Codon Table 9: Mitochondrial Genome of the Sea Cucumber Holothuria atra

15,788 base pairs comprise the complete mitochondrial genome of the sea cucumber Holothuria atra, sequenced by Jinjin Wang and published in April 2026. The data includes 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 18 non-coding regions, with an A+T content of 59.2%. Codon usage analysis shows leucine is the most abundant amino acid (16.58%), while cysteine is the least (1.03%).

Use Cases

• Phylogenetic analysis of Holothuroidea species based on shared mitochondrial sequences mentioned in the description
• Studying codon usage bias in mitochondrial genomes based on the 61 codons encoding 20 amino acids
• Predicting tRNA secondary structures based on the 22 tRNA sequences ranging from 62 to 72 base pairs
• Comparing mitochondrial genome organization based on the 18 non-coding and 7 overlapping gene regions

Strengths

• The complete mitochondrial genome is provided with a precise length of 15,788 bp
• Codon usage frequencies are quantified, identifying high-frequency (e.g., AGA, CUA) and low-frequency (e.g., GCG, CCG) codons
• Evolutionary relationships are analyzed, showing closest relation to Holothuria polii

Limitations

• Row count is unknown, which may limit suitability assessment
• Column-level documentation is absent; field semantics must be inferred after download
• The dataset is very small (14.1 KB), indicating limited scope to a single species' mitochondrial genome

Provenance

Source

Jinjin Wang via figshare

Collection Method

Genomic analysis of a Holothuria atra specimen's complete mitochondrial genome

Time Range

The study provides a snapshot; specific collection date is not stated.

Freshness

Last updated 2026-04-17 17:40:40; freshness should be verified

Geography

Associated with resource development in the Kiribati region, but specific sample location is not detailed.