Research summary
Illumina metagenomic sequencing of faecal samples from 124 European individuals produced 576.7 Gb of sequence and a non-redundant catalogue of 3.3 million microbial genes from the human gut, roughly 150 times the size of the human gene complement, with over 99% of genes bacterial and most shared across individuals of the cohort [1]. SOAPdenovo2 reduced memory consumption in graph construction, resolved more repeat regions in contig assembly, and increased coverage and length in scaffold construction compared with its predecessor, enabling more accurate de novo assembly of NGS short reads [2]. A whole-genome shotgun draft of the Oryza sativa ssp. indica genome covered 93% of the 420-megabase genome, predicted 32,000-50,000 genes, and detected homologs of 98% of known maize, wheat and barley proteins, with extensive synteny among cereals and limited synteny to Arabidopsis [3]. SOAP2 employed a Burrows-Wheeler Transform compression index in place of a seed index, reducing memory from 14.7 to 5.4 GB on the human genome and improving alignment speed by 20-30x while supporting both single- and paired-end reads [4]. The original SOAP tool was designed for gapped and ungapped alignment of short oligonucleotides from Illumina-Solexa sequencing, supporting resequencing, small RNA discovery and mRNA tag mapping with multi-threaded parallelism [5]. The tomato genome sequence was reported alongside a draft of Solanum pimpinellifolium; the two tomato genomes differed by only 0.6% nucleotides with signs of recent admixture, while differing by more than 8% from potato with nine large and several smaller inversions [6].
Recent publications
- A human gut microbial gene catalogue established by metagenomic sequencingDOI
- Enterotypes of the human gut microbiomeDOI
- A metagenome-wide association study of gut microbiota in type 2 diabetesDOI
- SOAPdenovo2: an empirically improved memory-efficient short-read de novo assemblerDOI
- Richness of human gut microbiome correlates with metabolic markersDOI
- Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseasesDOI
- A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica )DOI
- SOAP2: an improved ultrafast tool for short read alignmentDOI
- SOAP: short oligonucleotide alignment programDOI
- The tomato genome sequence provides insights into fleshy fruit evolutionDOI
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External profiles
- ORCID: https://orcid.org/0009-0008-8475-2934
- OpenAlex: openalex.org
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