µÎÁ¡¹ÚÀ̻罿¹ú·¹ Prosopocoilus blanchardi (Parry,1873)

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¢Ã ÇР   ¸í : Prosopocoilus blanchardi Parry,1873

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¡Ý ºÐ Æ÷ : Çѱ¹(Á¦ÁÖµµ), ¸ù°ñ, ŸÀÌ¿Ï, ³×ÆÈ, Áß±¹ µîÁö¿¡ ºÐÆ÷ÇÑ´Ù.


¨ç äÁýÁ¤º¸

- ä¡¡Áý¡¡ÀÚ : ºû°íÀ»»ýÅ¿¬±¸¼Ò Á¤Çåõ

- äÁýÁö¿ª : Á¦ÁÖÆ¯º°ÀÚÄ¡µµ ¼­±ÍÆ÷½Ã

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µÎÁ¡¹ÚÀ̻罿¹ú·¹ ¼­½ÄÁö ¹× Æ÷ȹÀå¼Ò ȯ°æ

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µÎÁ¡¹ÚÀ̻罿¹ú·¹ äÁýÇöȲ

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äÁýÀÏ

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DNAseq

RNAseq

Ç¥º»

2017.07.20

2 EA

1 EA

1 EA

¤Ñ


¨é NCBI Taxonomy À¯ÀüÁ¤º¸ ÇöȲ

À¯ÀüÁ¤º¸ Á¾·ù

Genus Prosopocoilus À¯ÀüÀÚ¿ø

Prosopocoilus blanchardi À¯ÀüÀÚ¿ø

Nucleotide

82

22

Protein

94

21

Genome

2

-

Gene

74

-


¨ê Sequencing °á°ú

Type

Total Reads

Total Bases

Total Bases (Gb)

GC Rate

ºñ°í

DNA

199,733,134 

30,159,703,234

30.1

34.5 

 

RNA

52,742,576 

7,615,641,533 

7.6

40.6 

 

 

- Illumina DNA Sequencing °á°ú

SOAP de novo

Pb_DNA hiseq

Input information

¡¡

 

¡¡

Region1

Region2

Total

raw data

Number Of Reads

 

 

101,597,184 

101,597,184 

203,194,368 

Number Of Bases

 

 

15,341,174,784 

15,341,174,784 

30,682,349,568 

error correction

Number Of Reads

 

 

101,232,007 

99,239,971 

200,471,978 

Number Of Bases

 

 

15,079,060,037 

14,311,680,780 

29,390,740,817 

pair reads

Number Of Reads

 

 

 

198,290,468 

198,290,468 

Number Of Bases

 

 

 

29,087,376,322 

29,087,376,322 

single reads

Number Of Reads

 

 

 

2,181,510 

2,181,510 

Number Of Bases

 

 

 

303,364,495 

303,364,495 

Assembly Results

Scaffold Metrics

> 100 bp

> 500 bp

> 1000 bp

> 2000 bp

Number Of Scaffold

 

501,865 

129,793 

85,553 

54,578 

Number Of Bases

 

464,763,262 

397,202,039 

366,052,470 

322,082,424 

Avg. Scaffold Size

¡¡

926 

3,060 

4,278 

5,901 

N50 Scaffold Size

¡¡

4,603 

5,801 

6,410 

7,362 

N80 Scaffold Size

¡¡

891 

2,111 

2,779 

3,791 

N90 Scaffold Size

¡¡

282 

1,171 

1,815 

2,863 

Largest Scaffold Size

¡¡

64,281 

64,281 

64,281 

64,281 

Contigs

> 0 bp

> 100 bp

> 500 bp

> 1000 bp

> 2000 bp

Number Of Contigs

11,999,088 

1,332,213 

168,391 

76,687 

22,343 

Number Of Bases

902,643,158 

409,580,444 

205,675,195 

141,488,989 

65,824,918 

Avg. Contig Size

75 

307 

1,221 

1,845 

2,946 

N50 Contig Size

83 

505 

1,438 

1,910 

2,854 

N80 Contig Size

38 

156 

791 

1,306 

2,273 

N90 Contig Size

35 

122 

633 

1,143 

2,132 

largest Contig Size

19,553 

19,553 

19,553 

19,553 

19,553 

 

