Identifying the molecular basis of reproductive isolation among diverging lineages represents an essential step toward understanding speciation in natural populations. Postzygotic barriers can lead to hybrid breakdown, a syndrome that has been documented in several systems, potentially involving the reactivation of transposable elements. In northeastern North America, two lake whitefish lineages have repeatedly colonized postglacial lakes ~12,000 years ago, and a dwarf limnetic species has evolved multiple times from the normal benthic species. Reproductive isolation is incomplete between them; viable hybrids can be generated in the laboratory but significant mortality occurs and is associated with a malformed phenotype in backcross embryos, thus revealing a hybrid breakdown syndrome. By means of RNA-seq analyses, the objective of this study was to determine which genes were misregulated in hybrids and rigorously test the hypothesis of transposable element reactivation. We compared the transcriptomic landscape in pure embryos, F1-hybrids, and healthy and malformed backcrosses at the late embryonic stage. Extensive expression differences consistent with previously documented adaptive divergence between pure normal and dwarf embryos were identified for the first time. Pronounced transcriptome-wide deregulation in malformed backcrosses was observed, with over 15% of transcripts differentially expressed in all comparisons, compared with 1.5% between pure parental forms. Convincing evidence of transposable elements and noncoding transcripts reactivation in malformed backcrosses is presented. We propose that hybrid breakdown likely results from extensive genomic incompatibilities, plausibly encompassing transposable elements. Combined with previous studies, these results reveal synergy amon gm any reproductive barriers, thus maintaining divergence between these two young whitefish species.

/pdf/rna-seq-reveals-transcriptomic-shock-involving-transposable-1wbwcyezpz.pdf

RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species

Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts.

Huanglongbing (HLB) is the most destructive disease that affects citrus worldwide. The disease has been associated with Candidatus Liberibacter. HLB diseased citrus plants develop a multitude of symptoms including zinc and copper deficiencies, blotchy mottle, corky veins, stunting, and twig dieback. Ca. L. asiaticus infection also seriously affects the roots. Previous study focused on gene expression of leaves and fruit to Ca. L. asiaticus infection. In this study, we compared the gene expression levels of stems and roots of healthy plants with those in Ca. L. asiaticus infected plants using microarrays. Affymetrix microarray analysis showed a total of 988 genes were significantly altered in expression, of which 885 were in the stems, and 111 in the roots. Of these, 551 and 56 were up-regulated, while 334 and 55 were down-regulated in the stem and root samples of HLB diseased trees compared to healthy plants, respectively. Dramatic differences in the transcriptional responses were observed between citrus stems and roots to Ca. L. asiaticus infection, with only 8 genes affected in both the roots and stems. The affected genes are involved in diverse cellular functions, including carbohydrate metabolism, cell wall biogenesis, biotic and abiotic stress responses, signaling and transcriptional factors, transportation, cell organization, protein modification and degradation, development, hormone signaling, metal handling, and redox. Microscopy analysis showed the depletion of starch in the roots of the infected plants but not in healthy plants. Collapse and thickening of cell walls were observed in HLB affected roots, but not as severe as in the stems. This study provides insight into the host response of the stems and roots to Ca. L. asiaticus infection.

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0073742&type=printable

Transcriptional and microscopic analyses of citrus stem and root responses to Candidatus Liberibacter asiaticus infection.

Understanding the molecular mechanisms underlying Alzheimer’s disease (AD) is necessary for the diagnosis and treatment of this neurodegenerative disorder. It is therefore important to detect the most important genes and miRNAs, which are associated with molecular events, and studying their interactions for recognition of AD mechanisms. Here we focus on the genes and miRNAs expression profile, which we have detected the miRNA target genes involved in AD. These are the most quintessential to find the most important miRNA, to target genes and their important pathways. A total of 179 differentially expressed miRNAs (DEmiRs) and 1404 differentially expressed genes (DEGs) were obtained from a comprehensive meta-analysis. Also, regions specific genes with their molecular function in AD have been demonstrated. We then focused on miRNAs which regulated most genes in AD, alongside we analyzed their pathways. The miRNA-30a-5p and miRNA-335 elicited a major function in AD after analyzing the regulatory network, we showed they were the most regulatory miRNAs in the AD. In conclusion, we demonstrated the most important genes, miRNAs, miRNA-mRNA interactions and their related pathways in AD using Bioinformatics methods. Accordingly, our defined genes and miRNAs could be used for future molecular studies in the context of AD.

/pdf/analysis-of-microrna-and-gene-expression-profiles-in-12uv77emrx.pdf

Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach.

New insights into the expression profile and function of micro-ribonucleic acid in human spermatozoa

Background: RNA-seq and microarray are the two popular methods employed for genome-wide transcriptome profiling. Current comparison studies have shown that transcriptome quantified by these two methods correlated well. However, none of them have addressed if they complement each other, considering the strengths and the limitations inherent with them. The pivotal requirement to address this question is the knowledge of a well known data set. In this regard, HrpX regulome from pathogenic bacteria serves as an ideal choice as the target genes of HrpX transcription factor are well studied due to their central role in pathogenicity. Results: We compared the performance of RNA-seq and microarray in their ability to detect known HrpX target genes by profiling the transcriptome from the wild-type and the hrpX mutant strains of γ-Proteobacterium Xanthomonas citri subsp. citri. Our comparative analysis indicated that gene expression levels quantified by RNA-seq and microarray well-correlated both at absolute as well as relative levels (Spearman correlation-coefficient, rs > 0.76). Further, the expression levels quantified by RNA-seq and microarray for the significantly differentially expressed genes (DEGs) also well-correlated with qRT-PCR based quantification (rs= 0.58 to 0.94). Finally, in addition to the 55 newly identified DEGs, 72% of the already known HrpX target genes were detected by both RNA-seq and microarray, while, the remaining 28% could only be detected by either one of the methods. Conclusions: This study has significantly advanced our understanding of the regulome of the critical transcriptional factor HrpX. RNA-seq and microarray together provide a more comprehensive picture of HrpX regulome by uniquely identifying new DEGs. Our study demonstrated that RNA-seq and microarray complement each other in transcriptome profiling.

