Complete mitochondrial genome of the Thai Red Junglefowl (Gallus gallus) and phylogenetic analysis

2018·0.2 MB·

by  Suwannapoom, Chatmongkon

ZOOLOGICAL RESEARCH
Complete mitochondrial genome of the Thai Red
Junglefowl (Gallus gallus) and phylogenetic analysis
DEAREDITOR, allvariantsthenoutput.UsingtheIntegrativeGenomicsViewer
(Thorvaldsdóttiretal.,2013),wecheckedthebamfileexported
byTorrentSuite5.0.2toconfirmthescoredvariants.
In this study, we sequenced the complete mitochondrial
Phylogenetic analysis was performed using complete
genome (mitogenome) of the Thai Red Junglefowl (RJF;
mtDNA sequences of all major haplogroups and
Gallus gallus) using the next-generation sequencing (NGS)
sub-haplogroups, as defined by Miao et al. (2013) and
platform of the Ion Torrent PGM. Samples were taken from
Pengetal.(2015).AllmitogenomeswerealignedbyClustalW,
Mae Wang District, Chiang Mai Province, northern Thailand.
thenanalyzedbymaximumparsimony(MP)inMEGA7.0with
Our data showed the complete mitogenome to be 16 785
1000bootstrapreplicates(Tamuraetal.,2011).
bp in length, composed by 13 protein-coding genes, 22
ThecompletemitogenomesequenceoftheThaiRJF(16785
tRNA genes, two rRNA genes, and one control region. The
bp; GSA accession No.: PRJCA000287, GenBank accession
genomenucleotidecompositionwas30.3%A,23.7%T,32.5%
No.: MG605671) had an overall base composition of 30.3%
C, and 13.5% G, resulting in a high percentage of A+T
for A, 23.7% for T, 32.5% for C, and 13.5% for G, with high
(50.4%). Phylogeneticanalysisrevealedthatthemitogenome
a A+T content of 54.0%. The mitogenome consisted of 13
belonged to haplogroup X, whereas those of all domestic
protein-coding genes, 22 tRNA genes, two rRNA genes, and
chickens belong to haplogroups A to G. This newly released
a displacement loop (D-loop). Most mitogenome genes were
mitogenome sequence will advance further evolutionary and
encodedontheheavystrand,exceptforeighttRNAgenesand
population genetics study of the RJF and domestic chicken.
one protein-coding gene (ND6), which were encoded on the
TheavailabilityoftheG.gallusmitogenomewillalsocontribute
light strand. Some protein-coding genes shared the start and
tofurtherconservationgeneticsresearchofauniquespecies,
stopcodons;forinstance,all13genesbeganwithATG,except
listedas‘datadeficient’inThailand.
for COX1, which started with GTG, and of the remaining 12
The Red Junglefowl (RJF; Gallus gallus) is a major wild
protein-coding genes, nine (ND1, COX2, ATPase8, ATPase6,
ancestor of the domestic chicken (Darwin, 1875; Liu et
ND3,ND4L,ND5,cytb,andND6)sharedthestopcodonTAA,
al., 2006; Miao et al., 2013). Early studies based on
two (COX3 and ND4) shard the stop codon “T– –”, and ND2
mitochondrial DNA (mtDNA) revealed that the Thai RJF has
usedTAG.Thelengthsofthe12SrRNAand16SrRNAgenes
acloserelationshipwiththedomesticchicken(Fumihitoetal.,
were976bpand1622bp,respectively.
1994; Fumihito et al., 1996), implying that Thailand is likely
As the RJF is a wild type of Gallus gallus, it differed
a domestication center of the chicken. To the best of our
from all major domestic haplogroups (A to G). We calculated
knowledge, no complete mtDNA genome (i.e., mitogenome)
the differences between the Thai RJF and randomly selected
sequenceoftheThaiRJFhasbeenreported.Inthisstudy,we
individualswithhaplogroupsAtoG(Table1). Comparedwith
collectedaRJFsamplefromtheMaeWangDistrictofChiang
the common domestic haplogroups, the RJF had 40 different
MaiProvinceinnorthernThailand(permissionprovidedbythe
basepairsonaverage(range:29–53).
Thai Institute of Animals for Scientific Purpose Development
(No. U1-01205-2558)). The complete mitochondrial genome
wassubmittedtoGenBank(accessionNo.:MG605671).
Genomic DNA was extracted from whole blood using Received:18September2017;Accepted:13February2018
the HiPure Tissue DNA Micro Kit (Magen, China). The Foundation items: This study was supported by the National Key
PCR amplification, library construction, and next-generation Research and Development Program (2016YFC1200705), Southeast
sequencing were in accordance with our earlier study (Chen Asia Biodiversity Research Institute, Chinese Academy of Sciences
et al., 2016). We used a de novo long fragment PCR
(Y4ZK111B01: 2015CASEABRI002), Ministry of Science and
and NGS strategy to obtain high quality mtDNA reads and
TechnologyofChina(2012FY110800),ChineseAcademyofSciences
excludeNTMTpseudogenes. Wefollowedcaveatsforquality
control in mtDNA genomic studies of domestic animals (Shi (KFZD-SW-208), and Yunnan Provincial Science and Technology
et al., 2014). The generated sequence was aligned against Department
areferencesequenceAP003321(Nishiborietal.,2005), with DOI:10.24272/j.issn.2095-8137.2017.028
SciencePress ZoologicalResearch39(2):127-129,2018 127
Table1Mitochondrialgenomedifferencesvs.ThaiRed replications using the MEGA 7 software package (Tamura et
Junglefowl(PRJA000287) al., 2013). The tree showed that the Thai RJF mitogenome
clusteredwithGU261692fromYunnan(Miaoetal.,2013)into
Haplogroup Sequence Differentbasenumber(n)
haplogroupX,asdefinedbyMiaoetal. (2013)andPengetal.
A GU261684 48 (2015).Tothebestofourknowledge,alldomesticchickensare
B GU261714 45 distributedinhaplogroupsAtoG.However,thearrangementof
C1 GU261679 53 theRJFwasidenticaltohaplogroupX,whichisonlyfoundin
wild chickens. In the MP tree, all haplogroups had very high
D GU261683 42
bootstrapvalues,alllargerthan90%. TherootoftheMPtree
E GU261712 29
wasinhaplogroupY,accordingtotheChickenReferenceTree
F GU261717 34
in dometree.org (Peng et al., 2015). Thus, our study strongly
G GU261676 31 supportedthepreviouslydefinedreferencetree.
Here, we assembled the first complete mitogenome of the
Thai RJF. This study will provide useful information for future
A phylogenetic tree (Figure 1) of all known Gallus gallus evolutionaryandpopulationgeneticsanalysesoftheRJFand
mitogenomeswasconstructedandtestedwith1000bootstrap domesticchicken.

