Complete Mitochondrial Genome of Crangon hakodatei (Rathbun, 1902) (Crustacea: Decapoda: Crangonidae)

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867 Copyright © 2016 The Korean Society of Fisheries and Aquatic Science pISSN:0374-8111, eISSN:2287-8815

서 론

현재까지자주새우속

(Fabricius, 1798)

에는

24

종이보고되 었으며이들은흔한저서성새우들로연안의저서생태계에가 장중요한구성요소중하나이다

(Hayashi and Kim, 1999).

자 주새우속에속하는새우들의형태학적특성은갑각의위쪽중 앙에 하나의위선

(gastric spine), 3

번째 악각

(maxilliped)

에 단하나의관절새

(arthrobranch),

첫번째흉지

(pereopod)

의장 절

(merus)

^에

1

^개의 ^복부^등뼈

(ventral spine)

^등을^들 ^수 ^있다

(Hayashi and Kim, 1999).

마루자주새우

[Crangon hakodatei (Rathbun, 1902)]

는발해만

,

황해

,

한국및일본연안을포함하

여북서태평양지역에서가장흔한종이며

,

조하대에서

200 m

깊이까지의대륙붕에서식하는것으로알려져있다

(Cha et al., 2001; Han and Li, 2015; Hayashi and Kim, 1999).

마루자주 새우는

3

^번째에서

5

^번째^복부절

(abdominal somites)

^까지^높고 무딘배중봉

(dorsomedial carina)

의존재에의해다른자주새우 류와분명히구분된다

(Han and Li, 2015; Maher et al., 2013).

C. hakodatei

는상업적으로중요한어류들의주요먹이원으로 서의역할뿐아니라소형생물의포식자로서도역할을하기때 문에경제적으로뿐아니라생태적으로도중요한종이다

(Han and Li, 2015).

따라서자주새우자원은효과적으로관리되어야

마루자주새우[ Crangon hakodatei (Rathbun, 1902)]의 전장 미토콘드리아 유전체에 대한 분석 연구

김경률

¹

·김현우

^1,2

*

1부경대학교 의생명기계전기융합공학협동과정, ²부경대학교 자원생물학과

Complete Mitochondrial Genome of Crangon hakodatei (Rathbun, 1902) (Crustacea: Decapoda: Crangonidae)

Gyungryul Kim

¹

and Hyun-Woo Kim

^1,2

*

1

Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan 48513, Korea

2

Department of Marine Biology, Pukyong National University, Busan 48513, Korea

Although shrimps belonging to family Crangonidae are known to be genetically divergent and ecologically impor- tant among the various benthos, any of their mitochondrial genome has not been reported yet. We here determined the complete mitochondrial genome sequence of Crangon hakodatei (Rathbun, 1902), which was collected from East China Sea (124°E and 34.5°N). Total mitochondrial genome length of C. hakodatei was 16,060 bp, in which 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs and a putative control region were encoded. Secondary structure pre- diction analysis showed that twenty tRNA genes exhibit the conserved structure but two genes, tRNA

^Cys

and tRNA

^Ser

(AGN), lack T and D arm, respectively. Based on the sequence similarity of the COI region from the currently reported five species belonging to genus Crangonidae, C. hakodatei was most closely related to Crangon crangon . Phylogenetic analysis of full COXI genes belonging to infraorder Caridea showed that only crangonid shrimps were clustered together with those of Dendrobranchiata. Gene order were well conserved from Penaeoidea to Caridea but tRNA

^Pro

and tRNA

^Thr

in Palaemonid shrimp were flipped each other by the recombination. Further study about mitochondrial genome sequences of shrimps belonging to Crangonidae should be made to know better about their evolutional relationships with other those in infraorder Caridea.

Key words: Crangonidae, Decapod crustacean, Barcode, Mitochondrial genome

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial Licens (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

http://dx.doi.org/10.5657/KFAS.2016.0867 Korean J Fish Aquat Sci 49(6) 867-874, December 2016 Received 8 December 2016; Accepted 19 December 2016

*Corresponding author: Tel: +82. 51. 629. 5926 Fax: +82. 51. 629. 5930

E-mail address: [email protected]

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하며이들에대한정확한유전정보를통한자원관리가필요 하다

.

일반적으로 미토콘드리아의

cytochrome oxidase subunit I (COXI)

유전자를 표적으로하는

COI

영역의

DNA

바코드가 종식별에가장널리사용되지만

(Folmer et al., 1994),

전장미 토콘드리아게놈정보는개체군과같은다양한유전자원학적 연구에더많은정보를제공한다

(Lang and Burger, 2007; Ma et al., 2015; Yamauchi et al., 2002).

