Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

BACKGROUND: Transposons, i.e. transposable elements (TEs), are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue of whether transposons mediate genomic changes in environment-adaptation genes, we scanned two alleles per each of the six xenobiotic-metabolizing Helicoverpa zea cytochrome P450 loci, including CYP6B8, CYP6B27, CYP321A1, CYP321A2, CYP9A12v3 and CYP9A14, for the presence of transposon insertions by genome walking and sequence analysis. We also scanned thirteen Drosophila melanogaster P450s genes for TE insertions by in silico mapping and literature search. RESULTS: Twelve novel transposons, including LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), MITEs (miniature inverted-repeat transposable elements), one full-length transib-like transposon, and one full-length Tcl-like DNA transpson, are identified from the alleles of the six H. zea P450 genes. The twelve transposons are inserted into the 5'flanking region, 3'flanking region, exon, or intron of the six environment-adaptation P450 genes. In D. melanogaster, seven out of the eight Drosophila P450s (CYP4E2, CYP6A2, CYP6A8, CYP6A9, CYP6G1, CYP6W1, CYP12A4, CYP12D1) implicated in insecticide resistance are associated with a variety of transposons. By contrast, all the five Drosophila P450s (CYP302A1, CYP306A1, CYP307A1, CYP314A1 and CYP315A1) involved in ecdysone biosynthesis and developmental regulation are free of TE insertions. CONCLUSION: These results indicate that TEs are selectively retained within or in close proximity to xenobiotic-metabolizing P450 genes

Characterization of Three Novel SINE Families with Unusual Features in Helicoverpa armigera

Although more than 120 families of short interspersed nuclear elements (SINEs) have been isolated from the eukaryotic genomes, little is known about SINEs in insects. Here, we characterize three novel SINEs from the cotton bollworm, Helicoverpa armigera. Two of them, HaSE1 and HaSE2, share similar 5′ -structure including a tRNA-related region immediately followed by conserved central domain. The 3′ -tail of HaSE1 is significantly similar to that of one LINE retrotransposon element, HaRTE1.1, in H. armigera genome. The 3′ -region of HaSE2 showed high identity with one mariner-like element in H. armigera. The third family, termed HaSE3, is a 5S rRNA-derived SINE and shares both body part and 3′-tail with HaSE1, thus may represent the first example of a chimera generated by recombination between 5S rRNA and tRNA-derived SINE in insect species. Further database searches revealed the presence of these SINEs in several other related insect species, but not in the silkworm, Bombyx mori, indicating a relatively narrow distribution of these SINEs in Lepidopterans. Apart from above, we found a copy of HaSE2 in the GenBank EST entry for the cotton aphid, Aphis gossypii, suggesting the occurrence of horizontal transfer

Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat

Transcriptome details for three transgenic lines with the most significantly reduced YPC and non-transformed controls. (DOCX 18 kb

Differential stepwise evolution of SARS coronavirus functional proteins in different host species

<p>Abstract</p> <p>Background</p> <p>SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known.</p> <p>Results</p> <p>We employed several methods to investigate selective pressure among different SARS-CoV groups representing different epidemic periods and hosts. Our results suggest that most functional proteins of SARS-CoV have experienced a stepwise adaptive evolutionary pathway. Similar to previous studies, the spike protein underwent strong positive selection in the early and middle phases, and became stabilized in the late phase. In addition, the replicase experienced positive selection only in human patients, whereas assembly proteins experienced positive selection mainly in the middle and late phases. No positive selection was found in any proteins of bat SARS-like-CoV. Furthermore, specific amino acid sites that may be the targets of positive selection in each group are identified.</p> <p>Conclusion</p> <p>This extensive evolutionary analysis revealed the stepwise evolution of different functional proteins of SARS-CoVs at different epidemic stages and different hosts. These results support the hypothesis that SARS-CoV originated from bats and that the spill over into civets and humans were more recent events.</p

Transposon insertion causes cadherin mis-splicing and confers resistance to Bt cotton in pink bollworm from China

