@article {499, title = {Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree. [Mass spectrometry - Metabolomics]}, journal = {PeerJ}, volume = {3}, year = {2015}, month = {2015}, pages = {e1066}, abstract = {

Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC-600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70\% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5\% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62\% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.

}, doi = {10.7717/peerj.1066}, author = {Kuravadi, Nagesh A and Yenagi, Vijay and Rangiah, Kannan and Mahesh, H B and Rajamani, Anantharamanan and Shirke, Meghana D and Russiachand, Heikham and Loganathan, Ramya Malarini and Shankara Lingu, Chandana and Siddappa, Shilpa and Ramamurthy, Aishwarya and Sathyanarayana, B N and Gowda, Malali} } @article {495, title = {Draft genome sequence of Staphylococcus aureus 118 (ST772), a major disease clone from India. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jul}, pages = {3727-8}, abstract = {

We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying staphylococcal cassette chromosome mec (SCCmec) type V from a pyomyositis patient. Our de novo short read assembly is \~{}2.8 Mb and encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes similar to those of ϕ7247PVL and novel lysogenic genes at the N termini.

}, keywords = {Cloning, Molecular, Genome, Bacterial, India, Molecular Sequence Data, Pyomyositis, Staphylococcal Infections, Staphylococcus aureus}, issn = {1098-5530}, doi = {10.1128/JB.00480-12}, author = {Prabhakara, Sushma and Khedkar, Supriya and Loganathan, Ramya Malarini and Chandana, S and Gowda, Malali and Arakere, Gayathri and Seshasayee, Aswin Sai Narain} } @article {494, title = {Draft genome sequence of Staphylococcus aureus ST672, an emerging disease clone from India. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Dec}, pages = {6946-7}, abstract = {

We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA) strain ST672, an emerging disease clone in India, from a septicemia patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs). The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune evasion cluster appear to be different from those of strain ST772 on preliminary examination.

}, keywords = {Bacteremia, Bacterial Proteins, Bacterial Typing Techniques, Base Sequence, DNA, Bacterial, Genome, Bacterial, Humans, Methicillin-Resistant Staphylococcus aureus, Molecular Sequence Data, Open Reading Frames, Penicillin-Binding Proteins, Sequence Analysis, DNA, Staphylococcal Infections}, issn = {1098-5530}, doi = {10.1128/JB.01868-12}, author = {Khedkar, Supriya and Prabhakara, Sushma and Loganathan, Ramya Malarini and S, Chandana and Gowda, Malali and Arakere, Gayathri and Seshasayee, Aswin Sai Narain} }