전형적인

Sanger

의디데옥 시종결방법을

(Dideoxy termination reaction)

이용하여전체 미토콘드리아게놈

(~15 kb)

을시퀀싱하는데비용이많이드는 반면

,

^최근에^개발^된^차세대^{염기서열법}

(NGS)

^은^전통적인^시 퀀싱기술보다훨씬저렴한비용으로전장미토콘드리아게놈 서열을결정할수있게되었다

(Williams et al., 2014; Zhou et al., 2013).

결과적으로

, 2015

년까지

5,319

개이상의미토콘드 리아게놈정보가

GenBank (http://www.ncbi.nlm.nih.gov)

에 기탁되었고그수는기하급수적으로증가하고있다

.

^자주새우 속에속하는새우들은유전자변형이가장큰분류군으로알려 져있지만

(Matzen da Silva et al., 2011)

아직이들의전장미토 콘드리아게놈에관한보고는아직없으며

,

이로인해다른십 각류종과비교분석할수있는분자계통발생학적연구가지연 되고있다

.

^본^연구^연구에서^전형적인

PCR

^과^차세대^염기서 열분석법을조합하여

C. hakodatei

^의^전장^{미토콘드리아}^게놈 을결정하고다른생이하목새우의미토콘드리아게놈과그특 성을비교했다

.

재료 및 방법

샘플링 및 DNA 추출

마루자주새우 샘플은 국립수산과학원의 한국 해양수산 자 원조사의일환인동중국해정기조사에서

(124

에서

DNA

추출

lva

^{채집되었다}

.

^채집된^새우를

99%

^에탄올

(SK

^케미칼

,

^한국

)

에넣고분석할때까지

-20%

에서보관했다

.

냉동된조직에서

genomic DNA

를분리하기위해

Tissue Lyser II (QIAGEN)

로 균질화하였다

. genomic DNA

는

AccuPrep® Genomic DNA Extraction Kit (Bioneer,

한국

)

를사용하여꼬리근육에서추출 되었다

.

^정제^된^게놈

DNA

^를^{정량화하고}

-70℃

^에서^보관^하 였다

.

MiSeq 시스템을 이용한 전장 미토콘드리아 게놈 분석

전체미토콘드리아 게놈을포함하는 두개의큰

PCR

산물 에대한서열특이적프라이머를디자인하기위해

, COXI

유전 자와시토크롬

b (cyt b)

^의^{부분서열을}

PCR

^을^통하여^얻었다

. COXI

유전자에대해서는

LCO1490

및

HCO2198 (Folmer et al., 1994)

프라이머를사용하였고

cytb

유전자는

Crus-mt-F10

및

Crus-mt-R10

프라이머를이용하여얻어졌다

(Table 1).

실 험에사용된프라이머는

IDT SciTools

프로그램을이용하여

분석하였고

(http://eu.idtdna.com/analyzer/Applications/Oli-

goAnalyzer/)

디자인된프라이머들은상업적으로합성하였다

(Macrogen, Korea).

예상되는크기로증폭된

PCR

산물을

Gel Extraction Kit (Bioneer, Daejeon, Korea)

를사용하여정제하 고

pGEM-T Easy vector (Promega, Madison, WI)

로클로닝 하였다

.

^복제된^인서트를^보유^한^벡터를

DH5d

^로^{형질전환시} 키고

37℃

에서밤새배양하였다

. M13

정방향및역방향프라 이머를사용하여

PCR

하여

PCR

산물의클로닝유무를확인하 였다

(Table 1).

클로닝된

DNA

염기서열은양방향으로읽어서 결정하였다

.

큰단편

PCR

기술을사용하여

(Yamauchi et al., 2002) Crh-F2

^와

Crh-R2

^및

Crh-F4

^와

Crh-R4

^{프라이머들을} 이용하여두개의큰

PCR

산물을증폭시켰다

(Table 1). 2

개의

PCR

산물을함께모아서

Covaris M220 (Covaris Inc, Woburn, MA, USA)

에의해

600 bp

로단편화하였다

. TruSeq ® Sample Preparation V2, (Illumina, San Diego, USA)

를사용하여단편 화된서열을포함하는라이브러리를구축하였다

.

