Bioinformatic study in profiling the gut microbial community of giant panda (Ailuropoda melanoleuca) from metagenomic shotgun data

As a miraculous member in mammals, giant panda is a strict vegetarian while its gastrointestinal tract possesses a typical digestive system of carnivores. Although it has evolved special pseudo-thumbs, and developed the teeth, mandible, skull and chewing muscles well to adapt the favorite food bamboo in morphology, no cellulolytic enzymes have been identified in the panda’s genome. Therefore, the gut microbiota in the giant panda is hypothesized to play the crucial role in lignocellulosic digestion. Besides the diet, the gut microbial community also interacts with the host health and aging in a dynamic ecosystem model, thus engages the unprecedented efforts in research and conservation of giant panda. As the result, deep shotgun metagenomic datasets were generated for the analysis of gut microbiota in giant panda. In Chapter 2 and 3 of this thesis, the quality of metagenomic assembly was compared between sequencing platforms and optimized with putative influencing factors, such as read length, library length and max k-mer length. The ultrahigh throughput Illumina sequencing platform was shown to provide more complete profiling with a comparable error rate, which was considered as more appropriate for metagenomic study despite of its inherent limitation in read length. On the other hand, numerous attempts to improve assembly quality with the adjustments of multiple putative influencing factors were performed for the optimization of both laboratory and computational designs. These two chapters provided computational analysis of the metagenomic assembly of the giant panda gut microbial community, to facilitate the metagenomic profiling more comprehensive with high accuracy. In Chapter 4, the descriptive metagenomic analysis revealed the giant panda gut microbiota was significantly distinguished from all other carnivores and herbivores. The microbial compositions vary remarkably during the growth state changing from juvenile to adult, and aging as well. Furthermore, the dramatic decrease of cellulolytic Clostridium species was discovered during the aging process in the gut of world’s oldest panda, and the booming of a virus family Myoviridae was found predominantly in the geriatric panda group. In Chapter 5, functional metagenomics not only discovered substantial evidence of cellulose, hemicellulose and lignin related protein coding genes in metagenomic data, but also identified the extreme low abundance of cellulose-related glycoside hydrolase enzymes in giant panda gut, which might reflect the low digestibility of the lignocellulosic diet. In addition, the putative cellulolytic population genome was recovered through pure bioinformatic computation, demonstrating the research value of assembling individual uncultivated bacterial genome from complex community metagenomic dataset. The success in reconstruction of uncultured experimental bacteria thus will hopefully spur more interaction among biologists and bioinformaticians in future metagenomic studies. This is the first study of deep shotgun metagenomic sequencing for the gut microbiota in giant panda, where comprehensive profiling for the microbial community structure and function is successfully constructed. The profiling results could provide guide for further experimental diet, health, and aging studies in giant panda.published_or_final_versionBiological SciencesDoctoralDoctor of Philosoph

The genome of the mesopolyploid crop species Brassica rapa

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops

LncRNAs Expression Signatures of Renal Clear Cell Carcinoma Revealed by Microarray

<div><h3>Background</h3><p>Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of cancers. In this study, we described lncRNAs profiles in 6 pairs of human renal clear cell carcinoma (RCCC) and the corresponding adjacent nontumorous tissues (NT) by microarray.</p> <h3>Methodology/Principal Findings</h3><p>With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 17157. From the data we found there were thousands of lncRNAs that differentially expressed (≥2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples. Compared with NT, many lncRNAs were significantly up-regulated or down-regulated in RCCC. Our data showed that down-regulated lncRNAs were more common than up-regulated ones. ENST00000456816, X91348, BC029135, NR_024418 were evaluated by qPCR in sixty-three pairs of RCCC and NT samples. The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.</p> <h3>Conclusions/Significance</h3><p>Our study is the first one to determine genome-wide lncRNAs expression patterns in RCCC by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development. Taken together, this study may provide potential targets for future treatment of RCCC and novel insights into cancer biology.</p> </div

Comparison between microarray data and qPCR result.

<p>ENST00000456816, X91348, BC029135 and NR_024418 determined to be differentially expressed in RCCC samples compared with NT samples in six patients by microarray were validated by qPCR. The heights of the columns in the chart represent the log-transformed median fold changes (T/N) in expression across the six patients for each of the four lncRNAs validated; the bars represent standard errors. The validation results of the four lncRNAs indicated that the microarray data correlated well with the qPCR results.</p

Summary of data from microarray for six pairs of renal cancer and adjacent normal tissues.

<p>Summary of data from microarray for six pairs of renal cancer and adjacent normal tissues.</p

Distributions of the lncRNAs expression levels.

<p>That most significantly different expressed were validated by qPCR in 63 pairs of RCCC and NT samples.</p