Figure1Phylogenetictreeof41completemitochondrialgenomesofGallusgallusconstructedwithmax imumparsimony
Blackdotrepresentsthenewsampleinthisstudy.Bootstrapsupportvalues(>50)areshownatthenodes.

COMPETINGINTERESFiTgSure 1 Phylogenetic tree of 41 complete mitochondrial gCehnaomtmeos nogf kGoanllSusu gwaalnlunsa poom1,2,#,Ya-JiangWu3,#,
XingChen4,#,AdeniyiC.Adeola4,JingChen5,
Theauthorsdeclarethatthecyohnasvteruncotecdom wpietthin gmianxteirmesutsm. parsimony. Wen-ZhiWang4,5,6,*
AUTHORS’CONTRIBUBTlaIcOkN dSot represents the new sample in this study. Boo1tSstcrhaopo sluopfpAogrrt icvualltuueres (a>n5d0N) aatruer alResources,Universityof
Phayao,Phayao56000,Thailand
Theauthorsaloneareresposnhsoibwlenf oartt htheec onnotdenetsa. ndwritingofthispaper. 2SoutheastAsiaBiodiversityResearchInstitute(CAS-SEABRI),
128 www.zoores.ac.cn
ChineseAcademyofSciences,YezinNayPyiTaw05282, ofAmerica,93:6792–6795.
Myanmar LiuYP,WuGS,YaoYG,MiaoYW,LuikartG,BaigM,Beja-PereiraA,DingZL,
3StateKeyLaboratoryforConservationandUtilizationof PalanichamyMG,ZhangYP.2006.Multiplematernaloriginsofchickens:out
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650091,China MiaoYW,PengMS,WuGS,OuyangYN,YangZY,YuN,LiangJP,Pianchou
4StateKeyLaboratoryofGeneticResourcesandEvolution, G,Beja-PereiraA,MitraB,PalanichamyMG,BaigM,ChaudhuriTK,Shen
KunmingInstituteofZoology,ChineseAcademyofSciences, YY,KongQP,MurphyRW,YaoYG,ZhangYP.2013.Chickendomestication:
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#Authorscontributedequallytothiswork PengMS,FanL,ShiNN,NingT,YaoYG,MurphyRW,WangWZ,Zhang
*Correspondingauthor,E-mail:[email protected] YP.2015.DomeTree: acanonicaltoolkitformitochondrialDNAanalysesin
domesticatedanimals.MolecularEcologyResouces,15:1238–1242.
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