Complete nuclear ribosomal DNA sequence analyses of the black-footed abalone Haliotis iris

Figures & data

Figure 1 . Schematic diagram of the tandemly repeated ribosomal DNA in eukaryotes, nrSSU: small subunit ribosomal RNA; nrLSU: large subunit ribosomal RNA; ITS1: internal transcribed spacer 1; ITS2: internal transcribed spacer 2; NTS: non-transcribed spacer; ETS: external transcribed spacer; IGS: intergenic spacer.

Figure 2. Schematic diagrams of the primers used in this study.

Table 1. Primers used in this study.

Region	Primers	Sequence(5′–3′)	Length (bp)	Reference
SSU	SSUF	AACCTGGTTGATCCTGCCAGT	1858 bp	Huang et al. (2007)
	SSUR	TGATCCTTCTGCAGGTTCA		Huang et al. (2007)
ITS	ITSF1	TACCGATTGAATGGTTTAGTGAG	637 bp	This paper
	ITSR1	GGTGTTTTGCGATTGCTTAGTC		This paper
	ITSF2	CGACATCTTGAACGCATATTGC	729 bp	This paper
	ITSR2	CCTCACGGTACTTGTTCGCTAT		This paper
LSU	LSUF1	AAGAGCCCAGCACCGAATC	1796 bp	This paper
	LSUR1	TGCGTTACCGCACGAGACC		This paper
	LSUF2	AAATCGTGCTCGCCCTTCC	662 bp	This paper
	LSUR2	GAAATCACATTGCGTCAGCACCAG		This paper
	LSUF3	CGTAACTTCGGGATAAGGATTGG	1233 bp	This paper
	LSUR3	CTTCGCACCATTGGCACCT		This paper
IGS	IGSF	CCGCAGGTTCAGACAGTTGGT	4138 bp	This paper
	IGSR	TTGGATGTGGTAGCCGTTTCTCA		This paper

Table 2. PCR reaction protocols for amplifying H. iris ribosomal DNA fragments.

Reaction step	SSUF/R	ITSF1/R1, ITSF2/R2	LSUF1/R1, LSUF3/R3	LSUF2/R2	IGS
Initial denaturation	95°C 5 min	95°C 5 min	95°C 5 min	95°C 5 min	95°C 5 min
Denaturation	95°C 1 min	95°C 30 s	95°C 1 min	95°C 30 S	95°C 30 S
Annealing	54°C 50 s	58°C 30 s	55°C 50 s	52°C 30 s	55°C 30 s
Extension	72°C 1 min 30 s	72°C 1 min	72°C 1 min 30 s	72°C 1 min	72°C 5 min
Cycle index	35cycles	35 cycles	35 cycles	35 cycles	35 cycles
A final extension	72°C 7 min	72°C 7 min	72°C 7 min	72°C 7 min	72°C 7 min

Table 3. GenBank accession number, the GC contents and the length of each region of the ribosomal DNA.

	SSU	ITS	LSU	IGS
Genbank NO.	KY933303–KY933304	KY933301–KY933302	KY933305	KY978225–KY978226
Length (bp)	1858 bp	749 bp	3412 bp	3560–3662 bp
GC contents (%)	50.75%	56.72%	54.37%	45.22–45.25%

Table 4. Collection information, GenBank accession numbers and the lengths of each ribosomal region for Haliotis species used in the present study.

Species	SSU		LSU		ITS
	GenBank accession number	Length (bp)	GenBank accession number	Length (bp)	GenBank accession number	Length (bp)
H. discus	AF082177.1	1858 bp	AY145418.1	3430 bp	AY146403.1	763 bp
H.asinina	GQ160786.1	1809 bp	GQ160634.1	2064 bp	–
H. diversicolor	AY698072.1	1860 bp	EF529461.1	1389 bp	AF296868.1	720 bp
H. tuberculata	AF120511.1	1937 bp	GQ160635.1	1693 bp	AF296861.1	710 bp
H. corrugata	FJ977644.1	1809 bp	FJ977675.1	2080 bp	AF296856.1	752 bp
H. discus hannai	AY319437.1	698 bp	–	–	AF296858.1	758 bp
H. kamtschatkana	AY923882.1	1477 bp		–	AF296853.1	750 bp
H. rufenscens	KR005646.1	547 bp	–	–	AF296855.1	748 bp
H. jacnensis	AY923878.1	588 bp	–	–	–	–
H. varia	AY923884.1	588 bp	–	–	–	–
H.midae	AY923883.1		–	–	AF296863.1	751 bp
H. pustulata	AY923880.1	587 bp	–	–	–
H. lamellosa	–	–	–	–	AF296862.1	710 bp
H. pourtalesii	–	–	–	–	AF296871.1	748 bp
H.virginea	AY923881.1	1442 bp	–	–	–	–
H.roei	–	–	–	–	AF296866.1	752 bp
H. cyclobates	–	–	–	–	AF296865.1	754 bp
H. scalaris	–	–	–	–	AF296864.1	751 bp
H. fulgens	–	–	–	–	AF296859.1	758 bp
H. cracherodii	–	–	–	–	AF296857.1	756 bp
H.sorenseni	–	–	–	–	AF296850.1	750 bp
H. roberti	–	–	–	–	AF306942.1	759 bp
H. madaka	–	–	–	–	AY146404.1	760 bp
H. walallensis	–	–	–	–	AF296854.1	749 bp
H. gigantea	–	–	–	–	AY146405.1	768 bp

Table 5. Pairwise distances of the nrSSU gene sequences.

