| Brain, which is also called cerebrum, consists of two hemispheres. It’s the senior nervous center controlling movements, producing feelings and realizing higher-level brain functions. The molecular mechanism and regulation mechanism of brain development has not yet been fully expounded. In this study, to help assess the expression changes of genes involved in postnatal brain development, we carried out a comparative study on mouse brain transcriptomes at three crucially developmental stages (infant stage,1weeks old; juvenile stage,4weeks old; adult stage,10weeks old) using the next-generation sequencing technology (SOLiD).Using SOLiD, we sequenced the transcriptomes at three developmental stages (RNA-seq), then aligned the obtained reads to the mouse genome and annotated genes using the GenBank database on NCBI. We acquired11,929,828,16,614,876and15,111,661uniquely-mapped reads from infant, juvenile, and adult cerebrum samples, respectively. Of these uniquely-mapped reads,33%-47%were mapped to exons,28%-34%were mapped to introns,1.2%-2.3%were mapped to junctions, and the others were mapped to intergenic regions. We identified15,344,16,048and15,775expressed genes in the mouse cerebrum of infancy, juvenile and adult, respectively. We used RPKM value to normalize the gene expression abundance among the three developmental stages. The gene expression profiles were clustered into two groups, one contains infant and juvenile cerebrums, and the other contains adult cerebrum only. Through comparative analysis of gene expression profiles, we found5,768expressed genes changed significantly between infant and juvenile cerebrums, while the number of that between juvenile and adult cerebrums was6,787. Compared to infant cerebrum,4,106differentially expressed genes were up-regulated in juvenile cerebrum, while compared to juvenile cerebrum,5,623differentially expressed genes were down-regulated in juvenile cerebrum. This phenomenon suggests that the abundance of cerebrum expressed genes during the three stages were up-regulated and then down-regulated. The gene expression was enhanced markedly during puberty comparied to other stages. These differently expressed genes reflected a vast repertoire of genes involved in energy metabolism, signal transduction, cell apoptosis, and so on. Remarkably, these differentially expressed genes also includes a large number of genes related to cancers and neurologic diseases, suggested these genes may play a role in the postnatal development of mouse cerebrum.In our research, we found1,493transcription factors(Tfs) which involved in the development of mouse cerebrum, some of which are essential for cerebrum development such as E2f family, Pax6, Six3, Rax, ISL-1. The function of most Tfs during cerebrum development are still unclear.In addition, we found254,304,382Tfs with low expression abundance (RPKM<1) in the three samples, respectively, including some important genes for the postnatal development of mouse cerebrum (Neurog2、Pax6、Six3). These lowly expressed Tfs undetected by DNA microarray before may help us understand the cerebrum transcriptome deeply.We studied the correlation between introns and exons and identified2,079,2,520and4,061genes have intronic regions showing significant exprssion in three stages, respectively.Our recearches indetated that9,145genes have alternative transcripts in the three samples totally. Moreover, we found23,266transciptional loci in the intergenic region in all,70.8%of which were annotated to the UTR extenstion region(16,477),20.7%of which were confirmed by EST,0.9%of which were annotated as the known ncRNA, and other7.6%(1,767) were identified as new transciptional loci. Chlorophyta is universally considered as the progenitor of land plants, the research of its development plays an important role in exploring the plant kingdom’s evolution. But because of the genes coded by genome are not conservative in Chlorophyta plants, researching their chloroplast genomes(cpDNA) is necessary for the study of evolution.Using Bryopsis hypnoides which is a pervasive algae in China sea as the study object, we sequence its cpDNA and perform comparative genomics and phylogeny analysis. The cpDNA of B. hypnoides is cyclic and double-stranded which has153,429bp. It has no inverted repeat sequence, the mean GC content is33.1%with scarcely bias.The cpDNA of B. hypnoides has111functional genes, including69protein-coding genes,5rRNA genes and37tRNA genes, and we predict29ORF with a standard of no less than300bp. Like the most algaes, all genes of B. hypnoides cpDNA have single copy. We also study genes arrangement and discover many gene clusters and gene pairs in B. hypnoides cpDNA. There are10genes have introns, as well as rrn16has2introns, the others has1intron respectively. Compared with other completely sequenced algaes, B. hypnoides cpDNA has10unusual tRNA genes,5of which correspond to those identified in some embryophyte cpDNAs, whereas the other five have been found previously only in some bacterial genomes. B. hypnoides cpDNA has5rRNA genes: rrn23, rrn16, rrn7, rrn5, and rrn3, the same situation can be found only in C. reinhardtii cpDNA, as genes rrn7and rrn3are absent from all other completely sequenced chlorophyte cpDNAs, and both C. reinhardti and B. hypnoides have the same rRNA genes arrangement.We conduct phylogenetic analysis using the concatenated sequences of42protein sequences from31algal/land plant organisms, including B. hypnoides, to elucidate their phylogenetic relationship. It’s distinctly that the tree identified two distinct lineages:the green lineage and the non-green lineage. Moreover, the chlorophytes and streptophytes form two distinct green lineages. The trees inferred with ML and MP methods both identified a clade uniting B. hypnoides and four complete sequenced members of the Chlorophyceae. The relationships with high bootstrap in the phylogeny are congruent with recently published phylogenies based on whole chloroplast genome sequences. |
PDF Full Text Request