- Illumina RNA Sequencing °á°ú

Total number of raw reads

- Number of sequences

59,658,056

- Number of bases

8,368,892,629

Contig information

- Total number of contig

167,098

- Number of bases

178,420,127

- Mean length of contig (bp)

1,067.8

- N50 length of contig (bp)

2,097

- GC % of contig

40.80

- Largest contig (bp)

27,439

- No. of large contigs (¡Ã500bp)

81,280

Transdecoder information

- Total number of contig

103,523

- Number of bases

211,950,910

- Mean length of contig (bp)

2,047.4

- N50 length of contig (bp)

3,218

- GC % of contig

42.60

- Largest contig (bp)

27,439

- No. of large contigs (¡Ã500bp)

82,287

Unigene information

- Total number of unigenes

26,991

- Number of bases

65,644,094

- Mean length of unigene (bp)

2,432.1

- N50 length of unigene (bp)

3,358

- GC % of unigene

42.36

- Length ranges (bp)

224 – 30,454

 

2) ÇöÀç »óȲ¿¡ ´ëÇÑ °íÂû

°¡) ´ë»óÁ¾ ¹× ½Ã·áÈ®º¸ »óȲ

(1) Ãʱ⠿¹ºñÁ¾À» Æ÷ÇÔÇÑ Ã¤Áý ´ë»óÁ¾ : 23Á¾(ÀýÁöµ¿¹°(°ïÃæ) 9Á¾, ¿¬Ã¼µ¿¹° 8Á¾, ¾ç¼­·ù 6Á¾)

(2) äÁý ¿Ï·á Á¾ : 9Á¾(ÀýÁöµ¿¹°(°ïÃæ) 5Á¾, ¿¬Ã¼µ¿¹° 1Á¾, ¾ç¼­·ù 3Á¾)


³ª) ¸êÁ¾À§±âµ¿¹°ÀÇ Genome survey

(1) Library QC data

 - DNA Library QC

Delivery name

Tape

Concentration 

 (ng/ul)

Volume

(ul)

Tape Quantity

(ug)

Main peak Size

(bp)

Result

µÎÁ¡¹ÚÀ̻罿¹ú·¹

80.559

23

1.853

470

pass

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- RNA  Library QC

Delivery name

Tape

Concentration 

 (ng/ul)

Volume

(ul)

Tape Quantity

(ug)

Main peak Size

(bp)

Result

µÎÁ¡¹ÚÀ̻罿¹ú·¹

377.058

30

11.312

280

pass


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(2) °íǰÁú genomic DNA äÃë ¹× Ç¥º»È®º¸

- °Ë¼ö¿ë DNA´Â ´ëºÎºÐ ¸¸Á·ÇÏ¿´°í, ¸êÁ¾À§±âÁ¾ÀÎ ´ë»óÁ¾µéÀº äÁý·®ÀÇ Á¦ÇÑÀ¸·Î ÀÎÇØ È®ÁõÇ¥º»À¸·Î Á¦Ãâ °¡´ÉÇÑ Ç¥º»À» È®º¸ÇÏÁö ¸øÇÏ¿© »çÁøÀ¸·Î ´ëüÇϰíÀÚ ÇÔ.


