Published May 20, 2025
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TABLE 1 in Confirming a new species of Amalthea D'Archino & W. A. Nelson (Halymeniales, Rhodophyta) from the mesophotic zone of Hawai'i through taxogenomics
Authors/Creators
- 1. Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 130 McAllister Way, Santa Cruz, California 95060 (United States) feresa @ hawaii. edu / feresa @ ucsc. edu (corresponding author)
- 2. School of Life Sciences, University of Hawai'i, 3190 Maile Way, Honolulu, Hawai'i 96822 (United States) celia @ hawaii. edu
- 3. Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina 29424 (United States) spaldinghl @ cofc. edu
- 4. Papahānaumokuākea Marine National Monument, National Oceanic Atmospheric Administration, 1845 Wasp Boulevard, Building 176, Honolulu, Hawai'i 96818 (United States) brian. hauk @ noaa. gov randall. kosaki @ noaa. gov
- 5. School of Life Sciences, University of Hawai'i, 3190 Maile Way, Honolulu, Hawai'i 96822, (United States) asherwoo @ hawaii. edu
Description
TABLE 1. — Functional classification of genes in the Amalthea mahilanii F.P.Cabrera & A.R.Sherwood, sp. nov. chloroplast genome. Categories for classification follow Ohta et al. (2003).
| Genetic system | Number | Genes | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Maintenance | 2 | dnaB | rne | ||||||
| RNA Polymerase | 4 | rpoA | rpoB | rpoC1 | rpoC2 | rpoZ | |||
| Transcription factors | 4 | ntcA | ompR | rbcR | ycf29 | ||||
| Translation | 4 | infB | infC | tsf | tufA | ||||
| Ribosomal proteins | |||||||||
| Large subunit | 28 | rpl1 | rpl2 | rpl3 | rpl4 | rpl5 | rpl6 | rpl9 | rpl11 |
| rpl12 | rpl13 | rpl14 | rpl16 | rpl18 | rpl19 | rpl20 | rpl21 | ||
| rpl22 | rpl23 | rpl24 | rpl27 | rpl28 | rpl29 | rpl311 | rpl32 | ||
| rpl33 | rpl34 | rpl35 | rpl36 | ||||||
| 18 | rps1 | rps2 | rps3 | rps4 | rps5 | rps6 | rps7 | rps8 | |
| Small subunit | rps9 rps18 | rps10 rps19 | rps11 | rps12 | rps13 | rps14 | rps16 | rps17 | |
| TRNA processing | 1 | tilS | |||||||
| Protein quality control | 4 | clpc | dnak | ftsH | groEL | ||||
| Photosystems | |||||||||
| Phycobilisomes | 11 | apcA cpeA | apcB cpeB | apcD nblA | apcE | apcF | cpcA | cpcB | cpcG |
| Photosystem I | 13 | psaA | psaB | psaC | psaD | psaE | psaF | psaI | psaJ |
| psaK | psaL | psaM | ycf3 | ycf4 | |||||
| 19 | psbA | psbB | psbC | psbD | psbE | psbF | psbH | psbI | |
| Photosystem II | psbJ psbY | psbK psbZ | psbL Psb30 | psbN | psbT | psbV | psbW | psbX | |
| Cytochrome complex | 11 | ccs1 petL | ccsA petM | petA petN | petB | petD | petF | petG | petJ |
| Redox system | 7 | acsF | bas1 | dsbD | ftrB | grx | pbsA | trxA | |
| ATP synthesis | |||||||||
| ATP synthase | 9 | atpA | atpB | atpD | atpE | atpF | atpG | atpH | atpl |
| clpC | sufB | sufC | |||||||
| Metabolism | |||||||||
| Carbohydrates | 5 | odpA | odpB | pgmA | rbcL | rbcS | cbbx | ||
| Lipids | 5 | accA | accB | accD | acpP | fabH | |||
| Nucleotides | 2 | carA | upp | ||||||
| Amino acids | 8 | argB | gltB | ilvB | ilvH | syfB | syh | trpA | trpG |
| Cofactors | 6 | chll | mоеB | preA | thiG | thiS | dfr | ||
| Transport | |||||||||
| Transport | 7 | cemA | secA | secG | secY | ycf38 | ycf63 | tatC | |
| Unknown | |||||||||
| 31 | ORF58 | ORF83 | ORF745 | ORF101 | ORF152 | ycf17 | ycf19 | ycf20 | |
| Conserved ORFs | ycf21 | ycf22 | ycf23 | ycf33 | ycf34 | ycf35 | ycf36 | ycf37 | |
| ycf39 | ycf41 | ycf45 | ycf46 | ycf52 | ycf53 | ycf54 | ycf55 | ||
| ycf58 | ycf60 | ycf62 | ycf65 | ycf80 | ycf86 | ycf92 | |||
| RNA genes | |||||||||
| rRNAs | 3 | rrn5 | rrn23 | rrn16 | |||||
| 29 | trnA-UGC | trnC-GCA | trnD-GUC | trnE-UUC | trnF-GAA | trnG-GCC | trnG-UCC | trnH-GUG | |
| tRNAs | trnI-GAU | trnK-UUU | trnL-CAA | trnL-UAA | trnL-UAG | trnM-CAU | trnM-CAU | trnM-CAU | |
| trnN-GUU | trnP-UGG | trnQ-UUG | trnR-ACG | trnR-CCG | trnR-UCU | trnS-GCU | trnS-UGA | ||
| trnT-GGU | trnT-UGU | trnV-GAC | trnW-CCA | trnY-GUA | |||||
| Miscellaneous RNAs | 1 | rnpB |
Notes
Published as part of Cabrera, Feresa P., Smith, Celia M., Spalding, Heather L., Hauk, Brian B., Kosaki, Randall K. & Sherwood, Alison R., 2025, Confirming a new species of Amalthea D'Archino & W. A. Nelson (Halymeniales, Rhodophyta) from the mesophotic zone of Hawai'i through taxogenomics, pp. 6 in Cryptogamie, Algologie 46 (1) on page 6, DOI: 10.5252/cryptogamie-algologie2025v46a1, http://zenodo.org/record/15496348
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Related works
- Is part of
- Journal article: 10.5252/cryptogamie-algologie2025v46a1 (DOI)
- Journal article: urn:lsid:plazi.org:pub:FFBCFFE0FFA1BB4EFFD8FFF5FFFECF06 (LSID)
- Journal article: http://publication.plazi.org/id/FFBCFFE0FFA1BB4EFFD8FFF5FFFECF06 (URL)
- Journal article: http://zenodo.org/record/15496348 (URL)
References
- OHTA N., MATSUZAKI M., MISUMI O., MIYAGISHIMA S. Y., NOZAKI H., TANAKA K., SHIN-I T., KOHARA Y. & KUROIWA T. 2003. - Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA research 10 (2): 67-77. https://doi.org/10.1093/dnares/10.2.67