/pdf/rna-seq-and-microarray-complement-each-other-in-1h5ok9byrm.pdf

RNA-seq and microarray complement each other in transcriptome profiling

Background: Huanglongbing (HLB) or citrus greening is a devastating disease of citrus. The gram-negative bacterium Candidatus Liberibacter asiaticus (Las) belonging to the α-proteobacteria is responsible for HLB in North America as well as in Asia. Currently, there is no cure for this disease. Early detection and quarantine of Las-infected trees are important management strategies used to prevent HLB from invading HLB-free citrus producing regions. Quantitative real-time PCR (qRT-PCR) based molecular diagnostic assays have been routinely used in the detection and diagnosis of Las. The oligonucleotide primer pairs based on conserved genes or regions, which include 16S rDNA and the β-operon, have been widely employed in the detection of Las by qRT-PCR. The availability of whole genome sequence of Las now allows the design of primers beyond the conserved regions for the detection of Las explicitly. Results: We took a complimentary approach by systematically screening the genes in a genome-wide fashion, to identify the unique signatures that are only present in Las by an exhaustive sequence based similarity search against the nucleotide sequence database. Our search resulted in 34 probable unique signatures. Furthermore, by designing the primer pair specific to the identified signatures, we showed that most of our primer sets are able to detect Las from the infected plant and psyllid materials collected from the USA and China by qRT-PCR. Overall, 18 primer pairs of the 34 are found to be highly specific to Las with no cross reactivity to the closely related species Ca. L. americanus (Lam) and Ca. L. africanus (Laf). Conclusions: We have designed qRT-PCR primers based on Las specific genes. Among them, 18 are suitable for the detection of Las from Las-infected plant and psyllid samples. The repertoire of primers that we have developed and characterized in this study enhanced the qRT-PCR based molecular diagnosis of HLB.

/pdf/repertoire-of-novel-sequence-signatures-for-the-detection-of-pqkk7azwvx.pdf

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

Citrus canker is a devastating disease that affects most commercial citrus varieties. Asiatic type canker is the most widespread and destructive form of citrus canker that is caused by Xanthomonas citri subsp. citri (XccA). Multiple variants of XccA including XccAw and XccA* have been reported. Citrus canker is also known to be caused by X. fuscans subsp. aurantifolii (Xau) B and C strains. XccAw, XccA*, XauB, and XauC, unlike XccA, are limited in host range. The complete genome sequence of XccA strain 306 was sequenced in 2002 using Sanger sequencing. With advances in sequencing technologies, other strains associated with citrus canker were also sequenced recently. Currently, draft sequences of XauB and XauC are available. The complete genome of XccAw strain 12879 has been sequenced, whereas XccA* strain 270 is currently being sequenced. Furthermore, the complete genome of another closely related citrus pathogen, X. axonopodis pv. citrumelo strain F1 causing citrus bacterial spot, has also been sequenced. Multilocus sequence phylogenetic analysis of XccA and other xanthomonads indicates that citrus canker pathogens XccA, XccAw, XauB, and XauC form a closely related group. In this review, the following topics were included: an introduction about citrus canker including the origin of citrus canker, its current distribution, economic losses, infection cycle; current understanding of the virulence mechanisms of XccA; genome information of XccA and related species; genome-enabled understanding of X. citri virulence and host specificity; and transcriptomics of X. citri. The advent of next generation sequencing will dramatically promote the genomic study of X. citri and investigation of the virulence mechanisms of X. citri to design innovative strategies to control citrus canker and other bacterial diseases.

Genomics of Xanthomonas citri and Related Species

Understanding the design principles of bacterial pathogenesis is central to combat several infectious diseases in humans, animals and plants [1]. This includes identification of common bacterial pathogenicity mechanisms employed by a wide variety of bacteria, which infect diverse hosts [2]. Recent studies have identified one such common virulence mechanism: Type III Secretion System (T3SS), employed by several animal and plant pathogenic bacteria [3-6]. Classically, the components of T3SS physically assemble to form a complex needle-like structure that enables the bacteria to inject virulence factors directly into their host cell’s cytoplasm. These factors in turn specifically interfere with their host cellular processes to elicit pathogenicity [7,8]. However, despite the common injection mechanism, each bacterial species injects unique set of species-specific virulence factors that define the host specificity [3,4].

/pdf/hrpx-transcription-factor-a-potential-common-target-for-y52o2d4q4q.pdf

HrpX Transcription Factor - A Potential Common Target for Several BacterialDiseases from a Synthetic Biology Perspective

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RNA-seq and microarray complement each other in transcriptome profiling

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

Genomics of Xanthomonas citri and Related Species

HrpX Transcription Factor - A Potential Common Target for Several BacterialDiseases from a Synthetic Biology Perspective