The Journal of Heredity 2002:93(6)
© 2002 The American Genetic Association 93:439-444
Brief Communication |
Complete Nucleotide Sequence of the Coturnix chinensis (Blue-Breasted Quail) Mitochondorial Genome and a Phylogenetic Analysis With Related Species
From the Department of Genome Research, National Institute of Agrobiological Sciences, Tsukuba, 305-0901, Japan (Nishibori, Hayashi, and Yasue), and the Laboratory of Animal Genetics, Graduate School of Biosphere Sciences, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan (Nishibori, Tsudzuki, and Yamamoto).
Address correspondence to Masahide Nishibori at the address above, or e-mail: nishibo{at} hiroshima-u.ac.jp.
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Abstract |
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Coturnix chinensis (blue-breasted quail) has been classically grouped in Galliformes Phasianidae Coturnix, based on morphologic features and biochemical evidence. Since the blue-breasted quail has the smallest body size among the species of Galliformes, in addition to a short generation time and an excellent reproductive performance, it is a possible model fowl for breeding and physiological studies of the Coturnix japonica (Japanese quail) and Gallus gallus domesticus (chicken), which are classified in the same family as blue-breasted quail. However, since its phylogenetic position in the family Phasianidae has not been determined conclusively, the sequence of the entire blue-breasted quail mitochondria (mt) genome was obtained to provide genetic information for phylogenetic analysis in the present study. The blue-breasted quail mtDNA was found to be a circular DNA of 16,687 base pairs (bp) with the same genomic structure as the mtDNAs of Japanese quail and chicken, though it is smaller than Japanese quail and chicken mtDNAs by 10 bp and 88 bp, respectively. The sequence identity of all mitochondrial genes, including those for 12S and 16S ribosomal RNAs, between blue-breasted quail and Japanese quail ranged from 84.5% to 93.5%; between blue-breasted quail and chicken, sequence identity ranged from 78.0% to 89.6%. In order to obtain information on the phylogenetic position of blue-breasted quail in Galliformes Phasianidae, the 2,184 bp sequence comprising NADH dehydrogenase subunit 2 and cytochrome b genes available for eight species in Galliformes [Japanese quail, chicken, Gallus varius (green junglefowl), Bambusicola thoracica (Chinese bamboo partridge), Pavo cristatus (Indian peafowl), Perdix perdix (gray partridge), Phasianus colchicus (ring-neck pheasant), and Tympanchus phasianellus (sharp-tailed grouse)] together with that of Aythya americana (redhead) were examined using a maximum likelihood (ML) method. The ML analyses on the first/second codon positions, the third codon positions, and amino acid sequence consistently demonstrated that blue-breasted quail and Japanese quail are in the same phylogenetic cluster.
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Introduction |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionReferences |
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The order Galliformes comprises three families—Phasianidae, Numididae, and Odontophoridae—and these families consist of 58 genera, including 214 species (Sibley and Monroe 1990). Although the 177 species belonging to the family Phasianidae are currently divided into 45 genera (Sibley and Monroe 1990), it has been proposed that these species be grouped differently, specifically, into two tribes, the Phasianini and Perdicini, based on their morphologic features (Johnsgard 1973, 1999). Thirty-eight species in Galliformes have the name of "quail"; 14 species of them are grouped into the Phasianidae spanning over 5 genera, and 24 into the Odontophoridae spanning 7 genera. According to the tribe-based classification, the species having the name of "quail" in the Phasianidae belong to the tribe Perdicini.
