Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae
Abstract
:1. Introduction
2. Results
2.1. Genomic Characteristics
2.2. Organellar Gene Analysis
2.3. PCGs
2.4. PCG Codon Use
2.5. Identification of Potential RNA Editing Sites in PCGs
2.6. Repeat Sequence Analysis
2.7. SNP Analysis
2.8. Phylogenetic Analysis and Ka/Ks
3. Discussion
3.1. Genomic Characteristics
3.2. Codon Use Preferences
3.3. RNA Editing Sites
3.4. Repeat Sequence
3.5. Phylogenetic Analysis and Ka/Ks
4. Materials and Methods
4.1. Sampling and DNA Extraction
4.2. Organellar DNA Sequencing and Genome Assembly
4.3. Genome Annotation
4.4. Codon Use Analysis
4.5. RNA Editing
4.6. Repeat Sequence Analysis
4.7. Comparative Genome and Phylogenetic Analyses
4.8. Ka/Ks Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Order | Species | Accession No. | Length | GC | PCG | Overlap | Spacer | Genes | PCG | tRNA | rRNA | ORFs | Note |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
bp | % | % | bp | bp | Number | Number | Number | Number | Number | ||||
Fucales | Sargassum hemiphyllum var. chinense * | MT873582 | 34,686 | 36.60 | 75.98 | 188 | 1597 | 65 | 35 | 25 | 3 | 2 | mtDNA |
Sargassum hemiphyllum var. chinense * | MT873582 | 124,323 | 30.60 | 75.34 | 75 | 19,859 | 173 | 137 | 28 | 6 | 2 | cpDNA | |
Sargassum confusum | MG459430 | 34,721 | 36.60 | 76.05 | 180 | 1596 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum confusum | MG459429 | 124,375 | 30.40 | 75.30 | 77 | 17,439 | 173 | 137 | 28 | 6 | 2 | cpDNA | |
Sargassum muticum | NC024614 | 34,720 | 36.60 | 76.01 | 171 | 1614 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum thunbergii | NC026700 | 34,748 | 36.60 | 76.04 | 168 | 1600 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum thunbergii | NC029134 | 124,592 | 30.40 | 75.00 | 75 | 17,848 | 173 | 137 | 28 | 6 | 2 | cpDNA | |
Sargassum fusiforme | MN883537 | 34,696 | 37.50 | 76.07 | 211 | 1570 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum fusiforme | MN794016 | 124,298 | 30.40 | 75.05 | 75 | 17,349 | 173 | 137 | 28 | 6 | 2 | cpDNA | |
Sargassum horneri | NC024613 | 34,606 | 36.20 | 76.30 | 164 | 1464 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum horneri | MN265366 | 124,075 | 30.60 | 75.45 | 75 | 17,365 | 173 | 137 | 28 | 6 | 2 | cpDNA | |
Sargassum yezoense | NC038156 | 34,767 | 36.60 | 75.90 | 81 | 1686 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum fluitans | NC033385 | 34,727 | 36.20 | 75.88 | 170 | 1643 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum natans | NC033384 | 34,727 | 36.20 | 75.90 | 161 | 1640 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum vachellianum | NC027508 | 34,877 | 36.20 | 75.57 | 158 | 1787 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum spinuligerum | NC034272 | 34,891 | 36.20 | 75.41 | 207 | 1835 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum ilicifolium | KT272403 | 34,925 | 35.60 | 75.49 | 160 | 1822 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum polycystum | KT280278 | 34,862 | 35.70 | 75.57 | 150 | 1598 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Sargassum aquifolium | NC033408 | 34,761 | 36.20 | 75.89 | 161 | 1701 | 64 | 35 | 24 | 3 | 2 | mtDNA | |
Fucus vesiculosus | NC007683 | 36,392 | 34.40 | 72.62 | 121 | 2086 | 66 | 35 | 25 | 3 | 3 | mtDNA | |
