Biology subjects

Feng Chen

Publications and source records attributed to Feng Chen.

3 recordsLinked to original sources

bioRxiv2015

Extensive sequencing of seven human genomes to characterize benchmark reference materials

The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.

Genomics↗

bioRxiv2014

Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing

Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor and Gloeophyllum trabeum1. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, and it involves up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed, and upstream transcription may interfere downstream transcription. Further comparative genomic analysis indicates that polycistronic transcription is likely a feature unique to these fungi. In addition, we also systematically demonstrated that short-read assembly is insufficient for mRNA isoform discovery, especially for isoform-rich loci. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a subset of fungi. Futhermore, our long-read sequencing approach combined with bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes.

Genomics↗

bioRxiv2014

Different profile of transcriptome between wheat Yunong 201 and its high-yield mutant Yunong 3114

Wheat is one of the most important crops in the world. With the exponentially increasing population and the need for ever increased food and feed production, an increased yield of wheat grain (as well as rice, maize and other grains) will be critical. Modern technologies are utilized to assist breeding programs. Such as the transcriptome sequencing, which greatly improves our genetic understanding, provides a platform for functional genomics research on crops. Herein, to get an overview of transcriptome characteristics of Yunong 3114, which is screened from the EMS mutagenized population of, a high quality Chinese winter noodle wheat, due to its different plant architecture as well as larger kernel size and higher grain weight, a high-throughput RNA sequencing based on next generation sequencing technology (Illumina) were performed. These unigenes were annotated by Blastx alignment against the NCBI non-redundant (nr), Clusters of orthologous groups (COG), gene orthology (GO), and the Kyoto Encyclopedia of Genesand Genomes (KEGG) databases. The 90.96% of the unigenes matched with protein in the NCBI nr database. Functional analysis identified that changes in several GO categories, including recognition of pollen, apoptotic process, defense response, receptor activity, protein kinase activity, DNA integration and so forth, played crucial roles in the high-yield characteristics of the mutant. Real-time PCR analysis revealed that the recognition of pollen related gene GsSRK is significantly up-regulated in Yunong 3114. In addition, alternative splicing (AS) analysis results indicated that mutation influence AS ratio, especially the retained introns, including the pollen related genes. Furthermore, the digital gene expression spectrum (DGE) profiling data provides comprehensive information at the transcriptional level that facilitates our understanding of the molecular mechanisms of various physiological aspects including development and high-yield of wheat. Together, these studies substantially increase our knowledge of potential genes and pathways for the genetic improvement of wheat and provide new insights into the yield and breeding strategies.

Plant Biology↗