귀이빨대칭이 (Cristaria plicata)

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▣ 국    명: 귀이빨대칭이

▣ 학    명: Cristaria plicata

▣ 지정번호: 멸종위기야생동물 Ⅰ급

▣ 계    통: 석패 목, 석패 과

  

1) 채집정보

- 채집허가: 2014.07.01 / 2마리

- 채 집 자: 강원대학교 이준상


2) 채집현황 및 샘플처리

귀이빨대칭이 채집현황

샘플처리

채집일

개체 수

DNAseq

RNAseq

표본

2014.10.25

2 EA

1 EA (발)

1 EA (내장)

1 EA


3) QC Data

샘플종

DNA QC

RNA QC

Result

Concentration (ug/ul)

Total Conc. (ug)

Concentration (ug/ul)

RIN (>7)

귀이빨

대칭이

84.1

17

349

7.4

pass


4) 기존 NCBI Taxonomy 유전정보 현황

유전정보 종류

Cristaria 속 유전자원

Cristaria plicata 유전자원 

Nucleotide

205

194

Protein

160

159

Genome

1

1

Gene

13

13


5) Sequencing 분석 결과

- Illumina DNA Sequncing 결과

Input information

　

　

　

Region1

Region2

Total

raw data

Number Of Reads

 

 

147,474,719 

147,474,719

294,949,438

Number Of Bases

 

 

18,581,814,594 

18,581,814,594

37,163,629,188

error correction

Number Of Reads

 

 

145,087,202 

142,393,434

287,480,636

Number Of Bases

 

 

16,980,344,416 

16,294,617,173 

33,274,961,589

pair reads

Number Of Reads

 

 

 

 

280,966,602

Number Of Bases

 

 

 

 

32,568,619,699

single reads

Number Of Reads

 

 

 

 

6,514,034 

Number Of Bases

 

 

 

 

706,341,890

Assembly Results

Scaffold Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Scaffolds

2,399,836

2,399,836

703,393

336,419

94,446

Number Of Bases

1,210,656,925

1,210,656,925

866,077,170

605,162,126

269,474,391

Avg. Scaffold Size

504

504

1,231

1,798

2,853

N50 Scaffold Size

999

999

1,429

1,861

2,793

N80 Scaffold Size

333

333

817

1,288

2,260

N90 Scaffold Size

175

175

653

1,137

2,122

largest Scaffold Size

13,098

13,098

13,098

13,098

13,098

Contig Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Contigs

19,767,574

4,196,594

598,163

175,313

20,811

Number Of Bases

2,183,645,096

1,285,251,032

550,888,568

256,864,390

52,553,165

Avg. Contig Size

110

306

920

1,465

2,525

N50 Contig Size

157

397

955

1,436

2,444

N80 Contig Size

53

179

653

1,141

2,139

N90 Contig Size

47

139

572

1,066

2,065

Largest Contig Size

11,456

11,456

11,456

11,456

11,456

 

- Illumina RNA Sequncing 결과

Input information

　

　

　

Region1

Region2

Total

raw data

Number Of Reads

 

 

143,076,292 

143,076,292

286,152,584

Number Of Bases

 

 

18,027,612,792 

18,027,612,792

36,055,225,584

error correction

Number Of Reads

 

 

140,951,928 

139,872,121

280,824,049

Number Of Bases

 

 

17,362,946,805 

17,221,984,593 

34,584,931,398

pair reads

Number Of Reads

 

 

 

 

278,287,810

Number Of Bases

 

 

 

 

34,323,357,010

single reads

Number Of Reads

 

 

 

 

2,536,239 

Number Of Bases

 

 

 

 

261,574,388

Assembly Results

Scaffold Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Scaffolds

248,154

248,154

56,916

27,544

10,956

Number Of Bases

122,240,873

122,240,873

82,066,573

61,580,866

38,432,323

Avg. Scaffold Size

492

492

1,441

2,235

3,507

N50 Scaffold Size

1,014

1,014

1,854

2,485

3,588

N80 Scaffold Size

276

276

877

1,458

2,488

N90 Scaffold Size

171

171

666

1,213

2,230

largest Scaffold Size

26,930

26,930

26,930

26,930

26,930

Contig Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Contigs

2,484,327

364,285

56,402

22,173

6,234

Number Of Bases

262,366,772

126,715,567

64,270,057

40,620,088

18,731,695

Avg. Contig Size

105

347

1,139

1,831

3,004

N50 Contig Size

91

513

1,292

1,895

2,934

N80 Contig Size

57

189

726

1,277

2,301

N90 Contig Size

47

146

601

1,131

2,144

Largest Contig Size

15,737

15,737

15,737

15,737

15,737

 

(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

귀이빨대칭이

602

996

599

2.08

○

2014.7.1

2014.10.25


(2) 유전체 서열확보 : 현재 20종 확보

Sample

구분

raw data size

trim data size

비고

귀이빨대칭이

DNA

37,163,629,188 

33,274,961,589 

　

RNA

36,055,225,584 

34,584,931,398 

　


(3) 기타분석

A. Genome Size estimation

샘 플 명

Kmer size

Kmer total

Pk depth

Genome_size

Coverage(X)

귀이빨대칭이

23

23,006,056,164

7

3,286,579,452 

8.97436

B. 반복서열


- 시퀀싱이 완료된 귀이빨대칭이 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: 175,313

 

sequences: 22,173

total length: 256,864,390 bp (256,864,390 bp excl N/X-runs)

 

total length: 40,620,088bp (40,620,088 bp excl N/X-runs)

GC level: 34.58%

 

GC level: 37.09%

bases masked: 1,027,933 bp (0.40%)

 

bases masked: 61,437 bp (0.15%)

 

number of

elements

length

occupied

percentage

of sequence

 

 

number of

elements

length

occupied

percentage

of sequence

SINEs:          

213

12,085

0.00%

 

SINEs:          

26

1,587 bp

0.00%

 

ALUs      

0

0

0.00%

 

 

ALUs      

0

0 bp

0.00%

 

MIRs      

76

4,930

0.00%

 

 

MIRs      

10

681 bp

0.00%

LINEs:          

3,402

878,128

0.34%

 

LINEs:          

158

38,248 bp

0.09%

 

LINE1     

81

5,526

0.00%

 

 

LINE1     

12

761 bp

0.00%

 

LINE2     

483

49,882

0.02%

 

 

LINE2     

19

1,962 bp

0.00%

 

L3/CR1    

148

10,775

0.00%

 

 

L3/CR1    

12

1,086 bp

0.00%

LTR elements:   

136

16,225

0.01%

 

LTR elements:   

25

2,373 bp

0.01%

 

ERVL      

7

433

0.00%

 

 

ERVL      

2

112 bp

0.00%

 

ERVL-MaLRs

3

133

0.00%

 

 

ERVL-MaLRs

1

64 bp

0.00%

 

ERV_classI 

103

11,930

0.00%

 

 

ERV_classI 

15

986 bp

0.00%

 

ERV_classII

7

435

0.00%

 

 

ERV_classII

4

327 bp

0.00%

DNA elements:   

1,007

86,630

0.03%

 

DNA elements:   

138

14,663 bp

0.04%

 

hAT-Charlie 

204

25,063

0.01%

 

 

hAT-Charlie 

37

5,773 bp

0.01%

 

TcMar-Tigger

192

19,924

0.01%

 

 

TcMar-Tigger

32

4,005 bp

0.01%

Unclassified:   

11

616

0.00%

 

Unclassified:   

2

128 bp

0.00%

Total interspersed repeats:

 

993,684

0.39%

 

Total interspersed repeats:

 

56,999 bp

0.14%

Small RNA:

635

37,708

0.01%

 

Small RNA:

50

4,603 bp

0.01%

Satellites:

10

1,311

0.00%

 

Satellites:

1

167 bp

0.00%

Simple repeats:

0

0

0.00%

 

Simple repeats:

0

0 bp

0.00%

Low complexity:

0

0

0.00%

 

Low complexity:

0

0 bp

0.00%




D. Mito-genome Map


그림입니다. 원본 그림의 이름: 슬라이드7.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

귀이빨대칭이

27,882

7,001

5,073

140

6

-

-

1

1

40,104


B. 바코드서열

>귀이빨대칭이(Cristaria plicata)

CCGGTCTTAACTCAGCTCGTGTAAGGGTATAATAGTCGAACAGACTATCCTGTCATAGCG

GTTGCACTAATGTGGATATCCTTAAGCCAACATCGAGGTCGCAAACCCAACTTTCGATAT

GTACTCTTGAGTTGGATTACGCTGTTATCCCCGGGGTAGCTTCTTTTTGGTCCTTAGTAA

GTTTTAGATGTGATTTCTAAAGAATCGGAAGCTTTGATGATTCCGAGATTGCCCCAATCA

AACCTTAAGCACTTTTAAGTGTGTAAACAGAAGCGCGAGAAGAGGTAAAGCTCCGCGGGG

TCTTTTCGTCTTCCTTTGTTATCTAAGTCTTTTCACTTAAACGAAAAGTTTTTTTGACAC

CACAAAGTAAAGGTGTTCCTAGTCTTGCCATTCACTGGCCTCCAATTAAAAGGCTAATTA

TTACGCTACCTTAGCACGCTCACGCTAACGCGGCCGTTTAAAGTTTCACTGGGCAGGCAT

TATCTTTTATCAGAGACTTCAAAAGACGATGTTTTTGGTAAACAGGC



그림입니다.