The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Pharmaceutical resource discovery from traditional medicinal plants: Pharmacophylogeny and pharmacophylogenomics

Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.

https://www.mdpi.com/2223-7747/8/11/476/pdf

Chloroplast Genome Sequence of Artemisia scoparia : Comparative Analyses and Screening of Mutational Hotspots

https://link.springer.com/content/pdf/10.1186/s43141-020-00057-3.pdf

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica.

Plants of the Agropyron genus are important pasture resources, and they also play important roles in the ecological restoration. Chloroplast genomes are inherited from maternal parents, and they are important for studying species taxonomy and evolution. In this study, we sequenced the complete chloroplast genomes of five typical species of the Agropyron genus (eg., A. cristatum × A. desertorum Fisch. Schult, A. desertorum, A. desertorum Fisch. Schult. cv. Nordan, A. michnoi Roshev, and A. mongolicum Keng) using the Illumina NovaSeq platform. We found that these five chloroplast genomes exhibit a typical quadripartite structure with a conserved genome arrangement and structure. Their chloroplast genomes contain the large single-copy regions (LSC, 79,613 bp-79,634 bp), the small single-copy regions (SSC, 12,760 bp-12,768 bp), and the inverted repeat regions (IR, 43,060 bp-43,090 bp). Each of the five chloroplast genomes contains 129 genes, including 38 tRNA genes, eight rRNA genes, and 83 protein-coding genes. Among them, the genes trnG-GCC, matK, petL, ccsA, and rpl32 showed significant nucleotide diversity in these five species, and they may be used as molecular markers in taxonomic studies. Phylogenetic analysis showed that A. mongolicum is closely related to A. michnoi, while others have a closer genetic relationship with the Triticum genus.

Analysis of Chloroplast Genomes Provides Insights Into the Evolution of Agropyron

Commiphora gileadensis and C. foliacea (family Burseraceae) are pantropical in nature and known for producing fragrant resin (myrrh). Both the tree species are economically and medicinally important however, least genomic understanding is available for this genus. Herein, we report the complete chloroplast genome sequences of C. gileadensis and C. foliacea and comparative analysis with related species (C. wightii and Boswellia sacra). A modified chloroplast DNA extraction method was adopted, followed with next generation sequencing, detailed bioinformatics and PCR analyses. The results revealed that the cp genome sizes of C. gileadensis and C. foliacea, are 160,268 and 160,249 bp, respectively, with classic quadripartite structures that comprises of inverted repeat’s pair. Overall, the organization of these cp genomes, GC contents, gene order, and codon usage were comparable to other cp genomes in angiosperm. Approximately, 198 and 175 perfect simple sequence repeats were detected in C. gileadensis and C. foliacea genomes, respectively. Similarly, 30 and 25 palindromic, 15 and 25 forward, and 20 and 25 tandem repeats were determined in both the cp genomes, respectively. Comparison of these complete cp genomes with C. wightii and B. sacra revealed significant sequence resemblance and comparatively highest deviation in intergenic spacers. The phylo-genomic comparison showed that C. gileadensis and C. foliacea form a single clade with previously reported C. wightii and B. sacra from family Burseraceae. Current study reports for the first time the cp genomics of species from Commiphora, which could be helpful in understanding genetic diversity and phylogeny of this myrrh producing species.

/pdf/first-complete-chloroplast-genomics-and-comparative-1kzauvsm94.pdf

First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees.

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First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees.