붉은발말똥게 (Sesarma intermedium)

그림입니다. 원본 그림의 이름: 20191126_004846.png 원본 그림의 크기: 가로 934pixel, 세로 721pixel

▣ 국명: 붉은발말똥게

▣ 학명: Sesarma intermedium

▣ 지정번호: 멸종위기야생동물 Ⅱ급

 ▣ 계통: 십각 목, Sesarmidae 과

1) 채집정보

- 채집허가: 2014.07.10 / 5마리

- 채 집 자: 신라대학교 고현숙



2) 채집현황 및 샘플처리

붉은발말똥게 채집현황

샘플처리

채집일

개체 수

DNAseq

RNAseq

표본

2014.09.29

5 EA

3 EA

2 EA

-


3) QC Data

샘플종

DNA QC

RNA QC

Result

Concentration (ug/ul)

Total Conc. (ug)

Concentration (ug/ul)

RIN (>7)

붉은발말똥게

108.4

20

353

6.3

pass


4) 기존 NCBI Taxonomy 유전정보 현황

유전정보 종류

Sesarma 속 유전자원

Sesarma intermedium 유전자원 

Nucleotide

716

-

Protein

161

-

Genome

1

-

Gene

37

-

 

5) Sequencing 분석 결과

 - Illumina DNA Sequncing 결과

Input information

　

　

　

Region1

Region2

Total

raw data

Number Of Reads

 

 

189,843,243

189,843,243

379,686,486

Number Of Bases

 

 

23,920,248,618

23,920,248,618

47,840,497,236

error correction

Number Of Reads

 

 

168,664,439

165,363,821

334,028,260

Number Of Bases

 

 

18,538,231,785

18,135,415,500

36,673,647,285

pair reads

Number Of Reads

 

 

 

 

308,096,906

Number Of Bases

 

 

 

 

34,351,794,449

single reads

Number Of Reads

 

 

 

 

25,931,354

Number Of Bases

 

 

 

 

2,321,852,836

Assembly Results

Scaffold Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Scaffolds

3,203,608

3,203,608

318,015

72,201

10,641

Number Of Bases

843,259,159

843,259,159

276,146,740

110,831,892

29,880,453

Avg. Scaffold Size

263

263

868

1,535

2,808

N50 Scaffold Size

321

321

864

1,484

2,683

N80 Scaffold Size

157

157

607

1,146

2,202

N90 Scaffold Size

126

126

549

1,069

2,093

largest Scaffold Size

259,778

259,778

259,778

259,778

259,778

Contig Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Contigs

42,215,912

4,464,853

147,548

17,176

1,266

Number Of Bases

3,021,343,702

892,697,805

107,928,053

23,583,775

3,519,700

Avg. Contig Size

71

199

731

1,373

2,780

N50 Contig Size

65

205

700

1,301

2,501

N80 Contig Size

48

139

559

1,090

2,153

N90 Contig Size

46

116

527

1,041

2,072

Largest Contig Size

45,085

45,085

45,085

45,085

45,085

 - Illumina RNA Sequncing 결과

Input information

　

　

　

Region1

Region2

Total

raw data

Number Of Reads

 

 

148,607,137

148,607,137

297,214,274

Number Of Bases

 

 

18,724,499,262

18,724,499,262

37,448,998,524

error correction

Number Of Reads

 

 

144,869,389

143,377,719

289,738,778

Number Of Bases

 

 

17,651,509,949

17,423,679,549

35,075,189,498

pair reads

Number Of Reads

 

 

 

 

284,329,580

Number Of Bases

 

 

 

 

34,683,772,704

single reads

Number Of Reads

 

 

 

 

3,917,528

Number Of Bases

 

 

 

 

391,416,794

Assembly Results

Scaffold Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Scaffolds

429,442

429,442

37,082

11,095

2,764

Number Of Bases

108,908,082

108,908,082

37,496,303

19,934,251

8,708,719

Avg. Scaffold Size

253

253

1,011

1,796

3,150

N50 Scaffold Size

302

302

1,060

1,815

3,094

N80 Scaffold Size

145

145

648

1,232

2,333

N90 Scaffold Size

119

119

566

1,106

2,157

largest Scaffold Size

15,520

15,520

15,520

15,520

15,520

Contig Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Contigs

6,071,178

559,812

25,602

6,322

1,109

Number Of Bases

449,202,856

113,481,169

22,996,315

10,066,265

3,115,851

Avg. Contig Size

73

202

898

1,592

2,809

N50 Contig Size

74

202

904

1,570

2,710

N80 Contig Size

49

130

612

1,172

2,207

N90 Contig Size

46

113

551

1,078

2,086

Largest Contig Size

11,458

11,458

11,458

11,458

11,458

 

(1) 고품질 genomic DNA 채취 및 표본확보

 

검수용  샘플 DNA 농도 및 총 양, 확증표본 현황표

　Sample명

농도(ng/ul)

Volume(ul)

DNA 총량(ug)

O.D A260/280

확증표본

채집허가일

채집일

붉은발말똥게

211

996

210

2.16

X

2014.7.10

2014.9.29


(2) 유전체 서열확보 : 현재 20종 확보

Sample

구분

raw data size

trim data size

비고

붉은발말똥게

DNA

47,840,497,236 

36,673,647,285 

　

RNA

37,448,998,524 

35,075,189,498 

　


