Analysis of RAPD and mitochondrial 16S rRNA gene sequences from Trichiurus lepturus and Eupleurogrammus muticus in the Yellow Sea*

Meng, Ze‐hong; Zhuang, Zhidong; Jin, Xin; Tang, Qiaoran; Su, Yan; 苏永全,

doi:10.1080/10020070412331343251

Cited by 4 publications

(3 citation statements)

References 2 publications

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“…From the perspective of modern genetics, species with higher genetic diversity will have a wider natural distribution and stronger environmental adaptability, survivability, and evolutionary potential than other species. Genetic variation is required for a species to adapt to environmental changes [ 23 ]. Therefore, evaluating genetic diversity is an important part of germplasm identification and collection.…”

Section: Discussionmentioning

confidence: 99%

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

Luo

Zhang

et al. 2020

BMC Genet

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Background Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. secundatum , limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49 S. secundatum accessions. Results Based on seven types of phenotypic data, the 49 S. secundatum accessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers ( h = 0.47, I = 0.66) and ISSR markers ( h = 0.45, I = 0.64) supports the notion that the S. secundatum accessions are highly diverse. S. secundatum could be divided into three classes based on the evaluated molecular markers. Conclusions Phenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum . Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum . The SNPs identified in this study could be used to distinguish S. secundatum accessions.

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Section: Discussionmentioning

confidence: 99%

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

Luo

Zhang

et al. 2020

BMC Genet

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“…However, the heterozygosity rate of the E. muticus genome was 2.4 times higher than that of L. savala, indicating that E. muticus may have a relatively high level of genetic variation. Meng et al [22] demonstrated that the randomly amplified polymorphic DNA (RAPD) polymorphism rate and genetic polymorphism were higher in E. muticus from the Yellow Sea than that of Trichiurus lepturus.…”

Section: Characterization Of the E Muticus Genomementioning

confidence: 99%

“…Thus, the widespread distribution, resource stability, and biological traits of E. muticus suggest that it may have a unique genomic characterization. However, only a few studies have investigated the biology of E. muticus in the northern Indian Ocean [12,[19][20][21] and its genetic variation in the Yellow Sea of China [16,22]. There is also a lack of research to reveal the genetic and evolutionary mechanisms of the species at the genomic level.…”

Section: Introductionmentioning

confidence: 99%

Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus

Han,

Wu,

Miao

et al. 2024

Animals

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Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids.

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Analysis of the genetic diversity and population structure of Perinereis aibuhitensis in China using TRAP and AFLP markers

Liu

Shi

et al. 2015

Biochemical Systematics and Ecology

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Analysis of RAPD and mitochondrial 16S rRNA gene sequences from Trichiurus lepturus and Eupleurogrammus muticus in the Yellow Sea*

Cited by 4 publications

References 2 publications

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus

Analysis of the genetic diversity and population structure of Perinereis aibuhitensis in China using TRAP and AFLP markers

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