First Draft Genome Assembly of Redlip Mullet (Liza haematocheila) From Family Mugilidae

Liyanage, D.S.; Oh, Minyoung; Omeka, W.K.M.; Wan, Qiang; Jin, Chang Nam; Shin, Ga-Hee; Kang, Byeong-Chul; Nam, Bo‐Hye; Lee, Jehee

doi:10.3389/fgene.2019.01246

Cited by 10 publications

(4 citation statements)

References 23 publications

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“…Genome size and heterozygosity rate estimations were made using a k-mer frequency distribution approach (Li & Waterman, 2003). Initially, the occurrence of unique 21-mers (where k=21) was counted and a distribution histogram generated using Jellyfish software v.2.0 (Marçais & Kingsford, 2011).…”

Section: De Novo Genome Assemblymentioning

confidence: 99%

A first draft genome of the Sugarcane borer, Diatraea saccharalis.

et al. 2020

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Background: The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Given its significant impact on yield reduction, whole-genome information of the species is needed. Here, we report the first draft assembly of the D. saccharalis genome. Methods: The genomic sequences were obtained using the Illumina HiSeq 2500 whole-genome sequencing of a single adult male specimen. We assembled the short-reads using the SPAdes software and predicted protein-coding genes using MAKER. Genome assembly completeness was assessed through BUSCO and the repetitive content by RepeatMasker. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori. The repeat content composes 41.18% of the genomic sequences which is in the range of other lepidopteran species. Conclusions: Functional annotation reveals that predicted gene models are involved in important cellular mechanisms such as metabolic pathways and protein synthesis. Thus, the data generated in this study expands our knowledge on the genomic characteristics of this devastating pest and provides essential resources for future genetic studies of the species.

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Section: De Novo Genome Assemblymentioning

confidence: 99%

A first draft genome of the Sugarcane borer, Diatraea saccharalis.

et al. 2020

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“…We sequenced and assembled data from different next-generation sequencing (NGS) tools to produce a standard draft genome of Risso's dolphin. Assembly of sequence reads appropriately is necessary to have a reliable reference genome [6]. In this study, we aimed to select recently developed assembly tools that suit large vertebrate genomes with Ivyspring International Publisher a high background noise.…”

Section: Introductionmentioning

confidence: 99%

Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus

Senevirathna¹,

Yonezawa²,

Saka³

et al. 2023

J. Genomics

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The Risso's dolphin (Grampus griseus) is one of the migratory marine mammals and they have commonly dispersed in tropical and temperate seas. It is a least concerned species in the IUCN red list of threatened species. However, their population size and factors affecting their population structure are unknown. Due to the wide distribution of this species, their populations might be genetically stable and less structured. To support genetic studies on dolphins and other marine mammals, we assembled the draft genome of Risso's dolphin that was found in Japan. The tissue samples were used to extract high molecular DNA and subjected to sequencing by Illumina HiSeq X, Oxford Nanopore MinION, and Bionano Saphyr. The assembled hybrid genome was 75.9% of complete eukaryotic BUSCOs and the genome size was 2.256 Gb with 2.042 Mb of scaffold N50. De novo assembly of this genome by Bionano Saphyr recovered 2.036 Gb total genome map length and structural variations. The gene structures of this draft genome were identified by BRAKER2, and 9947 genes were recovered. The data will be useful for future studies of cetaceans.

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“…Within the family Mugilidae, a draft genome assembly was first reported for redlip mullet, Liza haematocheila (0.74 Gb), which has 1,453 contigs with an N50 length of 3.9 Mb (Liyanage et al, 2019). Later, chromosome-level assembly of this fish was generated with Oxford Nanopore long-read, single-tube long fragment reads (stLFR), and HiC chromatin interaction data, which are 652.91 Mb length in 514 scaffolds with contig and scaffold N50 lengths of 7.21 and 28.01 Mb, respectively (Zhao et al, 2021).…”

Section: Introductionmentioning

confidence: 99%