Genomic Regions

Abstract Motivation Linked-Reads technologies combine both the high-quality and low cost of short-reads sequencing and long-range information, through the use of barcodes tagging reads which originate from a common long DNA molecule. This technology has been employed in a broad range of applications including genome assembly, phasing and scaffolding, as well as structural variant calling. However, to date, no tool or API dedicated to the manipulation of Linked-Reads data exist. Results We introduce LRez, a C ++ API and toolkit which allows easy management of Linked-Reads data. LRez includes various functionalities, for computing numbers of common barcodes between genomic regions, extracting barcodes from BAM files, as well as indexing and querying BAM, FASTQ and gzipped FASTQ files to quickly fetch all reads or alignments containing a given barcode. LRez is compatible with a wide range of Linked-Reads sequencing technologies, and can thus be used in any tool or pipeline requiring barcode processing or indexing, in order to improve their performances. Availability and implementation LRez is implemented in C ++, supported on Unix-based platforms, and available under AGPL-3.0 License at https://github.com/morispi/LRez, and as a bioconda module. Supplementary information Supplementary data are available at Bioinformatics Advances

scholarly journals Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish

2021 ◽  
Author(s):  
Brandon D. Pickett ◽  
Sheena Talma ◽  
Jessica R. Glass ◽  
Daniel Ence ◽  
Paul D. Cowley ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Indian Ocean ◽  
Genome Assembly ◽  
Anthropogenic Activities ◽  
Western Indian Ocean ◽  
Genetic Connectivity ◽  
High Quality ◽  
Widespread Species ◽  
High Quality Genome

ABSTRACTBackgroundBonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN’s Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking for Albula species.ResultsWe generated a high-quality genome assembly of an A. glossodonta individual from Hawai‘i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius.ConclusionsQuantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.

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

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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