(3) 기타분석

A. Genome Size estimation

샘 플 명

Kmer size

Kmer total

Pk depth

Genome_size

Coverage(X)

붉은발말똥게

23

29,615,545,908

202

146,611,613 

258.974

B. 반복서열


- 시퀀싱이 완료된 붉은발말똥게 DNA 및 RNA의 contigs 중 1kb 이상의 contigs의 반복서열을 탐색(Left; Repeat masking results of DNA contigs, Right; Repeat masking results of RNA contigs).

sequences: 17,176

 

sequences: 6,322

total length: 23,583,775 bp (23,583,775 bp excl N/X-runs)

 

total length: 10,066,265 bp (10,066,265 bp excl N/X-runs)

GC level: 39.60%

 

GC level: 48.04%

bases masked: 87,632 bp (0.37%)

 

bases masked: 15,587 bp (0.15%)

 

number of

elements

length

occupied

percentage

of sequence

 

 

number of

elements

length

occupied

percentage

of sequence

SINEs:          

5

302 bp

0.00%

 

SINEs:          

1

47 bp

0.00%

 

ALUs      

0

0 bp

0.00%

 

 

ALUs      

0

0 bp

0.00%

 

MIRs      

5

302 bp

0.00%

 

 

MIRs      

1

47 bp

0.00%

LINEs:          

218

38,074 bp

0.16%

 

LINEs:          

34

4,266 bp

0.04%

 

LINE1     

6

272 bp

0.00%

 

 

LINE1     

3

130 bp

0.00%

 

LINE2     

5

363 bp

0.00%

 

 

LINE2     

7

425 bp

0.00%

 

L3/CR1    

186

31,756 bp

0.13%

 

 

L3/CR1    

18

2,425 bp

0.02%

LTR elements:   

13

1,559 bp

0.01%

 

LTR elements:   

8

1,758 bp

0.02%

 

ERVL      

2

147 bp

0.00%

 

 

ERVL      

0

0 bp

0.00%

 

ERVL-MaLRs

1

67 bp

0.00%

 

 

ERVL-MaLRs

0

0 bp

0.00%

 

ERV_classI 

7

565 bp

0.00%

 

 

ERV_classI 

4

226 bp

0.00%

 

ERV_classII

0

0 bp

0.00%

 

 

ERV_classII

0

0 bp

0.00%

DNA elements:   

257

41,922 bp

0.18%

 

DNA elements:   

46

7,968 bp

0.08%

 

hAT-Charlie 

89

19,292 bp

0.08%

 

 

hAT-Charlie 

10

2,972 bp

0.03%

 

TcMar-Tigger

101

12,506 bp

0.05%

 

 

TcMar-Tigger

22

3,080 bp

0.03%

Unclassified:   

0

0 bp

0.00%

 

Unclassified:   

0

0 bp

0.00%

Total interspersed repeats:

 

81,857 bp

0.35%

 

Total interspersed repeats:

 

14,039 bp

0.14%

Small RNA:

109

5,775 bp

0.02%

 

Small RNA:

18

1,548 bp

0.02%

Satellites:

0

0 bp

0.00%

 

Satellites:

0

0 bp

0.00%

Simple repeats:

0

0 bp

0.00%

 

Simple repeats:

0

0 bp

0.00%

Low complexity:

0

0 bp

0.00%

 

Low complexity:

0

0 bp

0.00%



D. Mito-genome Map


그림입니다. 원본 그림의 이름: 슬라이드5.JPG 원본 그림의 크기: 가로 960pixel, 세로 720pixel

(4) Microsatellite 후보군

A. SSR statistics

Motif(-mer)

2

3

4

5

6

7

8

9

10

Total

붉은발말똥개

3,778

1,699

330

34

-

1

-

-

-

5,842


B. 바코드서열

>붉은발말똥게(Sesarma intermedium)

CCTGCAGGATTAAAGAAGGATGTATTTAAATTACGATCAATTAAAAGTATGGAAATAGGA

CCAGCTAAAACTGGAAGAGATAACAGTAATCAAATAGCATAAATAAATACTGATCATACA

AATAAAGGTATTTGATGTATAGTTATACCATAAGATCGTATTTTAATTACTGTTGTTATA

AAATTTATTGCTCCTCAAATAGATGAAACACCAGCTAGATGTCAAGAAAAAAATCCTAAA

TCTACAGAGGCCCCTGCATGAGCAATAGCAGCCGCTAAAGGAGGATACACAGTTCATCCT

GTTCCAACACCTCTTTCAACTATGCTTCTTGTTAATAATAATGATAAAGAAGGAGGTAGC

AATCAAAATCTTATATTATTTATACGTGGAAATGCCATATCTGGAGCTCCTAGTATTAAG

GGAACTAATCAATTGCCAAACCCTCCAATTATAATAGGAATAACTATAAAAAAAAATTAT

TACAAATGCATGGGCTGTTACAATTACATTATAAATTTGATCATTACCAATTAATCTTCC

TGGTTCATTTAATTCTGCTCGAATAATTAATCTTAATGATATACCTACTATTCCTGCTCA

AGCCAAAAAAACAAATATAAAGTGCCAATATCTTT


Neosarmatium fourmanoiri : family 까지 같음

chiromantes haematocheir : family 까지 같음


그림입니다.