Confirming a new species of Amalthea D’Archino & W. A. Nelson (Halymeniales, Rhodophyta) from the mesophotic zone of Hawai‘i through taxogenomics Author Cabrera, Feresa P. 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) feresa@ucsc.edu Author Smith, Celia M. School of Life Sciences, University of Hawai‘i, 3190 Maile Way, Honolulu, Hawai‘i 96822 (United States) celia @ hawaii. edu celia@hawaii.edu Author Spalding, Heather L. Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina 29424 (United States) spaldinghl @ cofc. edu spaldinghl@cofc.edu Author Hauk, Brian B. Author Kosaki, Randall K. 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 hauk@noaa.gov Author Sherwood, Alison R. School of Life Sciences, University of Hawai‘i, 3190 Maile Way, Honolulu, Hawai‘i 96822, (United States) asherwoo @ hawaii. edu asherwoo@hawaii.edu text Cryptogamie, Algologie 2025 2025-05-20 46 1 1 17 https://sciencepress.mnhn.fr/sites/default/files/articles/pdf/algologie2025v46a1.pdf journal article 10.5252/cryptogamie-algologie2025v46a1 55d929f9-bca9-4871-8f3f-ff422611f4f3 1776-0984 15496348

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