Abstract
White-bellied Erpornis (Erpornis zantholeuca) is a group of birds in the order Passeriformes, but its taxonomic status remains controversial. To understand the phylogenetic position of E. zantholeuca and phylogenetic relations within this family, we sequenced the complete mitochondrial genome of E. zantholeuca, which was 16,902 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the whole genome was 30.10% A, 30.48% C, 15.14% G, and 24.28% T and showed an elevated AT content (54.38%). All genes were encoded on the H-strand, with the exceptions of 8 tRNAs (trnQ, trnA, trnN, trnC, trnY, trnS2(UCN), trnP, trnE) and 1 PCG (Mt-ND6). Most PCGs used standard ATN as start codons, and TAN as stop codons. All tRNAs were predicted to form the typical cloverleaf secondary structures. The gene order of E. zantholeuca was consistent with that of Gallus gallus, which was considered to be a plesiomorphic or typical avian gene order. Phylogenetic relationships based on bayesian inference and maximum likelihood methods showed that E. zantholeuca was well supported as the sister group of (Vireo altiloquus + Vireo olivaceus). In addition, Pteruthius melanotis was sister to the other members of Vireonidae.
References
1.
Anmarkrud
JA
, Lifjeld
JT
. Complete mitochondrial genomes of eleven extinct or possibly extinct bird species
. Mol Ecol Resour
. 2017
;17
(2
):334
–41
.2.
Bankevich
A
, Nurk
S
, Antipov
D
, Gurevich
AA
, Dvorkin
M
, Kulikov
AS
, . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
. J Comput Biol
. 2012
;19
(5
):455
–77
.3.
Barker
FK
. Mitogenomic data resolve basal relationships among passeriform and passeridan birds
. Mol Phylogenet Evol
. 2014
;79
:313
–24
.4.
Barker
FK
, Cibois
A
, Schikler
P
, Feinstein
J
, Cracraft
J
. Phylogeny and diversification of the largest avian radiation
. Proc Natl Acad Sci U S A
. 2004
;101
(30
):11040
–5
.5.
Bernt
M
, Donath
A
, Jühling
F
, Externbrink
F
, Florentz
C
, Fritzsch
G
, . MITOS: improved de novo metazoan mitochondrial genome annotation
. Mol Phylogenet Evol
. 2013
;69
(2
):313
–9
.6.
Boore
JL
. Animal mitochondrial genomes
. Nucleic Acids Res
. 1999
;27
(8
):1767
–80
.7.
Boore
JL
. Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii
. Mol Biol Evol
. 2001
;18
(7
):1413
–6
.8.
Broughton
RE
, Milam
JE
, Roe
BA
. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA
. Genome Res
. 2001
;11
:1958
–67
.9.
Cibois
A
, Kalyakin
MV
, Lian-Xian
H
, Pasquet
E
. Molecular phylogenetics of babblers (Timaliidae): revaluation of the genera Yuhina and Stachyris
. J Avian Biol
. 2002
;33
(4
):380
–90
.10.
Coil
D
, Jospin
G
, Darling
AE
. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
. Bioinformatics
. 2015
;31
(4
):587
–9
.11.
Desjardins
P
, Morais
R
. Sequence and gene organization of the chicken mitochondrial genome: a novel gene order in higher vertebrates
. J Mol Biol
. 1990
;212
(4
):599
–634
.12.
Dong
Y
, Li
B
, Zhou
L
. A new insight into the classification of dusky thrush complex: bearings on the phylogenetic relationships within the Turdidae
. Mitochondrial DNA A DNA Mapp Seq Anal
. 2018
;29
(8
):1245
–52
.13.
Gibb
GC
, Kardailsky
O
, Kimball
RT
, Braun
EL
, Penny
D
. Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations
. Mol Biol Evol
. 2007
;24
(1
):269
–80
.14.
Gibb
GC
, England
R
, Hartig
G
, McLenachan
PAT
, Taylor Smith
BL
, McComish
BJ
, . New Zealand passerines help clarify the diversification of major songbird lineages during the oligocene
. Genome Biol Evol
. 2015
;7
(11
):2983
–95
.15.
Guindon
S
, Gascuel
O
. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
. Syst Biol
. 2003
;52
(5
):696
–704
.16.
Gutell
RR
, Lee
JC
, Cannone
JJ
. The accuracy of ribosomal RNA comparative structure models
. Curr Opin Struct Biol
. 2002
;12
(3
):301
–10
.17.
Kennedy
JD
, Weir
JT
, Hooper
DM
, Tietze
DT
, Martens
J
, Price
TD
. Ecological limits on diversification of the Himalayan core Corvoidea
. Evolution
. 2012
;66
(8
):2599
–613
.18.
Krajewski
C
, Sipiorski
JT
, Anderson
FE
. Complete mitochondrial genome sequences and the phylogeny of cranes (Gruiformes: Gruidae)
. Auk
. 2010
;127
(2
):440
–52
.19.
Kumar
S
, Stecher
G
, Tamura
K
. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets
. Mol Biol Evol
. 2016
;33
(7
):1870
–4
.20.
Larkin
MA
, Blackshields
G
, Brown
NP
, Chenna
R
, McGettigan
PA
, McWilliam
H
, . ClustalW and ClustalX version 2.0
. Bioinformatics
. 2007
;23
(21
):2947
–8
.21.
