Transcriptome Analysis of Sika Deer in China

Overview

Journal Mol Genet Genomics

Specialty Genetics

Date 2016 Jul 18

PMID 27423230

Citations 10

Authors

Bo-Yin Jia

Heng-Xing Ba

Gui-Wu Wang

Ying Yang

Xue-Zhe Cui

Ying-Hua Peng

Jun-Jun Zheng

Xiu-Mei Xing

Fu-He Yang

Affiliations

Soon will be listed here.

Abstract

Sika deer is of great commercial value because their antlers are used in tonics and alternative medicine and their meat is healthy and delicious. The goal of this study was to generate transcript sequences from sika deer for functional genomic analyses and to identify the transcripts that demonstrate tissue-specific, age-dependent differential expression patterns. These sequences could enhance our understanding of the molecular mechanisms underlying sika deer growth and development. In the present study, we performed de novo transcriptome assembly and profiling analysis across ten tissue types and four developmental stages (juvenile, adolescent, adult, and aged) of sika deer, using Illumina paired-end tag (PET) sequencing technology. A total of 1,752,253 contigs with an average length of 799 bp were generated, from which 1,348,618 unigenes with an average length of 590 bp were defined. Approximately 33.2 % of these (447,931 unigenes) were then annotated in public protein databases. Many sika deer tissue-specific, age-dependent unigenes were identified. The testes have the largest number of tissue-enriched unigenes, and some of them were prone to develop new functions for other tissues. Additionally, our transcriptome revealed that the juvenile-adolescent transition was the most complex and important stage of the sika deer life cycle. The present work represents the first multiple tissue transcriptome analysis of sika deer across four developmental stages. The generated data not only provide a functional genomics resource for future biological research on sika deer but also guide the selection and manipulation of genes controlling growth and development.

Citing Articles

The combination of SMRT sequencing and Illumina sequencing highlights organ-specific and age-specific expression patterns of miRNAs in Sika Deer.

Jia B, Wang X, Ma F, Li X, Han X, Zhang L Front Vet Sci. 2022; 9:1042445.

PMID: 36452144 PMC: 9701854. DOI: 10.3389/fvets.2022.1042445.

First Detection and Molecular Identification of Entamoeba bovis in Farm-Raised Sika Deer from Anhui Province, China.

Liu X, Ren Q, Guo J, Chen D, Li Q, Luo X Acta Parasitol. 2022; 67(4):1782-1787.

PMID: 36018470 DOI: 10.1007/s11686-022-00610-9.

VMP1 Regulated by chi-miR-124a Effects Goat Myoblast Proliferation, Autophagy, and Apoptosis through the PI3K/ULK1/mTOR Signaling Pathway.

Liu Y, Zhou Z, Li K, Wang P, Chen Y, Deng S Cells. 2022; 11(14).

PMID: 35883670 PMC: 9319091. DOI: 10.3390/cells11142227.

Growth Performance and Hematological Changes in Growing Sika Deers Fed with Spent Mushroom Substrate of .

Yuan C, Wu M, Chen X, Li C, Zhang A, Lu W Animals (Basel). 2022; 12(6).

PMID: 35327162 PMC: 8944863. DOI: 10.3390/ani12060765.

Development of novel EST microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in Sika deer.

Jia B, Wang G, Zheng J, Yang W, Chang S, Zhang J Hereditas. 2020; 157(1):24.

PMID: 32591015 PMC: 7320565. DOI: 10.1186/s41065-020-00137-x.

