2urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7Eurn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727AZooKeysZK1313-29891313-2970Pensoft Publishers10.3897/zookeys.995.3443234432Research ArticleAnimaliaAvesChordataPasseriformesVertebrataEvolutionary biologyGeneticsSystematicsAsiaSequence and organisation of the mitochondrial genome of Japanese Grosbeak (Eophonapersonata), and the phylogenetic relationships of FringillidaeSunGuolei1ZhaoChao1XiaTianhttps://orcid.org/0000-0002-0097-69491WeiQinguo1YangXiufeng1FengShi1ShaWeilai1ZhangHonghaizhanghonghai67@126.com1College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
2020181120209956780D177116D-8523-5002-86D5-A3CF95C58CC6C3518FBE-06B2-4CAA-AFBF-13EB96B3E1E942913921203201907102020Guolei Sun, Chao Zhao, Tian Xia, Qinguo Wei, Xiufeng Yang, Shi Feng, Weilai Sha, Honghai ZhangThis is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.http://zoobank.org/C3518FBE-06B2-4CAA-AFBF-13EB96B3E1E9
Mitochondrial DNA is a useful molecular marker for phylogenetic and evolutionary analysis. In the current study, we determined the complete mitochondrial genome of Eophonapersonata, the Japanese Grosbeak, and the phylogenetic relationships of E.personata and 16 other species of the family Fringillidae based on the sequences of 12 mitochondrial protein-coding genes. The mitochondrial genome of E.personata consists of 16,771 base pairs, and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one control region. Analysis of the base composition revealed an A+T bias, a positive AT skew and a negative GC skew. The mitochondrial gene order and arrangement in E.personata was similar to the typical avian mitochondrial gene arrangement. Phylogenetic analysis of 17 species of Fringillidae, based on Bayesian inference and Maximum Likelihood (ML) estimation, showed that the genera Coccothraustes and Hesperiphona are closely related to the genus Eophona, and further showed a sister-group relationship of E.personata and E.migratoria.
Eophonapersonatagene ordermitochondrial genomephylogenetic analysisQufu Normal UniversityCitation
Sun G, Zhao C, Xia T, Wei Q, Yang X, Feng S, Sha W, Zhang H (2020) Sequence and organisation of the mitochondrial genome of Japanese Grosbeak (Eophona personata), and the phylogenetic relationships of Fringillidae. ZooKeys 995: 67–80. https://doi.org/10.3897/zookeys.995.34432
Introduction
Eophonapersonata (Passeriformes: Fringillidae), commonly known as the Japanese Grosbeak, is a granivorous passerine with the adults reaching a size of ca. 23 cm. The species is mainly distributed in Far Eastern Asia including Eastern Siberia, Northeast China, North Korea, and Japan. Grosbeaks are migratory birds and move to South China during winter (Clement et al. 1993). Grosbeaks primarily feed on seeds, with preference for certain plants, and insects (Kominami 1987); for example, the seeds of Celtis and Aphananthe are favored during autumn and winter (Nimura 1993; Yoshikawa and Kikuzawa 2009).
The mitochondrial genome (hereafter mitogenome) is a useful molecular marker for phylogenetic analysis, and is widely used in the evolutionary analysis of a variety of species (Anderson et al. 1981; Boore 1999; Sun et al. 2016). The animal mitogenome is usually a short, closed, circular, double stranded molecule, and comprises of 37 genes: 13 protein-coding genes (PCGs; ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COI, COII, COIII, ATP6, ATP8, CYTB), two rRNA genes (12S rRNA and 16S rRNA), and 22 tRNA genes. Compared to nuclear DNA, the mitogenome is a more conserved molecule, and is maternally transmitted (Wolstenholme 1992; Boore 1999; da Fonseca et al. 2008).
With ca. 6000 species, passerines account for more than half of the total number of extant birds (Gill et al. 2020). Based on the analysis of hundreds of bird mitochondrial data, at least seven gene arrangements have been found (Zhou et al. 2014). Gene rearrangements in passerines are very common, and most reported passerines have the standard gene order consistent with chickens Gallusgallus (Desjardins and Morais 1990). In addition, Passeriformes have at least four gene arrangement (Harrison et al. 2004). The different rearrangements involve the initial tandem duplication, and the partial loss of the segment containing the control region (CR) (Caparroz et al. 2018).