Li
WJ
, Wang
ZQ
, Che
YL
. The complete mitogenome of the Wood-Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and its phylogenetic relationship among cockroach families
. Int J Mol Sci
. 2017
;18
(11
):2397
.22.
Lohse
M
, Drechsel
O
, Bock
R
. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes
. Curr Genet
. 2007
;52
(5-6
):267
–74
.23.
Lowe
TM
, Chan
PP
. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
. Nucleic Acids Res
. 2016
;44
:W54
–W57
.24.
Lu
HF
, Su
TJ
, Luo
AR
, Zhu
CD
, Wu
CS
. Characterization of the complete mitochondrion genome of diurnal moth Amata emma (Butler) (Lepidoptera: Erebidae) and its phylogenetic implications
. PLoS One
. 2013
;8
(9
):e72410
.25.
Master
RR
, Li
B
, Li
F
. The complete mitochondrial genome of Japanese marsh warbler, Locustella pryeri
. Mitochondrial DNA A DNA Mapp Seq Anal
. 2016
;27
(1
):373
–4
.26.
Milá
B
, Bruxaux
J
, Friis
G
, Sam
K
, Ashari
H
, Thébaud
C
. A new, undescribed species of Melanocharis berrypecker from western New Guinea and the evolutionary history of the family Melanocharitidae
. Ibis
. 2021
;163
(4
):1310
–29
.27.
Ojala
D
, Montoya
J
, Attardi
G
. tRNA punctuation model of RNA processing in human mitochondria
. Nature
. 1981
;290
(5806
):470
–4
.28.
Perna
NT
, Kocher
TD
. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes
. J Mol Evol
. 1995
;41
(3
):353
–8
.29.
Rambaut
A
, Drummond
AJ
. FigTree version 1
; 2012
. Available from http://tree.bio.ed.ac.uk/software/figtree30.
Reddy
S
, Cracraft
J
. Old world shrike-babblers (Pteruthius) belong with new world vireos (Vireonidae)
. Mol Phylogenet Evol
. 2007
;44
(3
):1352
–7
.31.
Ronquist
F
, Huelsenbeck
JP
. MrBayes 3: Bayesian phylogenetic inference under mixed models
. Bioinformatics
. 2003
;19
(12
):1572
–4
.32.
Ronquist
F
, Teslenko
M
, van der Mark
P
, Ayres
DL
, Darling
A
, Höhna
S
, . MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
. Syst Biol
. 2012
;61
(3
):539
–42
.33.
Sangster
G
, Cibois
A
, Reddy
S
. Pteruthiidae and Erpornithidae (Aves: corvides): two new family-group names for babbler-like outgroups of the vireos (Vireonidae)
. Bull Br Ornithol Club
. 2022
;142
(2
):241
–5
.34.
Santorum
JM
, Darriba
D
, Taboada
GL
, Posada
D
. Jmodeltest.org: selection of nucleotide substitution models on the cloud
. Bioinformatics
. 2014
;30
(9
):1310
–1
.35.
Shadel
GS
, Clayton
DA
. Mitochondrial DNA maintenance in vertebrates
. Annu Rev Biochem
. 1997
;66
:409
–35
.36.
Sheldon
FH
, Bledsoe
AH
. Avian molecular systematics, 1970s to 1990s
. Annu Rev Ecol Syst
. 1993
;24
(1
):243
–78
.37.
Sibley
CG
, Ahlquist
JE
. Phylogeny and Classification of Birds
. New Haven
: Yale University Press
; 1990
.38.
Spicer
GS
, Dunipace
L
. Molecular phylogeny of songbirds (Passeriformes) inferred from mitochondrial 16S ribosomal RNA gene sequences
. Mol Phylogenet Evol
. 2004
;30
(2
):325
–35
.39.
Stoneking
M
, Hedgecock
D
, Higuchi
RG
, Vigilant
L
, Erlich
HA
. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes
. Am J Hum Genet
. 1991
;48
(2
):370
–82
.40.
Sun
CH
, Liu
B
, Lu
CH
. Complete mitochondrial genome of the Siberian thrush, Geokichla sibirica sibirica (Aves, Turdidae)
. Mitochondrial DNA B
. 2019
;4
(1
):1150
–1
.41.
Taanman
JW
. The mitochondrial genome: structure, transcription, translation and replication
. Biochim Biophys Acta
. 1999
;1410
(2
):103
–23
.42.
Treplin
S
, Siegert
R
, Bleidorn
C
, Thompson
HS
, Fotso
R
, Tiedemann
R
. Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci
. Cladistics
. 2008
;24
(3
):328
–49
.43.
Wolstenholme
DR
. Animal mitochondrial DNA: structure and evolution
. Int Rev Cytol
. 1992
;141
:173
–216
.44.
Xiao
B
, Ma
F
, Sun
Y
, Li
QW
. Comparative analysis of complete mitochondrial DNA control region of four species of Strigiformes
. Yi Chuan Xue Bao
. 2006
;33
(11
):965
–74
.45.
Zhu
XY
, Xin
ZZ
, Wang
Y
, Zhang
HB
, Zhang
DZ
, Wang
ZF
, . The complete mitochondrial genome of Clostera anachoreta (Lepidoptera: Notodontidae) and phylogenetic implications for Noctuoidea species
. Genomics
. 2017
;109
(3-4
):221
–6
.46.
Zurita
P
, Dias
B
, Blackwood
N
. HBW-BirdLife Version 6.0 (2021). Available from http://datazone.birdlife.org© 2022 S. Karger AG, Basel
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