°Ë¼ö¿ë »ùÇà DNA ³óµµ ¹× ÃÑ ¾ç ÇöȲǥ

¡¡Sample ¸í

³óµµ(ng/ul)

Volume(ul)

DNA ÃÑ·®(ug)

O.D A260/280

ÃßÃâÀÏÀÚ

ÀúÀåÀå¼Ò

µÎÁ¡¹ÚÀ̻罿¹ú·¹

733

300

219.9

2.41

170927

1XTE pH8.0

(3) ±âŸºÐ¼®

A. Genome Size estimation – Jellyfish ÇÁ·Î±×·¥

°¢ ´ë»óÁ¾À» ´ë»óÀ¸·Î Jellyfish ÇÁ·Î±×·¥À¸·Î Genome size¸¦ ¿¹ÃøÇÑ °á°ú´Â ¾Æ·¡¿Í °°´Ù. °¢ ºÐ¼®Àº k-mer °ª 17mer, 19mer, 21mer¸¦ ´ë»óÀ¸·Î ÇÏ¿´°í ±×°ÍÀ» ÅëÇØ ¿¹ÃøµÈ genomeÀÇ Å©±â´Â Estimation genome size ¿¡ Ç¥½ÃµÇ¾ú°í, À̸¦ ÅëÇØ À̹ø »ç¾÷¿¡¼­ ºÐ¼®ÇÑ ¼­¿­ÀÇ ¾çÀÇ coverage´Â Genome coverage depth(Coverage Depth)¿¡ Ç¥±âµÇ¾ú´Ù. ±×¸®°í °¢ Á¾ÀÇ Ç¥ ¾Æ·¡ ±×·¡ÇÁ´Â kmer°ª º°·Î ³ªÅ¸³­ depthÀÇ ¿¹Ãø ±×·¡ÇÁ·Î peak°ªÀ» È®ÀÎÇÒ ¼ö ÀÖ´Ù.


»ùÇøí

K-mer

(K-mersize)

Estimateddepth

(K-merCoveragedepth)

Genomecoveragedepth

(Coveragedepth)

Estimatedgenome

size

µÎÁ¡¹ÚÀ̻罿¹ú·¹

17

43

24.61

623,437,265.5

19

43

23.84

643,448,832

21

42

24.21

633,772,909.7

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B. ¹Ýº¹¼­¿­

- ½ÃÄö½ÌÀÌ ¿Ï·áµÈ »ùÇà DNA ÀÇ contigs Áß 1kb ÀÌ»óÀÇ contigsÀÇ ¹Ýº¹¼­¿­À» Ž»ö (Repeat masking results of DNA contigs)

µÎÁ¡¹ÚÀ̻罿¹ú·¹ (Prosopocoilus blanchardi)

 

µÎÁ¡¹ÚÀ̻罿¹ú·¹ (Prosopocoilus blanchardi) ´Â 1kb ÀÌ»óÀÇ contig ÀÇ ¹Ýº¹¼­¿­Àº 26,991°³ read (65,644,094 bp) À̰í, GC level Àº 42.36%ÀÌ´Ù. Repeat Masking À¸·Î ³ª¿Â ¹Ýº¹¼­¿­Àº 645,606 bp (ÀüüÀÇ 0.98%) ¸¸Å­ ÀÖ´Ù. Small RNA Àº 31°³ read (10,221 bp) °¡ ÀÖ°í, Simple repeat ´Â 13,330°³ read (493.923 bp) °¡ ÀÖ´Ù.

sequences: 26,991

 

total length:  65,644,094 bp  (65,644,094 bp excl N/X-runs)

 

GC level: 42.36 %

 

bases masked: 645,606 bp ( 0.98%)

 

¡¡

number of

elements

length

occupied

percentage

of sequence

 

 

SINEs: 

4

156 bp

0.00%

 

¡¡

ALUs 

0

0 bp

0.00%

 

¡¡

MIRs 

0

0 bp

0.00%

 

LINEs: 

48

3,689 bp

0.01%

 

¡¡

LINE1 

1

34 bp

0.00%

 

¡¡

LINE2 

13

945 bp

0.00%

 

¡¡

L3/CR1 

27

2,229 bp

0.00%

 

LTRelements: 

58

16,338 bp

0.02%

 

¡¡

ERVL 

0

0 bp

0.00%

 

