Dr. Wen Wang, Professor, Head of CAS–Max Planck Junior Research Group, KIZ, CAS. This year we mainly focused on elite variety tag SNP analysis allele in upland rice, epigenetic changes and methylomics of silkworm, and transcriptomes of three orb-web spiders. Dr. Wen Wang was elected “Ten Thousand Elite Plan” of MOST, and gained funding from “the science and technology leading talent program of Yunnan”.
E-mail: wwang@mail.kiz.ac.cn
1. Analysis of elite variety tag SNPs reveals an important allele in upland rice
Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important talleles.
2. Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication
Domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection.By embryonic RNA interference,we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1.We omprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. We identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. Our results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance.
3. De novo assembly and analysis of transcriptomes of three orb-web spiders
As an ancient arthropod with a history of 390 million years (Ma), spiders evolved numerous morphological forms resulted from adaptation to different environments. The venom and silk of spiders, which have promising commercial applications in agriculture, medicine and engineering fields, are of special interests to researchers. However, little is known about their genomic components, which hinders not only understanding spider biology but also utilizing their valuable genes. Here we report on deep sequenced and de novo assembled trancriptomes of three orb-web spiders which spread in south China tropical forests, Gasteracanthaarcuata, Nasoonariasinensisand Gasteracanthahasselti. With Illumina paired-end RNA-seq technology, 54,871, 101,855 and 75,455 unigenes for G. arcuata, N. sinensisand G. hasseltiwere obtained respectively, among which 9,300, 10,001 and 10,494 unique genes are annotated respectively. From these annotated unigenes, we comprehensively analyzed silk and toxin gene components and structures for the three spiders. Our study provides valuable transcriptome data for three spider species which previously lack any genetic/genomic data. The results have laid the first fundamental genomic basis for exploiting gene resources from these spiders.
Highlights：
Publications：
1. Dong Y, et al., Wang W*. 2013. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology, 31(2)：135-141. ( IF= 32.438; 32.182).
2. Lyu J, et al., Wang W*. 2013. Analysis of elite variety tag SNPs reveals an important allele in upland rice. Nature Communication,Jul 5: 4: 2138. (IF= 10.015; 10.02).
3. Xiang H, et al., Wang W*. 2013. Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication. BMC Genomics, Sep 23; 14: 646. (IF= 4.379; 4.615).
4. Zhao YJ, Zeng Y, Chen L, Dong Y, Wang W*. 2013. Analysis of Transcriptomes of Three Orb-Web Spider Species Reveals Gene Profiles Involved in Silk and Toxin. Insect Sci, Oct 25. doi: 10.1111/1744-7917.12068. ( IF= 1.786; 1.59).
5. Song LT, Wang W*. 2013. Genomes and evolutionary genomics of animals. Current Zoology, 59(1): 1674-5507. ( IF= 1.392; 1.392).
6. Zhang Wen-guang. 2013.Development of Genome-Wide Scan for Selection Signature in Farm Animals. Journal of Integrative Agriculture, 12:8 1461-1470.
Lab Staff
Staff
Dr. Hui Xiang, Associate Professor, xiangh@mail.kiz.ac.cn
Dr. Xue-Yan Li, Assistant Professor, lixy@mail.kiz.ac.cn
Dr. Xiao-Fei Shi, Assistant Professor, shixiaofei1@163.com
Ms. Ruo-Ping Zhao, Assistant Professor, zhaorp@mail.kiz.ac.cn
Ms. Gui-Chun Liu, Assistant Professor, liuguichun@mail.kiz.ac.cn
Postdoctoral Fellows:
Wen-Guang Zhang, 2010；Bin Liu；Rui Su，2013
Graduate Students
Xun Xu, 2007
Ye-Sheng Zhang, 2010
Hui Liu, 2010
Tian Zhang, 2011
Lei Chen, 2011
Wen-Jing Sheng, 2011
Zhi-Heng Gou,
Xiao Wang,
Ling Kui,
Yan-Dong Ren, 2013
Ying-Jun Zhao, 2013
Ru Zhang, 2013