	H. iris	H. discus	H. tuberculata	H. discus hannai	H. diversicolor	H. jacnensis	H. pustulata	H. virginea	H. kamtschatkana	H. midae	H. varia	H. corrugata	H. asinina	H. rufenscens
H. iris
H. discus	0.030
H. tuberculata	0.062	0.061
H. discus hannai	0.030	0.061	0.062
H. diversicolor	0.030	0.000	0.061	0.061
H. jacnensis	0.061	0.063	0.030	0.030	0.063
H. pustulata	0.061	0.063	0.030	0.030	0.063	0.000
H. virginea	0.061	0.063	0.030	0.030	0.063	0.000	0.000
H. kamtschatkana	0.061	0.063	0.030	0.030	0.063	0.000	0.000	0.000
H. midae	0.094	0.061	0.094	0.062	0.061	0.061	0.061	0.061	0.061
H. varia	0.061	0.063	0.030	0.030	0.063	0.000	0.000	0.000	0.000	0.061
H. corrugata	0.062	0.061	0.000	0.062	0.061	0.030	0.030	0.030	0.030	0.094	0.030
H. asinina	0.062	0.061	0.000	0.062	0.061	0.030	0.030	0.030	0.030	0.094	0.030	0.000
H. rufenscens	0.842	0.750	0.825	0.842	0.750	0.827	0.827	0.827	0.827	0.670	0.827	0.825	0.825

Note: The GenBank accession numbers of species listed in Table 5 refer to Table 4 for accession numbers.

Figure 3. ML phylogenetic tree of Haliotidae based on ITS region sequence datasets.

Table 6. Pairwise distances of ITS gene sequences.

Species	H. iris	H. kamtschatkana	H.sorenseni	H. rufenscens	H. walallensis	H. madaka	H. discus	H. gigantea	H. discus hannai	H. corrugata	H. pourtalesii
H. iris
H. kamtschatkana	0.025
H.sorenseni	0.028	0.003
H. rufenscens	0.023	0.002	0.005
H. walallensis	0.023	0.002	0.005	0.000
H. madaka	0.028	0.009	0.012	0.011	0.011
H. discus	0.028	0.009	0.012	0.011	0.011	0.000
H. gigantea	0.026	0.008	0.011	0.009	0.009	0.002	0.002
H. discus hannai	0.029	0.008	0.011	0.009	0.009	0.008	0.008	0.006
H. corrugata	0.026	0.005	0.008	0.006	0.006	0.008	0.008	0.006	0.003
H. pourtalesii	0.036	0.020	0.023	0.018	0.018	0.020	0.020	0.018	0.017	0.017
H. roberti	0.040	0.025	0.028	0.023	0.023	0.022	0.022	0.020	0.021	0.021	0.011
H. cracherodii	0.036	0.014	0.017	0.012	0.012	0.014	0.014	0.012	0.014	0.014	0.018
H. fulgens	0.037	0.022	0.025	0.020	0.020	0.025	0.025	0.023	0.023	0.023	0.029
H. lamellosa	0.063	0.055	0.058	0.053	0.053	0.052	0.052	0.053	0.055	0.055	0.057
H. tuberculata	0.061	0.053	0.057	0.052	0.052	0.050	0.050	0.052	0.053	0.053	0.055
H.roei	0.052	0.047	0.050	0.045	0.045	0.044	0.044	0.045	0.047	0.047	0.047
H. cyclobates	0.053	0.049	0.052	0.047	0.047	0.042	0.042	0.044	0.048	0.048	0.050
H. scalaris	0.050	0.045	0.049	0.044	0.044	0.042	0.042	0.044	0.045	0.045	0.044
H.midae	0.042	0.034	0.037	0.032	0.032	0.031	0.031	0.032	0.034	0.034	0.036
H. diversicolor	0.061	0.057	0.060	0.055	0.055	0.048	0.048	0.050	0.055	0.055	0.057
Species	H. roberti	H. cracherodii	H. fulgens	H. lamellosa	H. tuberculata	H.roei	H. cyclobates	H. scalaris	H.midae	H. diversicolor
H. iris
H. kamtschatkana
H.sorenseni
H. rufenscens
H. walallensis
H. madaka
H. discus
H. gigantea
H. discus hannai
H. corrugata
H. pourtalesii
H. roberti
H. cracherodii	0.020
H. fulgens	0.034	0.029
H. lamellosa	0.062	0.060	0.062
H. tuberculata	0.060	0.058	0.060	0.002
H.roei	0.052	0.050	0.057	0.040	0.039
H. cyclobates	0.052	0.050	0.058	0.040	0.040	0.011
H. scalaris	0.048	0.048	0.055	0.039	0.037	0.017	0.018
H.midae	0.040	0.039	0.044	0.034	0.032	0.015	0.017	0.014
H. diversicolor	0.058	0.057	0.063	0.052	0.050	0.042	0.040	0.040	0.036

Note: The GenBank accession numbers of species listed in Table 6 refer to Table 4 for accession numbers.

Table 7. Pairwise distances of the nrLSU gene sequences.

species	H. iris	H. tuberculata	H. corrugata	H. asinina	H. discus	H. diversicolor supertexta
H. iris
H. tuberculata	0.014
H. corrugata	0.011	0.017
H. asinina	0.02	0.011	0.024
H. discus	0.011	0.017	0.007	0.024
H. diversicolor supertexta	0.038	0.026	0.042	0.03	0.042

Note: The GenBank accession numbers of species listed in Table 7 refer to Table 4 for accession numbers.

Huang B, Fang ZG, Liu JL, Zhou Z, Wang XB. 2007. Cloning and sequence of genes encoding Haliotis asinina 18S rRNAs. Oceanologia Et Limnologia Sinica. 38(3):212–216. (in Chinese with English Abstract).

 Google Scholar