¡¡

ERVL-MaLRs

0

0 bp

0.00%

 

¡¡

ERV_classI 

3

210 bp

0.00%

 

¡¡

ERV_classII

2

119 bp

0.00%

 

DNAelements: 

89

10,543 bp

0.02%

 

¡¡

hAT-Charlie 

8

872 bp

0.00%

 

¡¡

TcMar-Tigger

7

1,508 bp

0.00%

 

Unclassified: 

1

66 bp

0.00%

 

Total interspersed repeats:

 

30,792 bp

0.05%

 

Small RNA:

31

10,221 bp

0.02%

 

Satellites:

1

0 bp

0.00%

 

Simple repeats:

13,330

493.923 bp

0.75%

 


C. Mito-genome Map

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µÎÁ¡¹ÚÀ̻罿¹ú·¹´Â Reference·Î 21,628 bp Å©±âÀÇ Prosopocoilus astacoides blanchardi ¹ÌÅäÄܵ帮¾Æ genomeÀ» ÀÌ¿ëÇÏ¿© ¸ÊÇÎÇÏ¿´´Ù. °¸Àº 396 bp ·Î, Coverage ´Â 98.17%·Î È®ÀεǾú´Ù.

D. Transcriptome data ºÐ¼®

- µÎÁ¡¹ÚÀ̻罿¹ú·¹

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µÎÁ¡¹ÚÀ̻罿¹ú·¹ÀÇ KOG °á°ú, ¡°Infomation Storage and Processing¡± ºÎºÐ¿¡¼­´Â transcription °ü·ÃÀÌ 5.0%·Î °¡Àå ¸¹ÀÌ ¸ÅĪµÇ°í, ¡°Cellular Processes and Signaling¡± ¿¡¼­´Â signal transduction mechanisms (9.8%), post translational modification (6.1%) ·Î ¸¹ÀÌ ¸ÅĪµÈ´Ù. ¡°Metabolism¡± ºÎºÐÀº Æò±Õ 1% ´ë·Î ³·°Ô ¸ÅĪµÇ°í, Multiple Function Àº 20.3% ÀÌ´Ù.

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µÎÁ¡¹ÚÀ̻罿¹ú·¹ÀÇ GO °á°ú, Biological Process¿¡¼­ membrane (1,713°³), cell (1,601°³) ¼øÀ¸·Î ¸¹ÀÌ ¸ÅĪµÈ´Ù. Molecular Function ¿¡¼­´Â binding (2,981°³), catalytic activity (2,516°³) ¼øÀ¸·Î °¡Àå ¸¹ÀÌ ¸ÅĪµÈ´Ù. ¶ÇÇÑ, Cellular Component ºÎºÐ¿¡¼­´Â cellular process (2,429°³), metabolic process (2,408°³), single-organism process (1,445°³) ¼øÀ¸·Î ¸¹ÀÌ ¸ÅĪµÈ´Ù.


(4) Microsatellite È帱º

A. SSR statistics


µÎÁ¡¹ÚÀ̻罿¹ú·¹ 

Repeats

4

5

6

7

8

9

10

11

12

13

¡¦

Total

Di

0

0

374

230

102

96

40

21

2

0

 

869

Tri

0

1,947

907

291

168

14

11

2

7

0

 

3,357

Tetra

677

225

74

2

1

0

0

0

0

0

 

979

Penta

117

18

7

0

0

0

0

0

0

0

 

142

Hexa

66

2

0

0

0

0

0

0

0

0

 

68

Total

860

2,192

1,362

523

271

110

51

23

9

0

 

5,415


¡æ SSR °Ë»ö°á°ú ÃÑ 5,415°³ÀÇ SSR ¼­¿­À» È®ÀÎÇÒ ¼ö ÀÖ¾úÀ¸¸ç, Tri motif °¡ 3,357°³·Î °¡Àå ¸¹ÀÌ Á¸ÀçÇÏ´Â °ÍÀ» È®ÀÎ ÇÒ ¼ö ÀÖ¾úÀ¸¸ç, À̸¦ ±â¹ÝÀ¸·Î ÇÏ¿© SSR marker È帱º¿¡ ´ëÇÑ primer ¸¦ 7,942°³¸¦ µðÀÚÀÎ ÇÏ¿´´Ù.