The passerine family Fringillidae comprises ca. 50 genera and 230 species (Gill et al. 2020). The phylogenetic relationships between the species in the family Fringillidae and the superfamily Passeroidea are incompletely resolved (Van der Meij et al. 2005). Previous phylogenetic studies of Fringillidae have clarified several aspects of their relationships (Arnaiz-Villena et al. 2001; Van der Meij et al. 2005; Lerner et al. 2011; Zuccon et al. 2012; Tietze et al. 2013; Sangster et al. 2015; Zhao et al. 2016). The aim of this study is to determine the complete mitogenome of E.personata and provide a mitogenomic perspective on the phylogenetic relationships of E.personata and 16 other species of the family Fringillidae.
Materials and methodsSample collection and DNA extraction
The specimen of E.personata, which had died due to poaching activities, was collected from Shenyang City, Liaoning Province, China, and was stored in the laboratory and then frozen to -80 °C before further processing and analysis. All experiments involving animals were approved by the Qufu Normal University Institutional Animal Care and Use Committee (Permit number: QFNU2018-010) and executed in accordance with the Guide to Animal Experiments of the Ministry of Science and Technology (Beijing, China). DNA was extracted from muscle tissue using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Cloning and sequencing of mitochondrial genome
Primers were designed based on mitogenome sequences of a sparrowhawk (Accipiternisus, GenBank accession number KM360148) and Chinese Grosbeak E.migratoria (KX423959). MEGA5.1, Primer Premier 6.0, and the NCBI-Primer blast database (http://www.ncbi.nlm.nih.gov/BLAST) were used to determine the primers. All the amplified fragments were separated by gel electrophoresis and purified by Agarose Gel Extraction Kit (Qiagen). Purified fragments were cloned into PMD18-T vectors, and transformed into competent E.coli cells. Positive clones were identified by blue-white screening and sequenced. Bidirectional sequencing was conducted at Sangon Biotech (Shanghai) using the ABI 3730xl DNA Analyzer (PE Applied Biosystems, San Francisco, CA, USA).
Bioinformatics analysis and statistical procedures
The raw sequences were assembled using the software programs BioEdit (version 7.2. 5) and Chromas Pro 1.7.7 (Goodstadt and Ponting 2001). Genes were identified by aligning the identified sequences with the known sequence of the mitogenome of E.migratoria. The tRNA gene structure was predicted using Scan-SE 1.21 (http://lowelab.ucsc.edu/tRNAscan-SE) and ARWEN (http://130.235.46.10/ARWEN/) (Lowe and Eddy 1997).
Phylogenetic analysis of 17 Fringillidae species (accession numbers are provided in Table 2) and Phasianuscolchicus (NC_015526) was conducted using Bayesian inference and Maximum Likelihood (ML) estimation based on the sequences of 12 mitochondrial PCGs; ND6 gene, which is encoded on the L-strand, was excluded from analysis. The sequences were aligned with ClustalX 1.81 (Thompson et al. 1997; Jeanmougin et al. 1998), and phylogenetic analysis was performed using MrBayes 3.1.2 and PAUP* 4.0 (Swofford 2001; Ronquist and Huelsenbeck 2003).
Based on the Akaike Information criterion (AIC), GTR+I+G was estimated as the best-fit substitution model using Modeltest 3.7 (Posada and Crandall 1998). Bootstrap tests were based on 1000 replicates (Felsenstein 1981; Wilgenbusch and Swofford 2003). For Bayesian analysis, Metropolis-coupled Markov chain Monte Carlo analysis was performed, with 4 chains run in parallel, for 2,000,000 generations, and the first 25% of each of the sampled 1000 generations were excluded as burn-in.
Following Sangster and Luksenburg (2020), we verified the identity and integrity of our mitogenome sequence of E.personata with reference sequences of multiple protein-coding genes: NADH dehydrogenase subunit 2 (ND2, 1041 bp; n = 1), part of cytochrome oxidase subunit I (COX1, 698 bp; n = 6), and cytochrome b (CYTB, 1143 bp; n = 2). These markers are commonly used in avian systematics, and reference sequences were available for each marker.
ResultsComparison of mitogenomes of Japanese grosbeak and those of other species of Fringillidae
The complete mitochondrial genome of E.personata (KX812499, GenBank) was sequenced and a genome map was constructed (Fig. 1). The genome contains 13 PCGs, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region (Table 1).
Circular map of the mitochondrial genome of Eophonapersonata. tRNAs are denoted as one-letter symbols according to IUPAC-IUB single-letter amino acid codes; L1 = UUR, L2 = CUN, S1 = UCN, S2 = AGY.
https://binary.pensoft.net/fig/476810
Organization of the mitochondrial genome of Eophonapersonata.