^구체적인^라 이브러리구축방법은제조업체의매뉴얼에따랐으며

PCR

농 축단계후

,

생성물을

2%

아가로스겔에로딩하여확인하였다

. 500 bp

내지

700 bp

의생성물을잘라내어

MiniElute PCR

정제 키트

(Qiagen, Hilden, Germany)

로정제하였다

.

마지막으로구 축된라이브러리는

MiSeq System

^에^의해

300×2

^개의^쌍방향 읽기를사용하여염기서열을결정하였다

.

염기서열 조합 및 생물정보학적 분석

MiSeq sequencer

에서 얻은 초기 결과 중에서

CLC Ge-

Table 1. The primer sequences used in the study

Name Sequences (5' →3') Crus-mt-F10 GCWATACAYTAYACDGC Crus-mt-R10 TTRTTDGGRATDGAHCG

Crh-F1 CGCCCGCTAAACTAGAAGCAGAG Crh-R1 CTCTGCTTCTAGTTTAGCGGGCG Crh-F2 CCTCCTCTCTCAGCAGGAATTGCTCAC Crh-R2 TAAAGAAGAATGAAGCGCCGTTGGC Crh-F3 CTTAGAAATGAGAGCGACGGGCG Crh-R3 AGTATGTACACATCGCCCGTCGC Crh-F41 CGAACTATTCATGCCAACGGCGC Crh-R4 AGCTCCTAGAATGGAAGATACACCAGC Crh-F5 GTTAGTATAACCGCGGATGCTGGCAC Crh-R5 CCTGCATTATGTTTTGGTGTAAAGGCACG Crh-F6 GCTTCATGGTTTACGGCTTGACTTGG Crh-F7 GCGACGGGCGATGTGTACATAC Crh-R7 CAGGCCGACTACCATGTTCCATCTC

M13-F GTAAAACGACGGCCAGT

M13-R GCGGATAACAATTTCACACAGG

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nomic Workbench v.8.0 (CLC Bio Aarhus,

^덴마크

)

^을^사용하 여

QV 20

이하의값과

2

개이상의불확실한뉴클레오타이드 를가진서열을전체결과로부터제거했다

. Mothur

소프트웨어

(v.1.36.1)

를사용하여

7 bp

이상의서열이중첩되고불일치하 는서열이없는결과만서로쌍을이루어하나의서열을만들어 내었다

. Geneious R8 (Biomatters, Auckland, New Zealand)

^을 이용하여최소

20 bp

의중첩서열및

100%

중첩동일성을갖 는짧은서열들끼리더큰서열로조립하였다

.

생물정보학적분 석을통해구축된

C. hakodatei

전체미토콘드리아게놈서열

은여러

PCR

산물의염기서열을재확인함으로써확인되었다

(Table 1). 13

^개의^단백질과

2

^개의

rRNA

^에^대한^유전자의^위치 는기존의다른갑각류에서미리연구된완전한

mtDNA

서열 의다른뉴클레오티드또는아미노산서열과의비교에의해결 정되었다

. 22

개의

tRNA

유전자는

tRNAscan-SE (Lowe and Ward, 1997)

와

ARWEN (Laslett and Canbäck, 2008)

을사용 하여확인하였다

. C. hakodatei

^{미토콘드리아}^게놈의^그래픽지 도는

Organellar Genome DRAW (Laslett and Canbäck, 2008)

를사용하여그려졌다

.

분자계통진화도는

Evolutionary Genet- ics Analysis (MEGA6, http://www.megasoftware.net)

프로그 램을이용하였고

Minimum Evolution

알고리즘을사용하여작 성되었다

.

결과 및 고찰

Crangon hakodatei의 전장 미토콘드리아 게놈

본연구에서는자주새우과에서는최초로

Crangon hakodatei

의전장미토콘드리아게놈을결정했다

. C. hakodatei

^의^전장^미 토콘드리아게놈은

16,060 bps (GenBank Accession Number, KU641481)

이며다른십각류와마찬가지로

13

개의단백질

, 22

개의

tRNA

및

2

개의

rRNA

를암호화하고있다

(Fig. 1, Table 2). 9

^개의^단백질^코딩^유전자

(atp6, atp8, cox1, cox2, cox3, cob, nad2, nad3

및

nad6)

가

H

가닥에위치하고있고나머지

4

개의단백질이

(nad1, nad4, nad4L

및

nad5) L

가닥에암호화 되어있다

(Table 2).

