Comparative transcriptome analysis of Sweetpotato (Ipomoea batatas L.) and discovery of genes involved in starch biosynthesis
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Mating triggers substantial changes in gene expression and leads to subsequent physiological and behavioral modifications. However, postmating transcriptomic changes responding to mating have not yet been fully understood. Here, we carried out RNA sequencing (RNAseq) analysis in the sweet potato whitefly, Bemisia tabaci MED, to identify genes in females in response to mating. We compared mRNA expression in virgin and mated females at 24 h. As a result, 434 differentially expressed gene transcripts (DEGs) were identified between the mated and unmated groups, including 331 up- and 103 down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that many of these DEGs encode binding-related proteins and genes associated with longevity. An RT-qPCR validation study was consistent with our transcriptomic analysis (14/15). Specifically, expression of P450s (Cyp18a1 and Cyp4g68), ubiquitin-protein ligases (UBR5 and RNF123), Hsps (Hsp68 and Hsf), carboxylase (ACC-2), facilitated trehalose transporters (Tret1-2), transcription factor (phtf), and serine-protein kinase (TLK2) were significantly elevated in mated females throughout seven assay days. These combined results offer a glimpe of postmating molecular modifications to facilitate reproduction in B. tabaci females.
KEGG
RNA-Seq
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Cucumber mosaic virus (CMV) is one of the most severe viral diseases transmitted by aphids infecting Solanum crops in China, causing great losses of crop yields and income in rural communities. The tobacco cultivars NC82 and Taiyan 8 are closely related but differ in resistance to CMV. NC82 is susceptible to infection and Taiyan 8 is resistant, but the mechanisms underlying this difference in resistance are not clear. In this study, we conducted RNA sequencing to analyze changes in gene expression induced in the leaves of Taiyan 8 and NC82 upon systemic infection with CMV, compared with gene expression in the leaves of mock-inoculated plants. Leaves were sampled at one, three, eight, and 15 days after infection. In total, 3443 and 747 differentially expressed genes were identified in Taiyan 8 and NC82, respectively. Gene ontology and pathway enrichment analyses revealed that the different responses to CMV infection between cultivars were based on microtubule-based processes, pentose and glucuronate interconversions, plant–pathogen interaction, and hormone signal transduction pathways. Genes encoding pathogenesis-related proteins, disease-resistance proteins, lipoxygenase, cellulose synthase, an auxin response factor, and an ethylene receptor showed different expression patterns. The differences in gene expression following CMV infection likely contributed to the different resistance levels of these two tobacco cultivars. The comprehensive transcriptome dataset described here, which includes candidate response genes, will serve as a resource for further studies of the molecular mechanisms associated with tobacco defense responses against CMV.
Jasmonic acid
Pathogenesis-related protein
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Sexual Differentiation
Illumina dye sequencing
RNA-Seq
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Grass carp
KEGG
Hepatotoxin
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Ipomoea
Flesh
Candidate gene
Convolvulaceae
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In many animals, sperm competition and sexual conflict are thought to drive the rapid evolution of male-specific genes, especially those expressed in the testes. A potential exception occurs in the male pregnant pipefishes, where females transfer eggs to the males, eliminating testes from participating in these processes. Here, we show that testis-related genes differ dramatically in their rates of molecular evolution and expression patterns in pipefishes and seahorses (Syngnathidae) compared to other fish. Genes involved in testis or sperm function within syngnathids experience weaker selection in comparison to their orthologs in spawning and livebearing fishes. An assessment of gene turnover and expression in the testis transcriptome suggests that syngnathids have lost (or significantly reduced expression of) important classes of genes from their testis transcriptomes compared to other fish. Our results indicate that more than 50 million years of male pregnancy have removed syngnathid testes from the molecular arms race that drives the rapid evolution of male reproductive genes in other taxa.