Coturnix chinensis (blue-breasted quail; also known as Indian blue quail, Chinese painted quail, or button quail) occurs over a wide geographic range: from India through the southern and western parts of China, through southeast Asia to the islands of Indonesia and Philippines; and from the northern to southeastern coastlines of Australia (Sibley and Monroe 1990). The blue-breasted quail is generally accepted to be classified in the genus Coturnix as is evident by its scientific name (Monroe and Sibley 1993; Sibley and Monroe 1990). However, there is an additional classification that the quail is further grouped together with Coturnix adansonii (blue quail) into the subgenus Excalfactoria (Kuroda and Morioka 1987; Sibley and Monroe 1990; Uchida and Shimasaki 1987; Yamashina 1986). This quail is the smallest fowl in Galliformes, and the weight of adult blue-breasted quail is about half that of Coturnix japonica (Japanese quail), which is the smallest domestic fowl. In addition to its small size; the blue-breasted quail has lower mortality, short generation time, and an excellent reproductive performance (Tsudzuki 1994). The blue-breasted quail is therefore a possible model fowl for breeding and physiological studies of Japanese quail and Gallus gallus domesticus (chicken). It is considered that a closer genetic distance between the animal to be studied and a corresponding model animal is better. However, the phylogenetic position of blue-breasted quail in the family Phasianidae has not been determined conclusively, as described above. Therefore, in the present study, the sequence of the entire blue-breasted quail mitochondrial (mt) genome was determined, and then used to examine phylogenetic position of blue-breasted quail in the family Phasianidae through comparison with corresponding sequences of other species in the same family.
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Materials and Methods |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionReferences |
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DNA was prepared from the liver of a male blue-breasted quail (Tsudzuki 1994) kept at Hiroshima University, following the procedures described by Sambrook and Russell (2000). mtDNA fragments were amplified using the LA-PCR Kit (Takara Shuzo, Otsu, Japan) with blue-breasted quail DNA as the template and the two LA-PCR primer sets used for Japanese quail mtDNA amplification (Nishibori et al. 2001), according to the procedure described previously (Nishibori et al. 2001). Fragments of about 16 kbp thus amplified were purified through a 0.6% agarose gel and MagExtractor (MFX-6000, Toyobo, Osaka, Japan), and were used for segmental amplification through the appropriate primer pairs of the 37 primer sets described previously (Nishibori et al. 2001). Each primer set amplified a mtDNA fragment containing an overlap of at least 100 bp with the adjacent amplified fragment at both termini. The PCR products from the segmental amplification were sequenced using the PCR Product Pre-Sequence Kit (USB Co., Cleveland, OH, USA) and an ABI PRISMTM BigDye Terminator Cycle Sequencing Kit (Applied Biosystems, Foster, CA, USA). Sequences were assembled using AutoAssember ver.2.1 software (Applied Biosystems, Foster, CA, USA) and analyzed with the GENETYX program package (Software Development Inc., Tokyo, Japan), with reference to the structure of Japanese quail and chicken mtDNAs (Desjardins and Morais 1990; Nishibori et al. 2001).
Molecular phylogenetic analysis was performed for the blue-breasted quail mtDNA sequence together with those of related species by the maximum likelihood (ML) method (Adachi and Hasegawa 1996a). The NucML program was employed for the combined first and second bases of the codons, and separately for the third base of the codons, using the HKY85-F model (Hasegawa et al. 1985). The amino acid sequence was analyzed with ProtML using the mtREV24-F model (Adachi and Hasegawa 1996b). Local bootstrap values were calculated by the resampling of estimated log-likelihood of sites method with 1,000 repetitions (Hasegawa and Kishino 1994; Kishino et al. 1990).
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Results and Discussion |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionReferences |
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Following the procedure described above, the whole sequence of the blue-breasted quail mitochondrial genome and its genomic structure were determined and registered in a DNA database (DDBJ /EMBL/GenBank) under accession number AB073301. As presented in Table 1, blue-breasted quail mtDNA was found to consist of 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs, and a D-loop; these components are the same as those of Japanese quail and chicken mtDNAs. Blue-breasted quail mtDNA was shown to be 16,687 bp, which was smaller than Japanese quail and chicken mtDNAs by 10 bp and 88 bp, respectively (Table 1). The major differences between blue-breasted quail and Japanese quail/chicken mtDNA are ascribed to the D-loop and 16SrRNA, as shown in Table 1. Sequence identity of the genes, including those for 12SrRNA and 16SrRNA, between blue-breasted quail and Japanese quail ranged from 84.5% to 93.5%. The ATPase subunit 8 (ATPase8) showed the lowest similarity (84.5%), and NADH dehydrogenase subunit 4 (ND4) the highest (93.5%). The similarity of the sequences between blue-breasted quail and chicken ranged from 78.0% to 89.6%; ATPase8 again showed the lowest similarity (78.0%), and 12SrRNA the highest (89.6%).