Gene
Location (bp)
Size (bp)
Spacer (+) or overlap (–)
Strand
Start codon
Stop codon
Anticodon
D-loop
1–1187
1187
H
–
–
–
tRNAPhe
1188–1255
68
0
H
–
–
GAA
12S rRNA
1256–2230
975
0
H
–
–
–
TRNAVal
2231–2300
70
0
H
–
–
TAC
16S rRNA
2301–3904
1604
0
H
–
–
–
tRNALeu(UUR)
3905–3979
75
16
H
–
–
TAA
ND1
3996–4973
978
6
H
ATG
AGG
–
tRNAIle
4980–5053
74
3
H
–
–
GAT
tRNAGln
5057–5127
71
-1
L
–
–
TTG
tRNAMet
5127–5195
69
0
H
–
–
CAT
ND2
5196–6236
1041
-1
H
ATG
TA-
–
tRNATrp
6236–6305
70
1
H
–
–
TCA
tRNAAla
6307–6375
69
1
L
–
–
TGC
tRNAAsn
6384–6456
73
0
L
–
–
GTT
tRNACys
6457–6523
67
-1
L
–
–
GCA
tRNATyr
6523–6593
71
1
L
–
–
TGA
COX1
6595–8145
1551
-9
H
GTG
AGG
–
tRNASer(UCN)
8137–8209
73
3
L
–
–
GTC
tRNAAsp
8213–8281
69
8
H
–
–
GTC
COX2
8290–8973
684
1
H
ATG
TAA
–
tRNALys
8975–9043
69
1
H
–
–
TTT
ATPase8
9045–9212
168
-10
H
ATG
TAA
–
ATPase6
9203–9886
684
7
H
ATG
TAA
–
COX3
9894–10677
784
0
H
ATG
T--
–
tRNAGly
10678–10746
69
0
H
–
–
TCC
ND3
10747–11097
351
1
H
ATG
TAA
tRNAArg
11099–11168
70
1
H
–
–
TCG
ND4L
11170–11466
297
-7
H
ATG
TAA
–
ND4
11460–12837
1378
0
H
ATG
TAT
–
tRNAHis
12838–12907
70
0
H
–
–
GTG
tRNASer(AGY)
12908–12973
66
-1
H
–
–
GCT
tRNALeu(CUN)
12973–13043
71
0
H
–
–
TAG
ND5
13044–14861
1818
8
H
ATG
AGA
–
CYTB
14870–16012
1143
5
H
ATG
TAA
–
tRNAThr
16018–16086
69
18
H
–
–
TGT
tRNAPro
16105–16174
70
6
L
–
–
TGG
ND6
16181–16699
519
-71
L
ATG
TAG
–
tRNAGlu
16701–16771
71
1
L
–
–
TTC
The length of the complete mitogenome of E.personata is 16,771 bp, and is similar to that of other Fringillidae species (Table 2). The base composition of the genome is C (32.1%), A (30.7%), T (23.0%) and G (14.2%); the proportion of A+T (53.7%) is higher than G+C (46.3%), suggesting a strong A+T bias. The mitogenomes of 17 Fringillidae species showed a positive AT-skew and a negative GC-skew.
Base composition (in percentages) of the mitochondrial genomes of 17 species of Fringillidae.
Species
Total length (bp)
T (%)
C (%)
A (%)
G (%)
A + T content (%)
AT-skew
GC-skew
Accession number
Eophonapersonata
16771
23.0
32.1
30.7
14.2
53.7
0.142
-0.386
KX812499
Eophonamigratoria
16798
22.9
32.3
30.7
14.0
53.7
0.145
-0.397
KX423959
Oreomystisbairdi
16833
23.7
31.6
30.3
14.4
53.9
0.123
-0.373
KM078807
Paroreomyzamontana
16832
23.5
31.5
30.8
14.2
54.4
0.134
-0.379
KM078771
Melamprosopsphaeosoma
16840
24.2
31.0
30.5
14.3
54.7
0.114
-0.370
NC_025617
Acanthisflammea
16820
24.0
31.4
30.5
14.2
54.5
0.120
-0.378
NC_027285
Loxopscoccineus
15589
24.2
31.9
30.1
13.8
54.3
0.108
-0.395
KM078785
Loxiacurvirostra
16805
23.8
31.4
30.6
14.3
54.3
0.125
-0.375
KM078800
Carduelisspinus
16828
24.0
31.3
30.9
13.8
54.9
0.127
-0.388
HQ915866
Chlorissinica
16813
24.7
30.5
30.7
14.1
55.4
0.108
-0.369
HQ915865
Serinuscanaria
16805
23.9
31.1
31.1
13.8
55.0
0.130
-0.384
KM078794
Haemorhouscassinii
16812
24.3
30.5
30.9
14.2
55.2
0.120
-0.364
KM078786
Coccothraustescoccothraustes
16823
23.9
31.0
30.9
14.3
54.8
0.127
-0.369
KM078789
Hemignathusparvus
16833
23.8
31.5
30.3
14.4
54.1
0.120
-0.371
KM078799
Fringillamontifringilla
16807
23.3
32.1
30.3
14.3
53.6
0.130
-0.382
JQ922259
Hesperiphonavespertina
16810
23.6
31.6
30.8
14.0
54.4
0.132
-0.387
KM078770
Crithagradorsostriata
16804
24.2
30.8
31.1
13.8
55.4
0.125
-0.382
KM078798
Sequence analysis of the 13 PCGs in the mitogenome of E.personata revealed that the base composition of the ND6 gene was not consistent with the other genes, and the percentage of T and G is much higher than in the other genes, with a positive GC skew (Table 3), whereas the base composition and skewness are highly similar for the other genes. The encoded genes share the common start codon ATN, with ATG most commonly observed. However, the start codon for COI is GTG. The non-coding regions include a control region (D-loop) and a few intergenic spacers. The control region is 1187 bp and is located between the tRNAGlu and tRNAPhe.