Transgenic crops producing insecticidal proteins from Bacillus thuringiensis (Bt) are cultivated extensively, but rapid evolution of resistance by pests reduces their efficacy. We report a 3,370-bp insertion in a cadherin gene associated with resistance to Bt toxin Cry1Ac in the pink bollworm (Pectinophora gossypiella), a devastating global cotton pest. We found the allele (r15) harboring this insertion in a field population from China. The insertion is a miniature inverted repeat transposable element (MITE) that contains two additional transposons and produces two mis-spliced transcript variants (r15A and r15B). A strain homozygous for r15 had 290-fold resistance to Cry1Ac, little or no cross-resistance to Cry2Ab, and completed its life cycle on Bt cotton producing Cry1Ac. Inheritance of resistance was recessive and tightly linked with r15. For transformed insect cells, susceptibility to Cry1Ac was greater for cells producing the wild-type cadherin than for cells producing the r15 mutant proteins. Recombinant cadherin protein occurred on the cell surface in cells transformed with the wildtype or r15A sequences, but not in cells transformed with the r15B sequence. The similar resistance of pink bollworm to Cry1Ac in laboratory-and field-selected insects from China, India and the U.S. provides a basis for developing international resistance management practices.China's Key Project for Breeding Genetically Modified Organisms [2016ZX08012-004]; Agriculture and Food Research Initiative Competitive Grant from the USDA National Institute of Food and Agriculture [2018-67013-27821]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Comparison of low molecular weight glutenin subunits identified by SDS-PAGE, 2-DE, MALDI-TOF-MS and PCR in common wheat

Low-molecular-weight glutenin subunits (LMW-GS) play a crucial role in determining end-use quality of common wheat by influencing the viscoelastic properties of dough. Four different methods - sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis (2-DE, IEF × SDS-PAGE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and polymerase chain reaction (PCR), were used to characterize the LMW-GS composition in 103 cultivars from 12 countries

FERONIA interacts with ABI2-type phosphatases to facilitate signaling cross-talk between abscisic acid and RALF peptide in Arabidopsis

[EN] Receptor-like kinase FERONIA (FER) plays a crucial role in plant response to small molecule hormones [e.g., auxin and abscisic acid (ABA)] and peptide signals [e.g., rapid alkalinization factor (RALF)]. It remains unknown how FER integrates these different signaling events in the control of cell growth and stress responses. Under stress conditions, increased levels of ABA will inhibit cell elongation in the roots. In our previous work, we have shown that FER, through activation of the guanine nucleotide exchange factor 1 (GEF1)/4/10-Rho of Plant 11 (ROP11) pathway, enhances the activity of the phosphatase ABA Insensitive 2 (ABI2), a negative regulator of ABA signaling, thereby inhibiting ABA response. In this study, we found that both RALF and ABA activated FER by increasing the phosphorylation level of FER. The FER loss-of-function mutant displayed strong hypersensitivity to both ABA and abiotic stresses such as salt and cold conditions, indicating that FER plays a key role in ABA and stress responses. We further showed that ABI2 directly interacted with and dephosphorylated FER, leading to inhibition of FER activity. Several other ABI2-like phosphatases also function in this pathway, and ABA-dependent FER activation required PYRABACTIN RESISTANCE (PYR)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR)-A-type protein phosphatase type 2C (PP2CA) modules. Furthermore, suppression of RALF1 gene expression, similar to disruption of the FER gene, rendered plants hypersensitive to ABA. These results formulated a mechanism for ABA activation of FER and for cross-talk between ABA and peptide hormone RALF in the control of plant growth and responses to stress signals.We thank Dr. Alice Cheung, Dr. Daniel Moura, Grossniklaus Ueli, Dr. Jigang Li, and Dr. Nieng Yan for providing plant, ABI1 antibody, or plasmid materials, and Dr. Legong Li for assistance in laser confocal microscopy. This work was supported by grants from National Natural Science Foundation of China (NSFC-31400232, 31571444), the State Key Laboratory of Molecular Developmental Biology (2015-MDB-KF-12), the Fundamental Research Funds for the Central Universities of China, and a grant from the National Science Foundation.Chen, J.; Yu, F.; Liu, Y.; Du, C.; Li, X.; Zhu, S.; Wang, X.... (2016). FERONIA interacts with ABI2-type phosphatases to facilitate signaling cross-talk between abscisic acid and RALF peptide in Arabidopsis. Proceedings of the National Academy of Sciences. 113(37):E5519-E5527. https://doi.org/10.1073/pnas.1608449113SE5519E55271133

