Table 1.
Data on salmon genomes ever obtained. As we can assess, the great majority of studies focus on the mitochondrial genome.
| View | Genome | Genome Data Acquisition Approach | Characteristics and Features of the Genome | Reference |
|---|---|---|---|---|
| S. alpinus erythrinus | Mitochondrial | Sanger sequencing and annotation by comparison with other sequences using Geneious R11 Genome structure determined using MEGA X |
Size: 16,652 bp; two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 tRNA genes; the overall base composition was 28.0% A, 26.4% T, 17.0% G, and 28.6% C, and the mitogenome GC content was 45.6% | [183] |
| S. alpinus alpinus | Mitochondrial | Primers were designed using the mitoPrimer_V1 program; sequences annotated by comparison with published charr mitogenome sequences using Geneious R11 |
Size: 16,655 and 16,657 bp; GC content: 45.6%; 24 SNPs. The highest was the variability of NADH dehydrogenase subunit genes (42.6%Table of all variable sites). |
[184] |
| Salvelinus taranetzi | Mitochondrial | The sequenced fragments were de novo assembled into a complete mitochondrial genome and annotated by comparing with published genome sequences of charr using Geneious R11 | Size: 16,654 b.p. The overall base composition was 28.0% A, 26.4% T, 28.6% C, and 17.0% G, with a slight A + T bias (54.5%). Two substitutions were found in the control region and 12S rRNA. Other single nucleotide substitutions were found in common protein-coding sequences The total sequence discrepancy (D xy) was 0.0011 ± 0.0002 |
[185] |
| Salvelinus sp. | Mitochondrial | Size 16,654 b.p. The organization of the genome was identical to that of typical salmon genomes, including 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, a light chain origin of replication (OL), and a control region (CR). The overall base composition was 28.0% A, 26.4% T, 17.0% G, and 28.6% C, and the GC content was 45.6%. |
[186] | |
| Salvelinus boganidae and Salvelinus elgyticus | Mitochondrial | Libraries were prepared using an Ion Plus Fragment Library Kit and unique adapters (Ion Xpress), and preliminary fragmentation of PCR products was performed on a Covaris M220 ultrasonicator. Libraries were sequenced on the Ion S5 platform (Thermo Fisher Scientific). Clean reads were assembled into contig with the Bowtie2 algorithm in Geneious R11 Mitogenome of S. taranezi was used as a reference for correct contig position and orientation |
16,654 b.p. for s. elgyticus and 16,655 b.p. for s. boganidae. The gene arrangement, composition, and size are similar to s. Taranezi The genomic organization is identical to typical salmon mitogenomes, including two rRNA genes, 13 protein-coding genes, 22 tRNA genes, a light chain origin of replication (OL), and a control region (CR). |
[187] |
| Salvelinus levanidovi | Mitochondrial | Using Geneious R11, the sequenced fragments were combined into a full mitogenome and described by reference to previous char mitogenomes. | The complete mitogenome of native S. levanidovi was 16,624 bp long. the overall base composition was 28.1% A, 26.4% T, 28.6% C, and 16.9% G, with a slight A + T bias (54.5%) |
[188] |
| T. thymallus | Mitochondrial | The consensus sequence was controlled and annotated using MitoAnnotator. | Mitogenome has a total length of 16,660 bp and includes 13 protein-coding genes, 22 transfer RNA genes including 2 tRNA-Leu and 2 tRNA-Ser, two ribosomal RNA genes, and a control region following the standard vertebrate order. Intergenic spaces and overlapping sequences were found. Six coding genes have an incomplete codon stop: NADH2, COII, ATP6, NADH3, NADH4, and cytb. The base composition of the entire genome was 27.5% for A, 27.9% for T, 17.5% for G and 27.1% for C. |
[189] |
| Sl. Svetovidov | Mitochondrial | Genomes were matched using the MAFFT algorithm in Geneious, and maximum likelihood (ML) analysis was performed based on Tamura-Nei (TrN93) plus a nucleotide substitution gamma model. The machine learning tree was built using the MEGA X software and validated by bootstrap analysis. |
Genome length 16,655 bp. The overall base composition was 28.0% A, 26.4% T, 28.7% C, and 16.9% G with a slight A + T bias (54.5%) 18 single nucleotide differences and no difference in length between sequences MK695627, MK695628 and MK695629; only 13 substitutions were found in all sequences encoding the protein and five were found in the control region. | [190] |
| O. masou | Mitochondrial | Genome length 16,648 bp, with 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and one light chain origin of replication. The overall base composition is 28.6% A, 26.8% T, 28.1% C, and 16.4% G, respectively, with a slight AT bias (55.4%). |
[191] | |
| S. fontinalis × S. malma sp. hybrid | Mitochondrial | Genome length 16,623 bp. The overall base composition was 28.3% A, 26.5% T, 28.4% C and 16.8% G, with a slight A + T bias (54.8%) two non-coding regions, the L-chain origin of replication was located between tRNA-Asn and tRNA-Cys, and the control region was located within tRNA-Pro and tRNA-Phe. Eight tRNAs and the ND6 gene were encoded on the L-chain, the rest were encoded on the H-chain The complete mitogenome sequence contained 16s RNA and 12s RNA, which were located between tRNA-Phe and tRNA-Leu and were separated by the tRNA-Val gene. |
[192] | |
| S. malma | Mitochondrial | Genome length 16,652 bp. The overall base composition was 28.1% A, 26.4% T, 28.5% C, and 17.0% G. The 13 protein-coding genes code for 3808 amino acids in their entirety. |
[193] | |
| S. trutta | General | Sequencing with Illumina HiSeqX; Assembly of the genome using a software package; Gene annotation with Ensembl |
Size: 2.37 Gbp-p; most of the assembly consists of 40 chromosomal pseudomolecules; 43,935 protein-coding and 4441 non-protein-coding genes | [194] |