Base composition (in percentages) of the genes of Eophonapersonata.
Gene
Proportion of nucleotides
%A+T
AT skew
GC skew
%A+C
%G+T
T
C
A
G
ND1
25.3
33.3
27.3
14.1
52.6
0.039
-0.405
60.6
39.4
ND2
23.5
35.7
30.8
10.1
54.2
0.135
-0.559
66.4
33.6
COX1
23.3
32.7
27.5
16.5
50.8
0.081
-0.328
60.1
39.9
COX2
20.9
33.6
30.3
15.2
51.2
0.183
-0.377
63.9
36.1
ATP8
22.0
39.9
32.1
6.0
54.2
0.187
-0.740
72.0
28.0
ATP6
23.1
36.8
30.1
9.9
53.2
0.132
-0.575
67.0
33.0
COX3
24.0
33.3
27.6
15.2
51.5
0.069
-0.374
60.8
39.2
ND3
26.8
34.2
27.4
11.7
54.1
0.011
-0.491
61.5
38.5
ND4L
24.6
36.7
27.3
11.4
51.9
0.052
-0.524
64.0
36.0
ND4
23.1
35.6
30.5
10.9
53.6
0.138
-0.531
66.0
34.0
ND5
23.1
33.5
31.6
11.8
54.7
0.156
-0.480
65.1
34.9
CYTB
23.8
35.1
27.6
13.6
51.4
0.073
-0.442
62.6
37.4
ND6
38.9
9.6
10.4
41.0
49.3
-0.578
0.620
20.0
80.0
12S rRNA
20.0
27.7
31.4
20.9
51.4
0.222
-0.139
59.1
40.9
16S rRNA
21.4
24.2
34.7
19.7
56.1
0.236
-0.102
58.9
41.1
Total
23.6
31.9
29.3
15.2
52.9
0.108
-0.353
61.2
38.8
Based on the tRNA gene sequences identified, secondary structures of the tRNAs were determined (Fig. 2).
Predicted secondary structures for the 22 tRNAs in Eophonapersonata.
https://binary.pensoft.net/fig/476811Protein-coding genes and gene order
The 13 PCGs in the mitogenome of E.personata spans a length of 11,399 bp, and encode for six NADH dehydrogenase subunits, three cytochrome c oxidase subunits, two ATPases and cytochrome b. The light-strand has nine genes, which includes eight tRNA genes and ND6, and the heavy-strand has 28 genes, which includes 14 tRNA genes, two rRNA genes and 12 protein-coding genes. Relative synonymous codon usage (RSCU) values for the 13 PCGs are shown in Table 4. There are 3798 codons in the 13 PCGs, and codons of leucine, proline, isoleucine, and threonine take a higher proportion (Fig. 3). The codons AAA-lysine, GAA-glutamic acid, AAC-asparagine, UUC-phenylalanine, and AAU-asparagine are AT-rich, and the codons CUC-leucine, CCU-proline, GCC-alanine, and AGC-serine are GC-rich.
Relative synonymous codon usage (RSCU) values for the 13 protein-coding genes in Eophonapersonata.
Codon distribution in the mitochondrial genome of Eophonapersonata.
https://binary.pensoft.net/fig/476812
The gene order and arrangement of the region located between CYTB and tRNAPhe, is tRNAThr, tRNAPro, ND6, tRNAGlu, control region, and tRNAPhe, as shown in Fig. 4.
