Exome sequencing identifies SLC26A4, GJB2, SCARB2 and DUOX2 mutations in 2 siblings with Pendred syndrome in a Malaysian family

List of PCR primers used. (XLSX 9 kb

Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm

© 2020, The Author(s). Evaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted from E. oleifera × E. guineensis interspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids

First Draft Genome Assembly of the Malaysian Stingless Bee, Heterotrigona itama (Apidae, Meliponinae)

The Malaysian stingless bee industry is hugely dependent on wild colonies. Nevertheless, the availability of new queens to establish new colonies is insufficient to meet the growing demand for hives in the industry. Heterotrigona itama is primarily utilized for honey production in the region and the major source of stingless bee colonies comes from the wild. To propagate new colonies domestically, a fundamental understanding of the biology of queen development, especially from the genomics aspect, is necessary. The whole genome was sequenced using a paired-end 150 strategy on the Illumina HiSeq X platform. The shotgun sequencing generated approximately 89 million raw pair-end reads with a total output of 13.37 Gb and a GC content of 37.31%. The genome size of the species was estimated to be approximately 272 Mb. Phylogenetic analysis showed H. itama are much more closely related to the bumble bee (Bombus spp.) than they are to the modern honey bee (Apis spp.). The genome data provided here are expected to contribute to a better understanding of the genetic aspect of queen differentiation as well as of important molecular pathways which are crucial for stingless bee biology, management and conservation

Additional file 3: Table S2. of Exome sequencing identifies SLC26A4, GJB2, SCARB2 and DUOX2 mutations in 2 siblings with Pendred syndrome in a Malaysian family

List of non-synonymous heterozygous mutations inherited from mother. (XLSX 91 kb

Additional file 4: Table S3. of Exome sequencing identifies SLC26A4, GJB2, SCARB2 and DUOX2 mutations in 2 siblings with Pendred syndrome in a Malaysian family

List of other possible PDS causal mutations which uniquely inherited by the eldest sister. (XLSX 11 kb

Distributed under Creative Commons CC-BY 4.0 Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola

ABSTRACT Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011

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

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

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