Molecular characterization of Asian maize inbred lines by multiple laboratories

This study focuses on the standardization of techniques across laboratories to enable multiple datasets to be compared and combined in order to obtain reliable and robust wide-scale patterns of diversity. A set of protocols using a core collection of simple sequence repeat (SSR) markers, reference lines and standard alleles, plus a common system of allele nomenclature, was adopted in the study of maize genetic diversity in a network of laboratories in Asia. Pair-wise allele comparisons of the reference lines, done to assess the general agreement between datasets from four laboratories, showed error rates (raw) ranging from 5.8% to 9.7%, which were reduced to less than 8% after adjustments of correctable errors, and further reduced to less than 6% after the exclusion of all markers with greater than 10% individual error rates. Overall, 45% of the total mismatches were due to frameshift errors, 39% to wrong allele size, 15% to failed amplification and 1% to extra alleles. Higher genetic similarity values of the reference lines were achieved using fewer markers with data of higher quality rather than with more markers of questionable quality. Cluster analysis of the merged datasets showed the lines from southern China to be highly diverse, falling into six of the seven clusters observed and all well represented by tester lines. The lines from Indonesia fell into five of six groups, with two main groups represented by tester lines. The CIMMYT lines developed for the Asian region showed a relatively narrow genetic base, falling in two out of seven and in three out of six clusters in China and Indonesia, respectively. In contrast to the case in southern China where 95% of the lines clustered separately from the CIMMYT lines, lines in the Indonesian breeding program show a closer relationship with the CIMMYT lines, reflecting a long history of germplasm exchang

Genome-Wide Linkage Mapping Reveals QTLs for Seed Vigor-Related Traits Under Artificial Aging in Common Wheat (Triticum aestivum)

Long-term storage of seeds leads to lose seed vigor with slow and non-uniform germination. Time, rate, homogeneity, and synchrony are important aspects during the dynamic germination process to assess seed viability after storage. The aim of this study is to identify quantitative trait loci (QTLs) using a high-density genetic linkage map of common wheat (Triticum aestivum) for seed vigor-related traits under artificial aging. Two hundred and forty-six recombinant inbred lines derived from the cross between Zhou 8425B and Chinese Spring were evaluated for seed storability. Ninety-six QTLs were detected on all wheat chromosomes except 2B, 4D, 6D, and 7D, explaining 2.9–19.4% of the phenotypic variance. These QTLs were clustered into 17 QTL-rich regions on chromosomes 1AL, 2DS, 3AS (3), 3BS, 3BL (2), 3DL, 4AS, 4AL (3), 5AS, 5DS, 6BL, and 7AL, exhibiting pleiotropic effects. Moreover, 10 stable QTLs were identified on chromosomes 2D, 3D, 4A, and 6B (QaMGT.cas-2DS.2, QaMGR.cas-2DS.2, QaFCGR.cas-2DS.2, QaGI.cas-3DL, QaGR.cas-3DL, QaFCGR.cas-3DL, QaMGT.cas-4AS, QaMGR.cas-4AS, QaZ.cas-4AS, and QaGR.cas-6BL.2). Our results indicate that one of the stable QTL-rich regions on chromosome 2D flanked by IWB21991 and IWB11197 in the position from 46 to 51 cM, presenting as a pleiotropic locus strongly impacting seed vigor-related traits under artificial aging. These new QTLs and tightly linked SNP markers may provide new valuable information and could serve as targets for fine mapping or markers assisted breeding