Article of the Year 2020
Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing DataRead the full article
International Journal of Genomics publishes papers in all areas of genome-scale analysis, including bioinformatics, clinical and disease genomics, epigenomics, evolutionary and functional genomics, genome engineering, and synthetic genomics.
Chief Editor, Professor Nislow, is currently based at the University of British Columbia as a Tier 1 Canada Research Chair in Translational Genomics, with a background in yeast genetics and genomics.
Latest ArticlesMore articles
Genome-Wide Association Studies for Striga asiatica Resistance in Tropical Maize
Striga asiatica L. is a parasitic weed in cereal crops including maize leading to tremendous yield losses up to 100% under severe infestation. The available S. asiatica control methods include cultural control options such as uprooting and burning the Striga plants before they flower, field sanitation, crop rotation, intercropping, organic matter usage, improved fallows, and application of herbicides. Resource limitation among smallholder farmers renders almost all of the control methods impossible. Development and use of Striga resistant genotypes are seen as the most feasible management option. Marker identification formulates tools that are faster, cheaper, and easier to utilise in breeding for S. asiatica resistance which has low heritability. The objective of this study was to identify single nucleotide polymorphism (SNP) markers for Striga resistance using the genome-wide association study (GWAS). Genotyping by sequencing was done on tropical maize inbred lines followed by their evaluation for Striga resistance. Analysis of variance showed significant () variation among evaluated genotypes for Striga resistance traits such as germination distance, germination percentage, haustoria root attachments, total Striga plants emerged, total biomass, and growth rate. There were also significant differences () for cobs, leaves, stems, and roots weight. The broad sense heritability was fairly high (up to 61%) for most traits. The means for derived traits on stress tolerance indices were subjected to a -test, and significant differences () were found for leaves, stem, roots, shoots, and total biomass. The Manhattan plots from GWAS showed the presence of three SNP markers on chromosome numbers 5, 6, and 7 for total Striga plants emerged. The identified markers for resistance to S. asiatica should be validated and utilised to breed for Striga resistance in tropical maize.
Analysis of lncRNA, miRNA, and mRNA Expression Profiling in Type I IFN and Type II IFN Overexpressed in Porcine Alveolar Macrophages
Current data is scarce regarding the function of noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) in the interferon- (IFN-) mediated immune response. This is a comprehensive study that analyzes the lncRNA and miRNA expression profiles of the type I IFN and type II IFN in porcine alveolar macrophages using RNA sequencing. There was a total of 152 overexpressed differentially expressed (DE) lncRNAs and 21 DE miRNAs across type I IFN and type II IFN in porcine alveolar macrophages. Subsequent lncRNA-miRNA-mRNA network construction revealed the involvement of 36 DE lncRNAs and 12 DE miRNAs. LncRNAs such as the XLOC_211306, XLOC_100516, XLOC_00695, XLOC_149196, and XLOC_014459 were expressed at a higher degree in the type I IFN group, while XLOC_222640, XLOC_047290, XLOC_147777, XLOC_162298, XLOC_220210, and XLOC_165237 were expressed at a higher degree in the type II IFN group. These lncRNAs were found to act as “sponges” for miRNAs such as miR-34a, miR-328, miR-885-3p, miR-149, miR-30c-3p, miR-30b-5p, miR-708-5p, miR-193a-5p, miR-365-5p, and miR-7. Their target genes FADS2, RPS6KA1, PIM1, and NOD1 were found to be associated with several immune-related signaling pathways including the NOD-like receptor, Jak-STAT, mTOR, and PPAR signaling pathways. These experiments provide a comprehensive profile of overexpressed noncoding RNAs in porcine alveolar macrophages, providing new insights regarding the IFN-mediated immune response.
Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment
Blue light is an important signal that regulates the flowering of strawberry plants. To reveal the mechanism of early flowering under blue light treatment at the transcriptional regulation level, seedlings of cultivated strawberry (Fragaria × ananassa Duch.) “Benihoppe” were subjected to a white light treatment (WL) and blue light treatment (BL) until their flowering. To detect the expression patterns of genes in response to BL, a transcriptome analysis was performed based on RNA-Seq. The results identified a total of 6875 differentially expressed genes (DEGs) that responded to BL, consisting of 3138 (45.64%) downregulated ones and 3737 (54.36%) upregulated ones. These DEGs were significantly enriched into 98 GO terms and 71 KEGG pathways based on gene function annotation. Among the DEGs, the expression levels of genes that might participate in light signaling (PhyB, PIFs, and HY5) and circadian rhythm (FKF1, CCA1, LHY, and CO) in plants were altered under BL. The BBX transcription factors which responded to BL were also identified. The result showed that the FaBBX29, one of strawberry’s BBX family genes, may play an important role in flowering regulation. Our results provide a timely, comprehensive view and a reliable reference data resource for further study of flowering regulation under different light qualities.
A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
Identification of Isoflavonoid Biosynthesis-Related R2R3-MYB Transcription Factors in Callerya speciosa (Champ. ex Benth.) Schot Using Transcriptome-Based Gene Coexpression Analysis
The R2R3-MYB family is one of the largest plant transcription factor (TF) families playing vital roles in defense, plant growth, and secondary metabolism biosynthesis. Although this gene family has been studied in many species, isoflavonoid biosynthesis-related R2R3-MYB TFs in Callerya speciosa (Champ. ex Benth.) Schot, a traditional Chinese medicinal herb, are poorly understood. Here, a total of 101 R2R3-MYB TFs were identified from C. speciosa transcriptome dataset. 25 clades divided into five functional groups were clustered based on the sequence similarity and phylogenetic tree. Conserved motifs and domain distribution, expression patterns, and coexpression networks were also employed to identify the potential R2R3-MYB TFs in the regulation of isoflavonoid biosynthesis. In silico evaluation showed that the deduced R2R3-CsMYB proteins contain highly conserved R2R3 repeat domain at the N-terminal region, that is the signature motif of R2R3-type MYB TFs. Eight potential TFs (CsMYB17, CsMYB36, CsMYB41, CsMYB44, CsMYB45, CsMYB46, CsMYB72, and CsMYB81) had high degrees of coexpression with four key isoflavonoid biosynthetic genes (CsIFS, CsCHS7, CsHID-1, and CsCHI3), in which CsMYB36 as a potential regulator possessed the highest degree. HPLC analysis showed that formononetin and maackiain contents were significantly increased during the development of tuberous roots, which might be controlled by both related R2R3-CsMYBs and structural genes involved in the isoflavonoid biosynthesis pathway. The transcriptome data were further validated by reverse transcription real-time PCR (RT-qPCR) analysis, and similar expression profiles between TFs and key structural genes were identified. This study was the first step toward the understanding of the R2R3-MYB TFs regulating isoflavonoid biosynthesis in C. speciosa. The results will provide information for further functional analysis and quality improvement through genetic manipulation of these potential R2R3-CsMYB genes in C. speciosa.
The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea
Chenopodium album sensu stricto belonging to C. album aggregate is an annual cosmopolitan weed displaying the diversity of morphologies. We completed the six chloroplast genomes of C. album s. str. collected in Korea to understand the relationship between the diversity of chloroplast genomes and their morphological variations. All six C. album chloroplast genomes have a typical quadripartite structure with length ranging from 151,906 bp to 152,199 bp, similar to the previously sequenced C. album chloroplast genome (NC_034950). In total, 56 single nucleotide polymorphisms (SNPs) and 26 insertion and deletion (INDEL) regions (308 bp in total) were identified from the six chloroplast genomes, presenting a low level of intraspecific variations in comparison to the other angiosperm species. 376 normal simple sequence repeats were identified in all seven C. album chloroplast genomes. The phylogenetic analysis based on all available complete Amaranthaceae chloroplast genomes presents phylogenetic positions of six C. album samples as well as correlation with one of C. album morphological features. Our results provide the way to investigate intraspecific features of C. album chloroplast genomes and also the insights of understanding various intraspecific characteristics including morphological features.