B. Primer sequence

¡æ °¢ Á¾ÀÇ À¯ÀüÀÚ¸¦ ºÐ¼®ÇÏ¿© ±× Á¾À» ±¸º°ÇÒ ¼ö ÀÖ´Â primer¸¦ ¸¸µç´Ù. primer ÀÇ Á¶°ÇÀº Motif ¾à 4~6°³À̸ç, Forward ¿Í Reverse primer °¡ 18~22°³ Á¤µµÀ̰í Tm°ªÀÌ 54.5~55.5 Á¤µµ°¡ Àû´çÇÏ´Ù.


- µÎÁ¡¹ÚÀ̻罿¹ú·¹

Sequence

Motif

Forward Primer

Tm

Reverse Primer

Pb_Uni_00010

(AACT)6

GGAGCACCTCATTTTAAGTATC

54.79

CAAGACACTCTCTTCAGACCA

55.52

Pb_Uni_00250

(CCGAAA)4

GGTTGCACTCAGAGTTAGTGT

54.5

CGATGCTACATAACAATTCCT

54.56

Pb_Uni_00474

(CTT)10

TTCAGGGGTGACTTTTAAGTAT

54.73

TGTTCATCGAAATTTAAGTGG

55.41

Pb_Uni_00540

(AAG)8

AGCAATTAGGCCAAACATT

54.91

CATGTTTCGTCGTAAAGTCAT

55.34

Pb_Uni_02176

(CCATTC)4

TTCAAATACCTCAGAGTGACC

54.34

CTTCGTGTGTACCGTACTGAT

55.29

Pb_Uni_02200

(TTG)8

CAATAGACCGATATTTTGCAC

54.96

ATACAAAAACACGGCTAACAA

55.12

Pb_Uni_02211

(TAAAA)5

GACGACATCCATTTAGAAAAA

54.49

GACGCAAGCAAATCCTAATA

55.66

Pb_Uni_04330

(TTC)9

TATAAGTCTCGGGGTACTCGT

55.54

TCAAATGACGAATCAGAAAAC

55.36

Pb_Uni_04333

(GAA)9

AAGAACCCTACGAATCTTCC

54.97

TATAAGTCTCGGGGTACTCGT

55.54

Pb_Uni_08167

(TAA)9

TTCACTTTGTTTAAGGACGAG

54.8

AAATGTCGTGTGTTCAATTTC

55.13

Pb_Uni_08168

(TTA)9

AAATGTCGTGTGTTCAATTTC

55.13

TTGTTTAAGGACGAGCAACT

55.21

Pb_Uni_10329

(TGC)9

TGCTGCTGCTGCTGTTGT

60.52

TCAGCAAGTACAAACATTCAA

54.51

Pb_Uni_13287

(TTAAA)5

TTGACCGATTTTTATTAGTGC

54.71

TATTTGACGAATTGGAGGTTA

54.94

Pb_Uni_17182

(CAG)9

TCAGCAAGTACAAACATTCAA

54.51

CTGCTGCTGCTGTTGTTG

57.71

Pb_Uni_23230

(ACAA)7

CGCAGAGTATGTATGTATAAAA

50.32

TTAGCGTTAATTTAGCGAATC

54.37

C. ¹ÙÄÚµå ¼­¿­


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(5) Gene prediction


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Number of  Contig (>1kb)

Number of Bases (>1kb)

N50 Contig Size

Number of gene prediction

µÎÁ¡¹ÚÀ̻罿¹ú·¹

20,548

61,701,123

3,358

16,273


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