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Since blue-breasted quail was classically placed in the family Phasianidae, species in the family Phasianidae were screened under the condition that as many gene sequences as possible be available for comparison between species. Subsequently, eight species, Bambusicola thoracica (Chinese bamboo partridge; DDBJ/EMBL/GenBank accession numbers: AF222538 and AF028790), Japanese quail (AP003195), chicken (X52392), Gallus varius (green junglefowl; AF222551 and AB044988), Pavo cristatus (Indian peafowl; AF394612 and L08379), Perdix perdix (gray partridge; AF222560 and AF028791), Phasianus colchicus (ring-neck pheasant; AF222561 and AF028798), and Tympanchus phasianellus (sharp-tailed grouse; AF222569 and AF068191), were selected for the analysis of the concatenated sequence (2,184 bp) of NADH dehydrogenase subunit 2 (ND2) and cytochrome b (Cytb) genes. Then the sequences of blue-breasted quail ND2 and Cytb were analyzed with those of these eight species and additionally with those of Aythya americana (redhead; AF090337) as an outgroup using the ML method as described in Materials and Methods.
As shown in Figures 1a and 1c, ML analyses of both the first/second bases of the codons and the amino acid sequence indicated the same phylogenetic tree except for the position of Indian peafowl. The ML analysis of the third base of the codons revealed a phylogenetic tree that was different from the above two trees (Figure 1b). However, the cluster of blue-breasted quail and Japanese quail was consistently observed in the three ML analyses, though the position of the cluster was unstable in the trees (Figure 1a,b,c). In order to examine the possibility that the outgroup used in the present study affected the instability of the position of the cluster, mtDNA sequence of Numida meleagirs (helmeted guineafowl; AF397613 and L08383) was added as an additional outgroup to perform the ML analyses, indicating that the outgroup did not affect the positional instability of the cluster in the tree (data not shown). Although the instability of the position of the cluster was not resolved in the present study, the present findings strongly indicate that blue-breasted quail and Japanese quail are genetically very close, which is consistent with classical classification based on morphology and DNA–DNA hybridization (Sibley and Ahlquist 1990).
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Based on the similarity and genetic distance determined by "number of substitutions per 100 sites" between mitochondria genomes shown in Tables 2 and 3, respectively, it is possible that the tree construction using the third base of the codons was affected by mutational saturation, which may have resulted in deviation of the cluster positions based on the third base of the codons from those of the first/second bases of codons and of amino acid sequence. In addition, both of the topological instability and the low bootstrap values are attributable to insufficient phylogenetic signals. This indicates that a much longer sequence than that used in present study should be analyzed to clarify the inconsistency in the trees.
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Using a part of mitochondria D-loop sequence, Fumihito et al. (1995) indicated that blue-breasted quail formed a phylogenetic cluster as follows: (gray partridge, (blue-breasted quail, (Japanese quail, Chinese bamboo partridge))). This observation is contrast with the present observation. In order to resolve the discrepancy between the two observations, additional sequences, as described above, should be subjected to the analysis. However, in the particular genetic relationships between blue-breasted quail, Japanese quail, and Chinese bamboo partridge, the cluster of blue-breasted quail and Japanese quail seems to be more likely than the cluster of Japanese quail and Chinese bamboo partridge, because any of the present analyses using sequence longer than that used in their analysis (Fumihito et al. 1995) gave the cluster comprising blue-breasted quail and Japanese quail with high bootstrap values ranging from 991 to 1,000.
When the species examined in the present study were grouped based on the tribe-based classification proposed by Johnsgard (1973, 1999), chicken, green junglefowl, Indian peafowl, and ring-neck pheasant were classified into Phasianini; and Chinese bamboo partridge, gray partridge, Japanese quail, and blue-breasted quail were classified into Perdicini. Therefore, the results shown in Figure 1 do not support the tribe-classification, but rather support the conclusion stated by Kimball et al. (1999) that the tribe-based classification does not reflect the genetic relationships. The present observations further support those of Kimball et al. (1999) and Dimcheff et al. (2000) that sharp-tailed grouse and ring-neck pheasant were genetically very close. However, in order to provide conclusive evidence for the above matters, and to determine phylogenetic relationships between species in the family Phasianidae, more comprehensive molecular phylogenetic analyses are required.
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Received November 4, 2001
Accepted October 15, 2002
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