References

Gyurjan Jr I, Molnar A, Borsy A, Steger V, Hackler Jr L, Zomborszky Z . Gene expression dynamics in deer antler: mesenchymal differentiation toward chondrogenesis. Mol Genet Genomics. 2006; 277(3):221-35. DOI: 10.1007/s00438-006-0190-0. View

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

Garber M, Grabherr M, Guttman M, Trapnell C . Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011; 8(6):469-77. DOI: 10.1038/nmeth.1613. View

Yao B, Zhao Y, Wang Q, Zhang M, Liu M, Liu H . De novo characterization of the antler tip of Chinese Sika deer transcriptome and analysis of gene expression related to rapid growth. Mol Cell Biochem. 2011; 364(1-2):93-100. DOI: 10.1007/s11010-011-1209-3. View

Yue Y, Liu J, Yang M, Han J, Guo T, Guo J . De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries). Genet Mol Res. 2015; 14(1):1371-84. DOI: 10.4238/2015.February.13.16. View

Garcia-Seco D, Zhang Y, Gutierrez-Manero F, Martin C, Ramos-Solano B . RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit. BMC Genomics. 2015; 16:5. PMC: 4311454. DOI: 10.1186/s12864-014-1198-1. View

Abba S, Galetto L, Carle P, Carrere S, Delledonne M, Foissac X . RNA-Seq profile of flavescence dorée phytoplasma in grapevine. BMC Genomics. 2014; 15:1088. PMC: 4299374. DOI: 10.1186/1471-2164-15-1088. View

Khudyakov J, Preeyanon L, Champagne C, Ortiz R, Crocker D . Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights. BMC Genomics. 2015; 16:64. PMC: 4328371. DOI: 10.1186/s12864-015-1253-6. View

Molnar A, Gyurjan I, Korpos E, Borsy A, Steger V, Buzas Z . Identification of differentially expressed genes in the developing antler of red deer Cervus elaphus. Mol Genet Genomics. 2006; 277(3):237-48. DOI: 10.1007/s00438-006-0193-x. View

10.

Steger V, Molnar A, Borsy A, Gyurjan I, Szabolcsi Z, Dancs G . Antler development and coupled osteoporosis in the skeleton of red deer Cervus elaphus: expression dynamics for regulatory and effector genes. Mol Genet Genomics. 2010; 284(4):273-87. DOI: 10.1007/s00438-010-0565-0. View

11.

Lin G, Wang K, Deng X, Nevo E, Zhao F, Su J . Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia). BMC Genomics. 2014; 15:32. PMC: 3898070. DOI: 10.1186/1471-2164-15-32. View

12.

Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood P, Bowden J . De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013; 8(8):1494-512. PMC: 3875132. DOI: 10.1038/nprot.2013.084. View

13.

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

14.

Hobbs M, Pavasovic A, King A, Prentis P, Eldridge M, Chen Z . A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity. BMC Genomics. 2014; 15:786. PMC: 4247155. DOI: 10.1186/1471-2164-15-786. View

15.

Tian C, Tay W, Feng H, Wang Y, Hu Y, Li G . Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages. Sci Rep. 2015; 5:11042. PMC: 4457133. DOI: 10.1038/srep11042. View

16.

Hao L, Li H, Yan L . [Analysis of expressed sequence tags (ESTs) in sika deer (Cervus nippon hortulorum) velvet tip tissue]. Yi Chuan. 2011; 33(4):371-7. DOI: 10.3724/sp.j.1005.2011.00371. View

17.

Hishiki T, Kawamoto S, Morishita S, Okubo K . BodyMap: a human and mouse gene expression database. Nucleic Acids Res. 1999; 28(1):136-8. PMC: 102396. DOI: 10.1093/nar/28.1.136. View

18.

Ghaffari N, Sanchez-Flores A, Doan R, Garcia-Orozco K, Chen P, Ochoa-Leyva A . Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. Sci Rep. 2014; 4:7081. PMC: 4243063. DOI: 10.1038/srep07081. View

19.

Wang J, Lindsay B, Leebens-Mack J, Cui L, Wall K, Miller W . EST clustering error evaluation and correction. Bioinformatics. 2004; 20(17):2973-84. DOI: 10.1093/bioinformatics/bth342. View

20.

Shen L, Liu G, Zou Y, Zhou Z, Su Z, Gu X . The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species. PLoS One. 2015; 10(2):e0116872. PMC: 4332667. DOI: 10.1371/journal.pone.0116872. View