Multiple group I introns in the small-subunit rDNA of Botryosphaeria dothidea: implication for intraspecific genetic diversity.

Botryosphaeria dothidea is a widespread and economically important pathogen on various fruit trees, and it often causes die-back and canker on limbs and fruit rot. In characterizing intraspecies genetic variation within this fungus, group I introns, rich in rDNA of fungi, may provide a productive region for exploration. In this research, we analysed complete small subunit (SSU) ribosomal DNA (rDNA) sequences of 37 B. dothidea strains, and found four insertions, designated Bdo.S943, Bdo.S1199-A, Bdo.S1199-B and Bdo.S1506, at three positions. Sequence analysis and structure prediction revealed that both Bdo.S943 and Bdo.S1506 belonged to subgroup IC1 of group I introns, whereas Bdo.S1199-A and Bdo.S1199-B corresponded to group IE introns. Moreover, Bdo.S1199-A was found to host an open reading frame (ORF) for encoding the homing endonuclease (HE), whereas Bdo.S1199-B, an evolutionary descendant of Bdo.S1199-A, included a degenerate HE. The above four introns were novel, and were the first group I introns observed and characterized in this species. Differential distribution of these introns revealed that all strains could be separated into four genotypes. Genotype III (no intron) and genotype IV (Bdo.S1199-B) were each found in only one strain, whereas genotype I (Bdo.S1199-A) and genotype II (Bdo.S943 and Bdo.S1506) occurred in 95% of the strains. There is a correlation between B. dothidea genotypes and hosts or geographic locations. Thus, these newly discovered group I introns can help to advance understanding of genetic differentiation within B. dothidea

Cloud Radiative Feedbacks during the ENSO Cycle Simulated by CAMS-CSM

This study evaluated the simulated cloud radiative feedbacks (CRF) during the El Nino-Southern Oscillation (ENSO) cycle in the latest version of the Chinese Academy of Meteorological Sciences climate system model (CAMS-CSM). We conducted two experimental model simulations: the Atmospheric Model Intercomparison Project (AMIP), forced by the observed sea surface temperature (SST); and the preindustrial control (PIcontrol), a coupled run without flux correction. We found that both the experiments generally reproduced the observed features of the shortwave and longwave cloud radiative forcing (SWCRF and LWCRF) feedbacks. The AMIP run exhibited better simulation performance in the magnitude and spatial distribution than the PIcontrol run. Furthermore, the simulation biases in SWCRF and LWCRF feedbacks were linked to the biases in the representation of the corresponding total cloud cover and precipitation feedbacks. It is interesting to further find that the simulation bias originating in the atmospheric component was amplified in the PIcontrol run, indicating that the coupling aggravated the simulation bias. Since the PIcontrol run exhibited an apparent mean SST cold bias over the cold tongue, the precipitation response to the SST anomaly (SSTA) changes during the ENSO cycle occurred towards the relatively warmer western equatorial Pacific. Thus, the corresponding cloud cover and CRF shifted westward and showed a weaker magnitude in the PI-control run versus observational data. In contrast, the AMIP run was forced by the observational SST, hence representing a more realistic CRF. Our results demonstrate the challenges of simulating CRF in coupled models. This study also underscores the necessity of realistically representing the climatological mean state when simulating CRF during the ENSO cycle

Distribution of the different introns across hosts and populations.

<p>Four different colours represent four populations divided by presence or absence and types of introns. Hosts for each population are listed in the corresponding colours. Ratios of the four populations are marked at the relevant position of the pie chart.</p

His-Cys box homing endonucleases used for alignment.

<p>Note: ACT: Enzyme with demonstrated activity; FL: predicted full-length ORF.</p

Pairwise alignment between Bdo.S1199-A and Bdo.S1199-B.

<p>The two bars refer to the RNA sequences of Bdo.S1199-A (left) and Bdo.S1199-B (right), respectively. The pink bars correspond to the identical regions of two sequences. The purple stripes on the bars point to SNPs or insertion position whereas the white areas represent deletions.</p

Putative secondary structures of group IC1 introns of <i>B. dothidea</i>.

<p>A. Secondary structure of Bdo.S943. B. Secondary structure of Bdo.S1506. Putative Watson-Crick and wobble base pairs are shown by lines and hollow circles, respectively. Capital and small letters represent intron and exon nucleotides, respectively. The boldface letters indicate four conserved core sequence elements P, Q, R and S. Arrows point to the 5′ and 3′ splice sites. The guanosine cofactor binding-sites are marked with *.</p

Primary structure of the SSU rDNA in <i>Botryosphaeria dothidea</i>.

<p>The entire SSU rDNA is shown by the blue rectangle. The triangles in red, green, purple and yellow respectively indicate four different introns. The position and length of each intron are given separately above and below the triangles. The insertion sites correspond to the 16S rRNA of <i>E. coli</i> J01859. Primers are presented by black arrows.</p