Fucus vesiculosus | NC016735 | 124,986 | 28.90 | 74.99 | 77 | 17,912 | 172 | 137 | 27 | 6 | 2 | cpDNA | |
Fucus vesiculosus var. spiralis | MG922856 | 36,396 | 34.40 | 72.69 | 121 | 3196 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Fucus vesiculosus var. spiralis | MG922855 | 125,066 | 28.90 | 75.02 | 75 | 17,919 | 173 | 137 | 28 | 6 | 2 | cpDNA | |
Fucus distichus | NC034672 | 36,400 | 34.30 | 72.65 | 129 | 2220 | 64 | 35 | 23 | 3 | 3 | mtDNA | |
Coccophora langsdorfii | NC032287 | 35,660 | 36.40 | 74.08 | 194 | 2512 | 65 | 35 | 25 | 3 | 2 | mtDNA | |
Coccophora langsdorfii | NC032288 | 124,450 | 28.90 | 75.10 | 75 | 17,846 | 172 | 137 | 27 | 6 | 2 | cpDNA | |
Ectocarpales | Colpomenia peregrina | NC025302 | 36,025 | 32.00 | 75.30 | 123 | 1499 | 66 | 35 | 25 | 3 | 3 | mtDNA |
Scytosiphon lomentaria | NC025240 | 36,918 | 34.10 | 73.40 | 110 | 2221 | 67 | 35 | 25 | 3 | 4 | mtDNA | |
Scytosiphon promiscuus | MK107985 | 134,366 | 31.30 | 71.91 | 65 | 23,496 | 178 | 140 | 28 | 6 | 3 | cpDNA | |
Endarachne binghamiae | NC036747 | 37,460 | 34.40 | 72.26 | 153 | 2723 | 67 | 35 | 24 | 3 | 5 | mtDNA | |
Endarachne binghamiae | NC038231 | 136,274 | 31.20 | 70.80 | 65 | 26,270 | 177 | 140 | 28 | 6 | 2 | cpDNA | |
Ectocarpus siliculosus | NC030223 | 37,189 | 33.50 | 72.85 | 199 | 3153 | 66 | 35 | 25 | 3 | 5 | mtDNA | |
Ectocarpus siliculosus | NC013498 | 139,954 | 30.70 | 70.13 | 65 | 27,538 | 185 | 142 | 31 | 6 | 6 | cpDNA | |
Pleurocladia lacustris | NC032046 | 37,814 | 32.90 | 65.17 | 226 | 4134 | 69 | 35 | 24 | 3 | 7 | mtDNA | |
Pleurocladia lacustris | NC032045 | 138,815 | 29.80 | 69.62 | 65 | 26,578 | 180 | 139 | 30 | 6 | 5 | cpDNA | |
Cladosiphon okamuranus | NC040224 | 38,419 | 34.30 | 70.88 | 128 | 3628 | 64 | 35 | 24 | 3 | 2 | mtDNA | |
Cladosiphon okamuranus | NC046005 | 137,324 | 30.20 | 70.71 | 65 | 26,354 | 178 | 140 | 29 | 6 | 2 | cpDNA | |
Pylaiella littoralis | NC003055 | 58,507 | 38.00 | 54.35 | 135 | 8030 | 79 | 36 | 24 | 3 | 16 | mtDNA | |
Laminariales | Saccharina japonica rongfu | KX073815 | 37,638 | 35.30 | 72.43 | 95 | 2426 | 66 | 35 | 25 | 3 | 3 | mtDNA |
Saccharina japonica rongfu | MK058525 | 130,584 | 31.10 | 73.17 | 71 | 21,514 | 173 | 138 | 29 | 6 | 2 | cpDNA | |
Saccharina japonica | NC013476 | 37,657 | 35.30 | 72.40 | 95 | 2445 | 66 | 35 | 25 | 3 | 3 | mtDNA | |
Saccharina japonica | NC018523 | 130,585 | 31.10 | 73.17 | 71 | 21,516 | 173 | 138 | 29 | 6 | 2 | cpDNA | |
Saccharina latissima | NC026108 | 37,659 | 35.40 | 72.38 | 95 | 2519 | 66 | 35 | 24 | 3 | 3 | mtDNA | |
Saccharina latissima | NC049039 | 130,619 | 31.10 | 73.15 | 71 | 21,638 | 172 | 138 | 28 | 6 | 2 | cpDNA | |
Saccharina sculpera | NC029206 | 37,627 | 35.20 | 72.40 | 95 | 2624 | 64 | 35 | 24 | 2 | 3 | mtDNA | |
Saccharina longissima | NC021640 | 37,628 | 35.30 | 72.39 | 127 | 2519 | 65 | 35 | 24 | 3 | 3 | mtDNA | |
Laminaria solidungula | NC044690 | 130,784 | 31.00 | 72.67 | 71 | 22,118 | 173 | 138 | 29 | 6 | 2 | cpDNA | |
Laminaria hyperborea | NC021639 | 37,976 | 35.20 | 71.66 | 92 | 2969 | 64 | 35 | 23 | 3 | 3 | mtDNA | |
Laminaria digitata | NC004024 | 38,007 | 35.10 | 71.63 | 148 | 2405 | 67 | 35 | 25 | 3 | 4 | mtDNA | |
Laminaria digitata | NC044689 | 130,377 | 31.00 | 72.69 | 26 | 21,920 | 173 | 138 | 29 | 6 | 2 | cpDNA | |
