Additional file 1: Table S1. of De novo transcriptome analyses of host-fungal interactions in oil palm (Elaeis guineensis Jacq.)

DEGs in G-treated oil palm roots compared to untreated roots. Table S2. DEGs in T-treated oil palm roots compared to untreated roots. Table S3. Fungal transcripts in oil palm transcriptomes. Table S4. List of qRT-PCR primers used for verification of DEGs. (XLSX 833 kb

Genome Analysis of the First Extensively Drug-Resistant (XDR) <i>Mycobacterium tuberculosis</i> in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance

<div><p>The outbreak of extensively drug-resistant tuberculosis (XDR-TB) has become an increasing problem in many TB-burdened countries. The underlying drug resistance mechanisms, including the genetic variation favored by selective pressure in the resistant population, are partially understood. Recently, the first case of XDR-TB was reported in Malaysia. However, the detailed genotype family and mechanisms of the formation of multiple drugs resistance are unknown. We sequenced the whole genome of the UM 1072388579 strain with a 2-kb insert-size library and combined with that from previously sequenced 500-bp-insert paired-end reads to produce an improved sequence with maximal sequencing coverage across the genome. <i>In silico</i> spoligotyping and phylogenetic analyses demonstrated that UM 1072388579 strain belongs to an ancestral-like, non-Beijing clade of East Asia lineage. This is supported by the presence of a number of lineage-specific markers, including <i>fadD28</i>, <i>embA</i>, <i>nuoD</i> and <i>pks7</i>. Polymorphism analysis showed that the drug-susceptibility profile is correlated with the pattern of resistance mutations. Mutations in drug-efflux pumps and the cell wall biogenesis pathway such as <i>mmpL</i>, <i>pks</i> and <i>fadD</i> genes may play an important role in survival and adaptation of this strain to its surrounding environment. In this work, fifty-seven putative promoter SNPs were identified. Among them, we identified a novel SNP located at -4 T allele of <i>TetR/acrR</i> promoter as an informative marker to recognize strains of East Asian lineage. Our work indicates that the UM 1072388579 harbors both classical and uncommon SNPs that allow it to escape from inhibition by many antibiotics. This study provides a strong foundation to dissect the biology and underlying resistance mechanisms of the first reported XDR <i>M</i>. <i>tuberculosis</i> in Malaysia.</p></div

Comparative phylogenetic analysis of UM 1072388579 strain along with 50 previously published genomes.

<p>Phylogenetic tree was constructed based on overall SNPs extracted from genome sequences. The numbers on branches indicate Bayesian posterior probability values. <i>M</i>. <i>tuberculosis</i> isolates are clustered into respective genotype families based on spoligotyping-defined <i>M</i>. <i>tuberculosis</i> clade and lineage. The tree is rooted with <i>M</i>. <i>Bovis</i> BCG strain ATCC 35743 as outgroup.</p

The distribution of individual genic SNPs into various functional groups based on COGs analysis.

<p>C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; O: Posttranslational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport and V: Defense mechanisms.</p

Lineage-specific SNPs shared between the UM 1072388579 and FJ05194.

<p>Lineage-specific SNPs shared between the UM 1072388579 and FJ05194.</p

Comparison of short-insert paired-end (500-bp) and mate pair combined sequencing data.

<p>Comparison of short-insert paired-end (500-bp) and mate pair combined sequencing data.</p

Polymorphism of <i>TetR</i>/<i>acrR</i> promoter in <i>M</i>. <i>tuberculosis</i> strains.

<p>^a LAM: Latin American Mediterranean; EAI: East African Indian</p><p>Polymorphism of <i>TetR</i>/<i>acrR</i> promoter in <i>M</i>. <i>tuberculosis</i> strains.</p

Colonial characteristic and microscopic morphology of <i>C</i>. <i>bantiana</i>.

<p>The (A) surface and (B) close-up view of the colonial morphology of <i>C</i>. <i>bantiana</i> after being cultured for seven days. Light micrograph showing (C) smooth walled, pale olivaceous, ellipsoidal to spindle-shaped conidia arranged in long, strongly coherent chains (400× magnification, bars 20 μm).</p

CAZyme class annotation distribution of <i>C</i>. <i>bantiana</i> UM 956 genome.

<p>(A) Comparison of the distribution of CAZyme catalytic domains between <i>C</i>. <i>bantiana</i> and fungi from various lifestyles. (B) Comparison of the plant cell wall degrading potential from CAZyme analysis between <i>C</i>. <i>bantiana</i> and fungi from various lifestyles. AA: auxiliary activities; CBM: carbohydrate binding module; CE: carbohydrate esterase; GH: glycoside hydrolase; GT: glycosyltransferase and PL, polysaccharide lyase.</p

Genome content of <i>C</i>. <i>bantiana</i> UM 956 and other previously sequenced fungal genomes.

<p>Genome content of <i>C</i>. <i>bantiana</i> UM 956 and other previously sequenced fungal genomes.</p