Phylogenetic relationships of the 17 Fringillidae species, inferred from Bayesian and Maximum Likelihood analyses, recovered almost identical well-resolved topologies (Fig. 5). Four major clades can be distinguished: clade 1 consisted of the genus Fringilla; clade 2 comprised three genera of grosbeaks (Coccothraustes, Eophona, Hesperiphona); clade 3 comprised of five genera (Acanthis, Loxia, Carduelis, Serinus, and Haemorhous); and clade 4 consisted of three genera of honeycreepers (Hemignathus, Loxops, and Paroreomyza). Clades 3 and 4 were inferred as sister-groups, which together were sister to clade 2. Clade 1 was sister to all other cardeline finches.
The analysis recovered C.coccothraustes and H.vespertina as sister groups to Eophona, with strong support in both Bayesian and ML analysis (Fig. 5).
The phylogenetic tree generated for 17 species of Fringillidae. The values indicated at the nodes are Bayesian posterior probabilities (left) and ML bootstrap proportions (right).
https://binary.pensoft.net/fig/476814
No evidence for chimerism was found in comparisons of the ND2, COX1, and CYTB fragments with reference sequences on GenBank. Thus, in all cases the mitogenome of E.personata clustered with, and was very similar to, reference sequences of this species (data not shown).
Discussion
In this study, we obtained the complete mitogenome sequence of E.personata, and performed molecular phylogenetic analysis of 17 Fringillidae species based on the sequences of 12 mitochondrial PCGs. Our results revealed that the complete mitogenome of E.personata is 16,771 bp, and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region. Analysis of the base composition revealed an A+T bias, a positive AT skew and a negative GC skew. Phylogenetic analysis demonstrated that Coccothraustes is the closest genus to Eophona and that E.personata is the sister taxon of E.migratoria.
Our analysis showed that the mitogenome of E.personata is similar to that of other Fringillidae species. The genome structure was that of a typical vertebrate mitochondrial genome (Boore 1999). The A+T bias observed in the mitochondrial genome of E.personata was similar to that of other vertebrates (Yang et al. 2016), and the positive AT-skew value and a negative GC-skew value observed, is also consistent with the vertebrate mitogenome (Quinn and Wilson 1993). The gene order and arrangement in E.personata was similar to the typical arrangement seen in birds (Mindell et al. 1999; Haddrath and Baker 2001; Liu et al. 2013), including Passeriformes (Caparroz et al. 2018). It is generally believed that the rearrangement of the mitochondrial genome represents a rare evolutionary event that can be used to construct the phylogenetic relationships of distantly related groups (Bensch 2000). In birds, two major types of gene order are found which differ by the number of control region copies (Singh et al. 2008). One of these is believed to be the ancestral gene order and the other is the remnant control region 2 gene order (Singh et al. 2008).
The phylogenetic relationships observed in this study are in accordance with previous research (Arnaiz-Villena et al. 2001; Zuccon et al. 2012). In the current study, the three grosbeak genera (Coccothraustes, Eophona, Hesperiphona; clade 2) clustered together and formed a well-defined clade. The grosbeak consists of a group of fairly large and stocky finches, feeding primarily on hard seeds. Our study corroborates a previous study based on the nuclear and mitochondrial sequences (Zuccon et al. 2012). A close phylogenetic relationship between the four genera (Coccothraustes, Mycerobas, Hesperiphona, Eophona) has been recognised previously (Vaurie 1959; Clement et al. 1993; Dickinson and Christidis 2015), and their close evolutionary relationships are widely accepted.
Our analysis showed that the genus Fringilla diverged very early within the family Fringillidae and was followed a deep divergence between the grosbeak clade and a clade formed by the other members Carduelinae. Our study as well as previous studies suggests that the analysis of phylogenetic relationships of passerines are more accurately resolved and better supported with complete mitogenomes than with short sequences of single genes (Van der Meij et al. 2005; Nguembock et al. 2009).
Conclusions
In this study, the complete mitogenome of E.personata was sequenced and analysed for the first time, and the phylogenetic analysis confirmed the taxonomic classification of E.personata. The results showed that the genera Coccothraustes and Hesperiphona have a close relationship with the genus Eophona, and this is consistent with the morphologicl similarity observed between them. Our analysis shows the phylogenetic relationship of E.personata as a sister group to E.migratoria, and the mitogenome was observed to be very similar between them.
Acknowledgements
This work was supported by the Special Fund for Forest Scientific Research in the Public Welfare (201404420) and the National Natural Science Fund of China (31872242, 31672313, 31372220), and we thank all the funders of this work. There are no competing financial interests to declare. We are grateful to Ilze Skujina and an anonymous referee for providing constructive criticism on a previous version of the manuscript.
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