A First Insight into a Draft Genome of Silver Sillago (Sillago sihama) via Genome Survey Sequencing

Li, Zhiyuan; Tian, Changxu; Huang, Yang; Lin, Xinghua; Wang, Yaorong; Jiang, Dongneng; Zhu, Chunhua; Chen, Huapu; Li, Guangli

doi:10.3390/ani9100756

Cited by 16 publications

(15 citation statements)

References 33 publications

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“…As both sister chromatids would be separately assembled in high-heterozygosity regions, it might cause the imprecise assessment of genome size. The heterozygosity ratio of H. nehereus observed in the present study was 0.67%, which was higher than that of Scatophagus argus (female 0.37% and male 0.38%) [47], Sebastiscus marmoratus (0.17%) [48] and Acanthogobius ommaturus (0.17%) [49], but smaller than that of Sillago sihama (0.92%) [50]. Genome assembly becomes more difficult when the heterozygosity ratio is higher than 0.5% [25].…”

Section: Discussioncontrasting

confidence: 66%

Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus

Yang

Huang

Ning

et al. 2021

CIMB

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Harpadon nehereus forms one of the most important commercial fisheries along the Bay of Bengal and the southeast coast of China. In this study, the genome-wide survey dataset first produced using next-generation sequencing (NGS) was used to provide general information on the genome size, heterozygosity and repeat sequence ratio of H. nehereus. About 68.74 GB of high-quality sequence data were obtained in total and the genome size was estimated to be 1315 Mb with the 17-mer frequency distribution. The sequence repeat ratio and heterozygosity were calculated to be 52.49% and 0.67%, respectively. A total of 1,027,651 microsatellite motifs were identified and dinucleotide repeat was the most dominant simple sequence repeat (SSR) motif with a frequency of 54.35%. As a by-product of whole genome sequencing, the mitochondrial genome is a powerful tool to investigate the evolutionary relationships between H. nehereus and its relatives. The maximum likelihood (ML) phylogenetic tree was constructed according to the concatenated matrix of amino acids translated from the 13 protein-coding genes (PCGs). Monophyly of two species of the genus Harpadon was revealed in the present study and they formed a monophyletic clade with Saurida with a high bootstrap value of 100%. The results would help to push back the frontiers of genomics and open the doors of molecular diversity as well as conservation genetics studies on this species.

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Section: Discussioncontrasting

confidence: 66%

Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus

Yang

Huang

Ning

et al. 2021

CIMB

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“…The genome assembled here appears to be of higher quality than that of S. sihama in spite of the same sequencing strategy being employed, also in our lab [51]. This might be due to the heterozygosity rate of S. argus being substantially lower than that of S. sihama (0.92%) [51]. Male-specific Dmrt1 is the candidate sex determination gene in S. argus [38].…”

Section: Discussionmentioning

confidence: 66%

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Huang

Jiang

et al. 2019

Animals

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Simple Summary: The spotted scat, Scatophagus argus, is a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding. However, genomic data from S. argus is lacking. In the present study, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained. This information will serve to support the breeding and aquaculture of S. argus. Abstract:The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.

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“…Recently, the K-mer method has been successfully applied for estimating genome size using genome survey sequences without prior knowledge of the genome size for non-model species [27,33]. Based on Illumina sequencing data, the genome size was estimated using K-mer depth distribution of sequenced reads [34].…”

Section: Discussionmentioning

confidence: 99%

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Peng

Zhende

et al. 2021

Preprint

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The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber, fruit and nut industry. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for it. The genome size of B. horsfieldi was estimated as approximate 520 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.26% and 51.03%, respectively. The assembled genome was 528.56Mb with GC content of 35.40%. A total of 121750 microsatellite motifs were identified. The most frequent repeat motif was mononucleotide with a frequency of 85.84%, followed by 8.08% of dinonucleotide, 5.04% of trinonucleotide, 0.73% of tetranonucleotide, 0.20% of pentanonucleotide and 0.12% of hexanonucleotide motifs. The AT/AT, TA/TAand GA/TC repeats were the most abundant motifs of dinucleotide motifs, and AAT/ATT, TAA/TTA and ATA/TAT were the most abundant motifs of trinucleotide motifs, respectively. ninety six pairs of SSR primers were randomly selected for PCR amplification and agarose gel electrophoresis detection, among which 56 pairs of primers can be effectively amplified to obtain the target fragment. In summary, various candidate microsatellite markers were identified and characterized in this study using genome survey analysis.

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A First Insight into a Draft Genome of Silver Sillago (Sillago sihama) via Genome Survey Sequencing

Cited by 16 publications

References 33 publications

Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus

Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

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