Lessonia spicata | NC044181 | 37,097 | 32.70 | 73.21 | 166 | 1861 | 66 | 35 | 25 | 3 | 3 | mtDNA | |
Lessonia spicata | NC044182 | 130,305 | 30.90 | 73.31 | 71 | 21,426 | 173 | 138 | 27 | 6 | 2 | cpDNA | |
Costaria costata | NC023506 | 37,461 | 34.90 | 72.76 | 150 | 2134 | 66 | 35 | 25 | 3 | 3 | mtDNA | |
Costaria costata | NC028502 | 129,947 | 30.90 | 73.50 | 71 | 21,064 | 171 | 138 | 27 | 6 | 2 | cpDNA | |
Undaria pinnatifida | NC023354 | 37,402 | 32.50 | 72.70 | 160 | 2107 | 65 | 35 | 24 | 3 | 3 | mtDNA | |
Undaria pinnatifida | NC028503 | 130,383 | 30.60 | 73.24 | 71 | 21,449 | 172 | 138 | 28 | 6 | 2 | cpDNA | |
Macrocystis integrifolia | NC042669 | 37,366 | 32.00 | 72.93 | 128 | 2253 | 64 | 35 | 24 | 3 | 2 | mtDNA | |
Nereocystis luetkeana | NC042395 | 37,399 | 35.30 | 72.85 | 129 | 2403 | 63 | 35 | 24 | 2 | 2 | mtDNA | |
Dictyotales | Dictyopteris divaricata | NC043845 | 32,021 | 38.30 | 74.67 | 160 | 1370 | 65 | 35 | 24 | 3 | 3 | mtDNA |
Dictyopteris divaricata | NC036804 | 126,099 | 31.20 | 75.64 | 97 | 17,191 | 172 | 137 | 27 | 6 | 2 | cpDNA |
Total Value of Shared CDS (mtDNA) | Total Value of Shared CDS (cpDNA) | |
---|---|---|
GCall | 35.68% a/32.44% b/34.59% c | 31.13% a/31.59% b/31.74% c |
GC1 | 41.79% a/42.41% b/43.13% c | 41.93% a/42.83% b/42.95% c |
GC2 | 36.63% a/36.28% b/37.18% c | 34.27% a/34.74% b/34.98% c |
GC3 | 28.62% a/18.83% b/23.47% c | 17.20% a/17.21% b/17.30% c |
ENC | 47.12 a/39.41 b/42.77 c | 39.44 a/38.87 b/38.28 c |
Type | Effect | a mtPCGs | b cpPCGs | Percentage/% |
---|---|---|---|---|
Hydrophilic | CAT(H)→TAT(Y) | 3 | a 6.25/b 5.00 | |
Hydrophilic | CAC(H)→TAC(Y) | 1 | 1 | |
Hydrophilic | CGC(R)→TGC(C) | 1 | ||
Hydrophobic | CTC(L)→TTC(F) | 1 | a 56.25/b 30.00 | |
Hydrophobic | CTT(L)→TTT(F) | 12 | ||
Hydrophobic | CGG(R)→TGG(W) | 1 | ||
Hydrophobic | CCC(P)→CTC(L) | 1 | ||
Hydrophobic | CCT(P)→CTT(L) | 8 | ||
Hydrophobic | GCT(A)→GTT(V) | 12 | 3 | |
Hydrophobic | GCG(A)→GTG(V) | 5 | 1 | |
Hydrophobic | GCC(A)→GTC(V) | 4 | ||
Hydrophobic | GCA(A)→GTA(V) | 1 | 2 | |
Hydrophilic–hydrophobic | ACG(T)→ATG(M) | 1 | a 21.25/b 50.00 | |
Hydrophilic–hydrophobic | TCA(S)→TTA(L) | 5 | 3 | |
Hydrophilic–hydrophobic | TCG(S)→TTG(L) | 1 | ||
Hydrophilic–hydrophobic | TCT(S)→TTT(F) | 3 | ||
Hydrophilic–hydrophobic | ACA(T)→ATA(I) | 2 | 4 | |
Hydrophilic–hydrophobic | ACT(T)→ATT(I) | 3 | 3 | |
Hydrophilic–hydrophobic | ACC(T)→ATC(I) | 2 | ||
Hydrophilic–hydrophobic | CCA(P)→TCA(S) | 2 | a 16.25/b 15.00 | |
Hydrophilic–hydrophobic | CCG(P)→TCG(S) | 4 | ||
Hydrophilic–hydrophobic | CCC(P)→TCC(S) | 4 | 1 | |
Hydrophilic–hydrophobic | CCT(P)→TCT(S) | 3 | 2 |
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Jia, X.; Chen, W.; Liu, T.; Chen, Z. Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae. Int. J. Mol. Sci. 2024, 25, 8584. https://doi.org/10.3390/ijms25168584
Jia X, Chen W, Liu T, Chen Z. Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae. International Journal of Molecular Sciences. 2024; 25(16):8584. https://doi.org/10.3390/ijms25168584
Chicago/Turabian StyleJia, Xuli, Weizhou Chen, Tao Liu, and Zepan Chen. 2024. "Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae" International Journal of Molecular Sciences 25, no. 16: 8584. https://doi.org/10.3390/ijms25168584