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Draft genome of the Reindeer ( Rangifer tarandus) Zhipeng Li ICG12, ShenZhen, China 27 Oct, 2017
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Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Jan 28, 2018

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Page 1: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Draft genome of the Reindeer (Rangifer tarandus)

Zhipeng Li

ICG12, ShenZhen, China

27 Oct, 2017

Page 2: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Chinese Academy of Agricultural Sciences (CAAS)

43 institutes, established in 1957 Institute of Special Animal and Plant

Sciences (ISAPS)

ISAPS,CAAS

Page 3: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Background

Material and Methods

Sequencing Result

Genome Assembly

Assessment of Genome

Ongoing work

Acknowledgement

Outline

Page 4: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Background-Ruminantia genome project (RGP)

200 species in 6 families (Tragulidae, Girffidae,

Antilocapridae, Moschidae, Cervidae, and Bovidae)

The most important group of large terrestrial herbivorous

mammals

They are commonly found in most of the continents of the

world (except Australia and Antarctica)

They are ecologically, behaviourally and physiologically

very diverse

A good scientific treasure for understanding the processes

of evolution(Cantalapiedra et al., 2014)

Page 5: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Profs. Wen Wang & Qiang Qiu groups, Northwestern

Polytechnical University

Profs. Rasmus Heller & Guojie Zhang groups, University of

Copenhagen

Prof. Yu Jiang group, Northwest A&F University

Profs. Guangyu Li & Zhipeng Li group, ISAPS, CAAS

45 species coverage 2/3 genus from all families in

Ruminantia are sequences in this project(Cantalapiedra et al., 2014)

Background-Ruminantia genome project (RGP)

Page 6: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Reindeer is the only species with a circumpolar distribution, digest lichen, and resist cold. The only domesticated deer in the world. Antlers are the defining characteristic of male cervids. Interestingly, reindeer is the only species that females regularly grow antlers in cervid. Reindeer milk contains greater amount of proteins, and lower amount of lactose compared to that of bovids.

(CAFF Map, 2001)

Background- Reindeer (Rangifer tarandus)

(Wang et al., Science, 2015) (Park and Haenlein, 2006)

Page 7: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Material and methods Reindeer distribution

- Greater Khingan Mountains

- Inner Mongolia Autonomous Region, China

Animal

- A two-year-old, female reindeer

Library Construction

Short-insert libraries(200, 250, 350, 400 and 450 bp)

Long-insert libraries(3, 6.5, 11.5 and 16 kb)

Illumina Hiseq 4000

Page 8: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Sequencing result

Insert Size (bp) TypeBases

sequenced (Gb)Reads Length

(bp)Sequence

Coverage (×)Physical

coverage (×)

200 Paired-end 78.82 150 28.61 19.07

250 Paired-end 74.96 150 27.20 22.66

350 Paired-end 78.62 150 28.53 33.28

400 Paired-end 91.43 150 33.18 44.22

450 Paired-end 105.47 150 38.28 57.39

3000 Mate-paired 81.26 150 29.49 293.48

6500 Mate-paired 64.53 150 23.42 498.86

11500 Mate-paired 72.35 150 26.25 1,002.05

16000 Mate-paired 75.80 150 27.51 1,463.27

Total 723.24 262.47 3,434.28

A total of 723.2 Gb raw data were obtained, and finally, clean reads amounting to 615 Gb were used to further analysis.

