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Draft genome of the Reindeer (Rangifer tarandus)
Zhipeng Li
ICG12, ShenZhen, China
27 Oct, 2017
Chinese Academy of Agricultural Sciences (CAAS)
43 institutes, established in 1957 Institute of Special Animal and Plant
Sciences (ISAPS)
ISAPS,CAAS
Background
Material and Methods
Sequencing Result
Genome Assembly
Assessment of Genome
Ongoing work
Acknowledgement
Outline
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)
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)
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)
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
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.
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
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
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
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
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
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
Species-specific genes and phylogeny
The divergence time between Reindeer, and ancestors of cattle and goat,is estimated to be about 29.5 Mya.
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.
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
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
Ongoing work-HologenomeHow the rumen microbiome contribute to host adaption and evolution?
Ongoing work-hologenome
16S rRNA and mtDNA Metabolome and mtDNA
The relationship between rumen microbiota and host phylogeny
Home message
Reporting the reference genome of reindeer
Reindeer re-sequencing project
Rumen evolution and development
Rumen microbiome and host evolution
Acknowledgement
Prof. Wen Wang Prof. Qiang Qiu Prof. Tom Gilbert Prof. Guojie Zhang Prof. Yu Jiang
Assistant ProfessorRasmus Heller
Associate ProfessorBent Petersen
Thanks for your attention!
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