Whole-genome sequencing and analysis of the Chinese herbal plant

Background@# () (2n = 2x = 16) is genus of flowering plants belonging to the Gelsemicaeae family.@*Method@#Here, a high-quality genome assembly using the Oxford Nanopore Technologies (ONT) platform and high-throughput chromosome conformation capture techniques (Hi-C) were used.@*Results@#A total of 56.11 Gb of raw GridION X5 platform ONT reads (6.23 Gb per cell) were generated. After filtering, 53.45 Gb of clean reads were obtained, giving 160 × coverage depth. The genome assemblies 335.13 Mb, close to the 338 Mb estimated by k-mer analysis, was generated with contig N50 of 10.23 Mb. The vast majority (99.2%) of the assembled sequence was anchored onto 8 pseudo-chromosomes. The genome completeness was then evaluated and 1338 of the 1440 conserved genes (92.9%) could be found in the assembly. Genome annotation revealed that 43.16% of the genome is composed of repetitive elements and 23.9% is composed of long terminal repeat elements. We predicted 26,768 protein-coding genes, of which 84.56% were functionally annotated.@*Conclusion@#The genomic sequences of could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.

The evolution study on Oryza rufipogon. dw by whole-genome sequencing

The species of Oryza rufipogon. dw was first discovered at Dongxiang, Jiangxi in 1978. It is recognized as abundant in genetic resources with the characteristics of cold and insect resistance. A total of 100.15 Gb raw data was obtained from seven pair-end libraries by Illumina Hiseq4000 platform. Subsequently, a draft assembly genome of O. rufipogon. dw was generated with a final size of 422.7 Mb with a contig N50 of 15 kb and a scaffold N50 of 296.2 bb. The assembly genome size was higher than the estimated genome size (413 Mb) based on k-mer analysis. The identified repeat sequences accounted for 40.09% of the entire genome, and 32,521 protein-coding genes with an average of 4.59 exons per gene was annotated in five databases. Phylogenetic analysis using 1460 single-copy gene, O. rufipogon. dw was close with O. rufipogon by Bayes method. The wild rice species of O. rufipogon. dw divergence was estimated at ∼0.3 million years ago (Mya) from O. rufipogon, and ∼0.6 Mya from the O. sativa. The draft genome of O. rufipogon. dw provided an essential resource for its origin and evolution study.

Complete and de novo assembly of the Leishmania braziliensis (M2904) genome

Leishmania braziliensis is the etiological agent of American mucosal leishmaniasis, one of the most severe clinical forms of leishmaniasis. Here, we report the assembly of the L. braziliensis (M2904) genome into 35 continuous chromosomes. Also, the annotation of 8395 genes is provided. The public availability of this information will contribute to a better knowledge of this pathogen and help in the search for vaccines and novel drug targets aimed to control the disease caused by this Leishmania species.

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes / 基因组蛋白质组与生物信息学报·英文版

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.

Genome Analysis Of Streptococcus Gordonii SK12

The gram-positive, mesophilic and non-motile coccus Streptococcus gordonii is an important causativeagent of infective endocarditis (IE). This pioneer species of dental plaque also causes bacteraemiain immune-supressed patients. In this study, we analysed the genome of a representative strain,Streptococcus gordonii SK12 that was originally isolated from the oral cavity. To gain a better understandingof the biology, virulence and phylogeny, of this potentially pathogenic organism, high-throughput IlluminaHiSeq technology and different bioinformatics approaches were performed. Genome assembly of SK12was performed using CLC Genomic Workbench 5.1.5 while RAST annotation revealed the key genomicfeatures. The assembled draft genome of Streptococcus gordonii SK12 consists of 27 contigs, with agenome size of 2,145,851 bp and a G+C content of 40.63%. Phylogenetic inferences have confirmedthat SK12 is closely related to the widely studied strain Streptococcus gordonii Challis. Interestingly, wepredicted 118 potential virulence genes in SK12 genome which may contribute to bacterial pathogenicityin infective endocarditis. We also discovered an intact prophage which might be recently integratedinto the SK12 genome. Examination of genes present in genomic islands revealed that this oral strainmight has potential to acquire new phenotypes/traits including strong defence system, bacitracinresistance and collateral detergent sensitivity. This detailed analysis of S. gordonii SK12 further improvesour understanding of the genetic make-up of S. gordonii as a whole and may help to elucidate howthis species is able to transition between living as an oral commensal and potentially causing the lifethreateningcondition infective endocarditis.