Page 9: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Genome size evaluation and assembly

K-mer analysisG = N*(L − 17 + 1)/K_depth

Estimated genome size=2.76 Gb(220-fold mean coverage)

Constructing contigs and scaffoldsSOAPdenovo

(pregraph −K 79 −d 0; map -k 79; scaff -L 200)

Closing gapsGapCloser

(200, 250 and 350 bp)

Genome assembly = 2.64 Gb

Type Scaffold (bp) Contig (bp)

Total number 58,765 117,102

Total length 2,832,785,815 2,732,476,387

N50 length 986,392 91,805

N90 length 151,297 17,480

Max length 4,664,725 770,474

GC content(%) 41.24 40.98

Page 10: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Quality assessments

92.6% (3,803 genes)

FRC method

Average nuclear distance = 7.18%

83.95%1:1 aligned

69.88 per Mb

Break

Reindeer genome assembly is of good level of contiguity and correctness

2.64 Gb

Points

Page 11: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Genome annotation-repeat

Repbase TE library

Repeats

Repeat sequences cover about 1.03 Gb, accounting for 39.1% of the reindeer genome assembly

2.64 Gb

Tandem repeats

Transposable elements

De novo libraryconstruction

De novo library

Repbase

TE library

Page 12: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Genome annotation-gene structure prediction

2.64 Gb

glimmerHMM

De novo gene prediction

Homology-based prediction

TblastN

Bos taurus Ovis aries Homo sapiens

21,555 protein-coding genes

Comparinggenomes

Page 13: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Genome annotation-gene function

21,555 protein-coding genes

Pfam PRINTS ProDom SMART

KEGG TrEMBL SwissProt

BLASTP

19,004 genes(88.17%)

Annotation type Numbers Percent(%)

InterPro 17,513 81.25

GO 14,138 65.595

KEGG 5,240 24.31

Swissprot 18,536 85.99

TrEMBL 18,892 87.65

Annotated 19,004 88.17

Page 14: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Genome annotation-rRNA-coding sequences

Type Copy (w) Average length (bp) Total length (bp) Percent (%)

miRNA 547 92.9049 50,819 0.0017

tRNA 863 73.1483 63,127 0.0022

rRNA rRNA 159 91.4088 14,534 0.0005

18S 16 91.8125 1,469 0.0000

28S 36 140.3611 5,053 0.0002

5.8S 2 130.5000 261 0.0000

5S 105 73.8191 7,751 0.0003

snRNA snRNA 1,339 119.7214 160,307 0.0056

CD-box 102 130.8235 13,344 0.0004

HACA-box 267 137.9588 36,835 0.0013

splicing 951 112.6330 107,114 0.0037

Page 15: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Species-specific genes and phylogeny

The divergence time between Reindeer, and ancestors of cattle and goat,is estimated to be about 29.5 Mya.

Page 16: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Conclusion

In summary, we report the first sequencing, assembly and

annotation of the reindeer genome, which will be useful in analysis

of the genetic basis of the unique characteristics of reindeer, and

broader studies on ruminants.

Page 17: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Ongoing work-Reindeer resequencing project

Where the reindeer originate?

How and when the reindeer to be

domesticated?

What is the genetic diversity of reindeer?

Why the female reindeer grows antler?

The cairngorm reindeer(http://www.christmasreindeer.co.uk/)

Distribution: Europe, North American,and ChinaPopulations: Wild and domesticated

Page 18: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Ongoing work-Rumen development and evolution

Lesser Mouse DeerTragulus kanchil

Why the rumen begin to function in ruminant?

How the rumen evolve in host adaption?

Rumen plays important roles in host development and healthy

Page 19: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Ongoing work-HologenomeHow the rumen microbiome contribute to host adaption and evolution?

Page 20: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Ongoing work-hologenome

16S rRNA and mtDNA Metabolome and mtDNA

The relationship between rumen microbiota and host phylogeny

Page 21: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Home message

Reporting the reference genome of reindeer

Reindeer re-sequencing project

Rumen evolution and development

Rumen microbiome and host evolution

Page 22: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Acknowledgement

Prof. Wen Wang Prof. Qiang Qiu Prof. Tom Gilbert Prof. Guojie Zhang Prof. Yu Jiang

Assistant ProfessorRasmus Heller

Associate ProfessorBent Petersen

Page 23: Zhipeng Li at #ICG12: Draft Genome of the Reindeer (Rangifer tarandus)

Thanks for your attention!