The complete mitochondrial genome and phylogenetic analysis of Upogebia major (De Haan, 1841)

Conservation Genet Resour

Song

Zhang

et al. 2022

The mud shrimp Upogebia major (De Haan, 1841) (Crustacea, Decapoda, Gebiidea) is an important species widely distributed in coastal shallow waters. As an active initiation species, it has contributed signi cantly to the maintenance of coastal benthic biodiversity. However, there is still a lack of effective molecular markers to effectively protect and manage this species. In this study, we used the DNeasy Blood & Tissue kit to extract DNA and Illumina HiSeq 4000 sequencing technology to obtain SNP marker resources. 177 single nucleotide polymorphism (SNP) markers were developed and characterized in U. major. The minor allele frequency raged from 0.0500 to 0.5000. The observed heterozygosity and expected heterozygosity ranged from 0.0333 to 0.9000 and from 0.0966 to 0.5085, respectively. Polymorphic information content ranged from 0.0905 to 0.3750. The inbreeding coe cient values varied from − 0.2902 to 0.5968. Seventeen loci showed signi cant deviations from the Hardy-Weinberg equilibrium (P < 0.05). The polymorphic SNPs will be helpful for the further population genetic analysis and natural resource conservation of U. major.

Section: Introductionmentioning

confidence: 99%

Development and characterization of 177 SNP markers in the mud shrimp Upogebia major

Conservation Genet Resour

Song

Zhang

et al. 2022

“… 2020 ; Emami-Khoyi et al. 2021 ; Sun and He 2021 ). Two rRNA genes, 12SrRNA (827 bp) and 16SrRNA (1402 bp) are separated by a trnV-GTA.…”

mentioning

confidence: 99%

Complete mitogenome and phylogenetic analysis of the tropical rocky shore crabGrapsus albolineatus(Lamarck, 1818) (Crustacea: Grapsoidea)

Mitochondrial DNA Part B

Chen

et al. 2022

In this study, the complete mitogenome of Grapsus albolineatus (Lamarck, 1818) (Crustacea: Grapsoidea) was sequenced. The mitogenome of G. albolineatus was a circular molecule with 15,578 bp length. Its nucleotide composition was 26.81% A, 16.37% G, 34.51% T, and 22.31% C. It comprised 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA). All PCGs were initiated by ATN codons, except for the atp8 and nad1 genes. Ten PCGs used a common stop codon of TAA or TAG, and the other three ended with a truncated stop codon (a single stop nucleotide T). Phylogenetic analysis revealed that G. albolineatus was closely related to species from the genera Pachygrapsus and Metopograpsus .

Development and Characterization of 177 SNP Markers in The Mud Shrimp Upogebia Major

Song

et al. 2021

Preprint

The mud shrimp Upogebia major (De Haan, 1841) (Crustacea, Decapoda, Gebiidea) is an important species widely distributed in coastal shallow waters. As an active initiation species, it has contributed significantly to the maintenance of coastal benthic biodiversity. However, there is still a lack of effective molecular markers to effectively protect and manage this species. In this study, we used the DNeasy Blood & Tissue kit to extract DNA and Illumina HiSeq 4000 sequencing technology to obtain SNP marker resources. 177 single nucleotide polymorphism (SNP) markers were developed and characterized in U. major. The minor allele frequency raged from 0.0500 to 0.5000. The observed heterozygosity and expected heterozygosity ranged from 0.0333 to 0.9000 and from 0.0966 to 0.5085, respectively. Polymorphic information content ranged from 0.0905 to 0.3750. The inbreeding coefficient values varied from − 0.2902 to 0.5968. Seventeen loci showed significant deviations from the Hardy-Weinberg equilibrium (P < 0.05). The polymorphic SNPs will be helpful for the further population genetic analysis and natural resource conservation of U. major.