단백질을암호화하고있는유전자는

ACG

를사용하고있는

COI

를제외하고는

ATN

으로시작하였으며

Nad4

^와

Cytb

^{유전자에서는}^보존된^정지^코돈이^확인되지^않았 다

(Table 2). COXI

와

COXII

를제외하고

11

개의유전자가

7 bp

까지중첩되어있는것으로밝혀졌는데이런사실은이미알 려진여러미토콘드리아게놈에서흔하게발견되는공통적인 특성이다

(Cook, 2005; Yamauchi et al., 2003). C. hakodatei

^의 미토콘드리아게놈에서

LrRNA

^와

SrRNA

^유전자의^길이는^각 각

1297 bp

와

853 bp

였다

. LrRNA

유전자는

tRNA

^Leu와

tRNA-

Val유전자사이에끼어있는반면

, SrRNA

유전자는

tRNA

^Val유 전자와잠정적인고도가변조절영역

(control region)

사이에위 치한다

.

잠정적으로추정되는

C. hakodatei

^의^고도^가변^영역

은높은

A/T (85.1 %)

^{뉴클리오티드}^서열의^비율을^가지는^단 ^백질을^{암호화하고}^있지^않은

1,138 bp

의크기를가지고있었

다

. tRNA

유전자의크기는

63

에서

70

개의뉴클레오타이드로 Table 2. Location of genes in the mitochondrial genome of the Crangon hakodatei

Featrures

(anticodon) Start Stop Str. L_nt In./term. L_aa

COI 1 1535 + 1535 ACG/TA- 511

trnL1 (taa) 1536 1599 + 64

CO2 1602 2288 + 687 ATG/TAA 228

trnK (ttt) 2292 2359 + 68 trnD (gtc) 2360 2423 + 64

Atp8 2424 2582 + 159 ATC/TAG 52

Atp6 2576 3253 + 678 ATG/TAA 225

CO3 3257 4045 + 789 ATG/TAA 262

trnG (tcc) 4045 4107 + 63

Nad3 4108 4461 + 354 ATG/TAG 117

trnA (tgc) 4460 4524 + 65 trnR (tcg) 4526 4590 + 65 trnN (gtt) 4594 4658 + 65 trnS1 (tct) 4658 4726 + 69 trnE (ttc) 4726 4791 + 66 trnF (gaa) 4790 4853 - 64

Nad5 4853 6577 - 1725 ATG/TAA 574

trnH (gtg) 6578 6641 - 64

Nad4 6643 7971 - 1329 ATG/--- 343

Nad4L 7965 8264 - 300 ATG/TAA 99

trnT (tgt) 8267 8329 + 63 trnP (tgg) 8329 8396 - 68

Nad6 8398 8913 + 516 ATC/TAA 171

Cyt b 8913 10049 + 1137 ATG/--- 378 trnS2 (tga) 10048 10117 + 70

Nad1 10117 11076 - 960 ATA/TAA 319

trnL2 (tag) 11088 11152 - 65

rrnL 11153 12449 - 1297

trnV (tac) 12450 12515 - 66

rrnS 12516 13368 - 853

CR(non-coding) 13369 14506 + 1138 trnI (gat) 14507 14573 + 67 trnQ (ttg) 14683 14753 - 70 trnM (cat) 14761 14828 + 68

Nad2 14829 15830 + 1002 ATT/TAA 333 trnW (tca) 15828 15896 + 69

trnC (gca) 15909 15975 - 67 trnY (gta) 15989 16051 - 63

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다양하며두가닥모두에서미토콘드리아게놈전체에퍼져있 었다

(Table 2). 20

개의

tRNA

유전자는

tRNAscan-SE (Lowe and Eddy, 1997)

^와

ARWEN ARWEN (Laslett and Canback,

2008)

에의해전형적인클로버잎모양의

2

차구조로예측되었

다

. tRNA

^Ser

(AGN)

유전자에는후생동물의미토콘드리아게

놈에서흔히볼수있는

D arm

이결여된형태로예측되었으나

(Wolstenholme, 1992) T arm

이결여된

tRNA

^Cys의예측된

2

차 구조는

C. hakodatei

^의^{미토콘드리아}^게놈에서^{특이적으로}^확 인되었다

(Fig. 2).

모든사용된안티코돈은다른연갑강

(Mala-

costraca)

에속하는종들에서기술된것들과일치하였다

(Abas-

cal et al., 2006).

