Decoding the Mitochondrial Genome of the Tiger Shrimp: Comparative Genomics and Phylogenetic Placement Within Caridean Shrimps

Genes, Journal Year: 2025, Volume and Issue: 16(4), P. 457 - 457

Published: April 16, 2025

Background/Objectives: Freshwater shrimps of the family Atyidae, particularly hyperdiverse genus Caridina, are keystone decomposers in tropical aquatic ecosystems and valuable aquaculture resources. However, their evolutionary relationships remain unresolved due to conflicting morphological molecular evidence. Here, we sequenced characterized complete mitochondrial genome Caridina mariae (Tiger Shrimp), aiming (1) elucidate its genomic architecture, (2) reconstruct a robust phylogeny Caridea using 155 decapod species address long-standing taxonomic uncertainties. Methods: Muscle tissue from wild-caught C. (voucher ID: KIZ-2023-001, Guangdong, China) was subjected Illumina NovaSeq 6000 sequencing (150 bp paired-end). The mitogenome assembled MITObim v1.9, annotated via MITOS2, validated by PCR. Phylogenetic analyses employed 13 protein-coding genes under Bayesian inference (MrBayes v3.2.7; 106 generations, ESS > 200) maximum likelihood (RAxML v8.2.12; 1000 bootstraps), with Harpiosquilla harpax as outgroup. best-fit substitution model (MtZoa + F I G4) selected jModelTest v2.1.10. Results: 15,581 circular encodes 37 (13 PCGs, 22 tRNAs, 2 rRNAs) an A T-rich control region (86.7%). Notably, trnS1 lacks dihydrouracil arm—a rare structural deviation Decapoda. PCGs exhibit moderate nucleotide skew (AT = 0.030; GC −0.214), while nad5, nad4, nad6 show significant GC-skew. Phylogenomic strongly support (PP 1.0; BS 95) novel sister-group relationship between Halocaridinidae Typhlatyinae, contradicting prior morphology-based classifications. monophyly Penaeoidea, Astacidea, confirmed, but Eryonoidea Crangonoidea formed unexpected clade. Conclusions: This study provides first mitogenomic framework for mariae, revealing both conserved features (e.g., PCG content) lineage-specific innovations tRNA truncation). resolved challenges traditional classifications highlights convergent adaptation freshwater lineages. These findings offer tools conservation prioritization threatened underscore utility mitogenomics systematics.

Language: Английский

Development and Application of a 40 K Liquid Capture Chip for Beef Cattle

Animals, Journal Year: 2025, Volume and Issue: 15(9), P. 1346 - 1346

Published: May 7, 2025

The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics species by exploring genetic diversity aid selection. SNP chip is a cost-effective genotyping platform essential for molecular breeding livestock. In this study, we developed liquid capture suitable five Hubei (China) indigenous beef cattle breeds based on whole-genome sequencing datasets. panel consisted 42,686 SNPs (~40 K). These were evenly distributed each bovine chromosome, with majority having minor allele frequencies >0.05 located within intergenic regions. performance evaluation was proceeded 200 individuals, revealing that has high call rate 99.48%. further used examine population structure 205 individuals demonstrated ability differentiate between foreign breeds. also determine runs homozygosity (ROH) local 195 individuals. We identified 2547 ROH several genes associated economically important traits in study population. Our findings demonstrate not only contributes understanding but provides valuable information future programs, thereby improving their production efficiency economic value.

Language: Английский