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Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolution and morphological divergences among nematodes, we compared 48 transcriptomes of different developmental stages across eight nematode species. The transcriptomes were clustered broadly into embryo, larva, and adult stages, with the developmental plastic stages were separated from common larval stages within the larval branch. This suggests that development was the major determining factor after lifestyle changes, such as parasitism, during transcriptome evolution. Such patterns were partly accounted for by tissue-specific genes-such as those in oocytes and the hypodermis-being expressed at different proportions. Although nematodes typically have 3-5 larval stages, the transcriptomes for these stages were found to be highly correlated within each species, suggesting high similarity among larval stages across species. For the Caenorhabditis elegans-Caenorhabditis briggsae and Strongyloides stercoralis-Strongyloides venezuelensis comparisons, we found that ∼50% of genes were expressed at multiple stages, whereas half of their orthologs were also expressed in multiple but different stages. Such frequent changes in expression have resulted in concerted transcriptome evolution across adjacent stages, thus generating species-specific transcriptomes over the course of nematode evolution. Our study provides a first insight into the evolution of nematode transcriptomes beyond embryonic development.
Caenorhabditis
Developmental Biology
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Wheat is one of the most important staple crops worldwide. Fusarium head blight severely reduces wheat yield and quality. Cultivation of a novel type of cleistogamous wheat mutant, ZK001, which was created by static magnetic field treatment, is a new strategy for controlling Fusarium head blight. However, little is known about the mechanism of cleistogamy in wheat. The present study demonstrated that anthers of ZK001 were retained on the glumes at all flowering stages, whereas those of YM18 were extruded from the paleae and lemmae. There was a clear difference in the morphological characteristics of lodicules between YM18 and ZK001. Lodicule calcium and potassium contents were significantly higher in YM18 than in ZK001 from white to yellow anther stages. In Fusarium head blight resistance, the diseased kernel rate and deoxynivalenol content of ZK001 were markedly lower than those of YM18 and QM725. Comparative transcriptome analysis of YM18 and ZK001 was performed to identify regulatory mechanisms of cleistogamy. The main differentially expressed genes identified in the spikelets of YM18 and ZK001 at the green anther stage were associated with cell walls, carbohydrates, phytohormones, water channel, and ion binding, transport, and homeostasis. These differentially expressed genes may play an important role in regulating cellular homeostasis, osmotic pressure, and lodicule development. The results indicate that ZK001 lost the ability to push the lemmae and paleae apart during the flowering stage because of the thin lodicules. ZK001 was speculated to provide structural barriers for Fusarium head blight during the flowering stage. The thin lodicule of ZK001 results from low levels of soluble sugar, calcium ions, and potassium ions in the lodicules. These levels are regulated by differentially expressed genes.
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Histotylenchus gen. n. is proposed for H. histoides sp. n. (Type) from soil around roots of Napier grass in Malawi, H. historicus (Jairajpuri & Baqri) comb. n. and H. baoulensis (Netscher & Germani) comb. n. Telotylenchoides gen. n. is proposed for T. housei (Raski et al.) comb. n. (Type) and T. lobatus (Loof & Yassin) comb. n. T. lobatus is briefly described from specimens collected around roots of Citrus nobilis and Ipomoea batatas in Central Sudan. Tylenchorhynchus dissitus Colbran and Tylenchorhynchus bursifer Loof are transferred to Paratrophurus Arias whose diagnosis is emended.
Ipomoea
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The genus Ipomoea (Convolvulaceae) has a sporophytic self-incompatibility system that is under the genetic control of a single multiallelic S-locus. Self-incompatibility reactions occur on the stigma surface at an early stage after pollination, and result in the complete arrest of pollen germination such that no seed is set. In a genetic analysis of 224 plants of diploid I. trifida, collected from six native populations in Central America, we identified 49 different S-alleles that showed a linear dominance-recessive hierarchy. We also obtained a spontaneous self-compatible mutant and showed that this self-compatibility trait is due to mutation at the S-locus. To investigate the molecular basis of sporophytic self-incompatibility in Ipomoea, we analysed stigma proteins and mRNAs extracted from several different S-genotypes, using two-dimensional gel electrophoresis (2D-PAGE) and AFLP-based mRNA fingerprinting (AMF), respectively. From the 2D-PAGE analyses, S-locus-linked stigma proteins (SSPs) were identified. The amino acid sequences of these proteins have a high homology to non-metallo short-chain alcohol dehydrogenases reported in several plant species. The SSP gene was mapped at a distance of 1·2 cM from the S-locus. In the AMF analysis, we obtained a clone homologous to the Brassica SRK, which showed no genetic linkage to the S-locus of Ipomoea. This suggests that the sporophytic self-incompatibility system of Ipomoea is mediated through a different molecular mechanism to that of Brassica.
Ipomoea
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