그러나유전자의배열은연갑강내에서보존 되지않고그전위현상들이동일한분류군내에서종종발생하 기때문에

(Abascal et al., 2006),

분석된

C. hakodatei

^미토콘 드리아게놈의유전자서열을생이하목및수상새아목내의미 토콘드리아게놈유전자배열들과비교하였다

(Fig. 3). World

Class of Marine Species (WoRMS; http://www.marinespe-

cies.org)

^에^따르면^현재^{생이하목내}

15

^개의^직접적인^하위^분 류군이알려져있으며이에해당하는

19

개의미토콘드리아게 Fig. 1. The Map of Crangon hakodatei mitochondrial genome. Genes encoded by the heavy strand were shown outside the circle, and encoded by the light strand were shown inside the circle respectively. The gray arrow indicate the direction of transcription for the two DNA strands. The inner circle denotes the GC content of this genome. The map of complete mitochondria genome was drawn using OGDRAW (Lohse et al., 2013).

(5)

놈을

GenBank

데이터베이스에서확보하여비교하였다

.

줄새 우속에속하는새우를제외하고는다른모든유전자배열은생 이하목에속하는미토콘드리아게놈상에서서잘보존되어있 었다

(Fig. 3).

대조적으로

,

줄새우속에속하는새우들의미토콘 드리아게놈상에서

tRNA

^Pro^와

tRNA

^Thr^이

^재조합에^의해서^서 로뒤집혀서다른종들과는구분되는독특한구조를가지고있 었다

(Fig. 3).

미토콘드리아 게놈을 통한 Crangon hakodatei의 분 자계통학적 분석

본연구로분석된

C. hakodatei

^의^{미토콘드리아}^게놈과^생이

하목에속하는

9

종의염기서열동일성은

70-73%

정도이며

,

자 주새우류와 밀접하게 관련이 없는 브레실리아상과에

(super-

family Bresilioidea)

속하는

Opaepele loihi

에가장높은동일 성을 보였다

.

그이유는아직자주새우류의전체미토콘드리 아게놈의서열이데이터베이스에확보되어있지않기때문이 다

.

하지만자주새우상과에해당하는새우종에서

COI

영역을

(Folmer et al., 1994)

비교하였을때

, C.hakodatei

^는

Crangon

crangon

과

94%

의서열동일성을보이면서가장가까운것으로 분석되었다

(Fig. 4A).

전체

COXI

유전자를데이터베이스에존 재하는생이하목에속한다른십각류와함께분자계통학적으로 분석한결과

, C. hakodatei

^는^다른^{생이하목에}^속하는^새우와^군 Fig. 2. Predicted secondary structure of 22 tRNAs of the Crangon hakodatei mitochondrial genome. The tRNAs are labeled with the three letters of abbreviations for each corresponding amino acids.

(6)

Fig. 3. Gene orders of mitochondrial genomes from Decapoda. All genes are transcribed from left to right except for those underlined to indicate opposite orientation. tRNA genes are designed by the corresponding single-letter amino acid code. Red colars indicate genes that are located differently from their positions in Crangon hakodatei mitochondrial genome.

Fig. 4. Phylogenetic trees of mitochondrial COXI genes (A) and COI regions (B) from shrimps belonging to Caridea with other decapod crustaceans. Molecular Evolutionary Genetics Analysis ver. 6.0 (MEGA6) program was used for constructing phylogenetic tree with the minimum evolution algorithm. The evolutionary distances were computed using the Kimura 2-parameter method

(A)

(B)

(7)

집을이루지않고수상새아목의새우와같은군집을형성했다

(Fig. 4B).

미토콘드리아와핵유전자를기반으로한십각류의 분자계통발생에관한많은연구에도불구하고

(Bracken et al., 2009; Lin et al., 2012; Shen et al., 2013; Shen et al., 2015)

생 이하목내의속간상관관계는아직뚜렷하게정리되지않았다

.

최근의연구에따르면생이하목새우는다른십각류에비해보 리새우상과

(Penaeoidea)

와진화적으로가장근연한것으로보 고되었다

(Liu and Cui, 2011).

결론적으로본연구에서는기존 의

PCR

방법과

NGS

방법의조합에의해

C. hakodatei

의완전 한미토콘드리아게놈을결정하고다른생이하목새우의서열 의특성을비교했다

.

^하지만^십각류의^{미토콘드리아}^게놈에^대 한연구는아직부족하여더많은유전정보가밝혀져야자주새 우의분자계통학적위치가명확해질것으로생각한다

.

사 사

이논문은부경대학교자율창의학술연구비

(2015

년

)

에 의하 여연구되었음

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