title: Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during development.
abstract: Vertebrates diverged from other chordates approximately 500 million years ago and have adopted several modifications of developmental processes. Amphioxus is widely used in evolutionary developmental biology research, such as on the basic patterning mechanisms involved in the chordate body plan and the origin of vertebrates. The fast development of next-generation sequencing has advanced knowledge of the genomic organization of amphioxus; however, many aspects of gene regulation during amphioxus development have not been fully characterized. In this study, we applied high-throughput sequencing on the transcriptomes of 13 developmental stages of Chinese amphioxus to gain a comprehensive understanding of transcriptional processes occurring from the fertilized egg to the adult stage. The expression levels of 3,423 genes were significantly changed (FDR ≤ 0.01). All of these genes were included in a clustering analysis, and enrichment of biological functions associated with these clusters was determined. Significant changes were observed in several important processes, including the down-regulation of the cell cycle and the up-regulation of translation. These results should build a foundation for identifying developmentally important genes, especially those regulatory factors involved in amphioxus development, and advance understanding of the developmental dynamics in vertebrates.
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.|Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Kevin Yi
authors.initials: KY
authors.lastname: Yang
authors.affiliation: Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors.forename: Zuming
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Patrick Kwok-Shing
authors.initials: PK
authors.lastname: Ng
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Wayne Junwei
authors.initials: WJ
authors.lastname: Zhou
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Yinfeng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.|Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Minghua
authors.initials: M
authors.lastname: Liu
authors.affiliation: Nanjing Institute of Paleontology and Geology, Chinese Academy of Sciences, Nanjing, China.
authors.forename: Junyuan
authors.initials: J
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors.forename: Bingyu
authors.initials: B
authors.lastname: Mao
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.|Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Stephen Kwok-Wing
authors.initials: SK
authors.lastname: Tsui
mesh_terms: D000199:Actins / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D054262:Gastrulation; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D005801:Genes, Homeobox; D064175:Lancelets / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017411:Ribonucleoproteins, Small Nuclear / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics; D059467:Transcriptome
chemical_list: D000199:Actins; D018797:Cell Cycle Proteins; D012333:RNA, Messenger; D017411:Ribonucleoproteins, Small Nuclear