Histogram presentation of eggNOG classification of the assembled unigenes.

<p>Histogram presentation of eggNOG classification of the assembled unigenes.</p

Known non-reducing PKSs with MeT domains and their products.

<p>The genes <i>ATEG-10080</i>, <i>ATEG-03629</i>, <i>ATEG-03432</i> and <i>ATEG-0776</i> are from <i>Aspergillus terreus</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0199110#pone.0199110.ref029" target="_blank">29</a>]. Both <i>Tspks2</i> and <i>Tspks3</i> are from <i>Talaromyces stipitatus</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0199110#pone.0199110.ref043" target="_blank">43</a>]. <i>PksCT</i> is from <i>Monascus purpureus</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0199110#pone.0199110.ref042" target="_blank">42</a>]. <i>Cupks1</i> is from <i>Cladonia uncialis</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0199110#pone.0199110.ref010" target="_blank">10</a>]. <i>Nppks6</i> and <i>Nppks7</i> are from <i>Nephromopsis pallescens</i>. 1: 3,5-dimethylorsellinic acid; 2: 5-methylorsellinic acid; 3: 6-acetyl-2,7-dihydroxy-3-methylnaphthalene-1,4-dione; 4: 2,4-dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde; 5: 2,4-dihydroxy-6-(5,7-dimethyl-2-oxo-trans-3-trans-5-nonadienyl)-3-methylbenzaldehyde; 6: beta-orsellinic acid; 7: methylphloracetophenone. KS, beta-ketoacyl-ACP synthase; AT, acyl transferase; PT, product template domain; ACP, acyl carrier protein; MeT, C-methyltransferase; R, reductive releasing domain; TE, thioesterase domain; CLC, Claisen cyclase domain.</p

Phylogenetic relationships between <i>Nephromopsis pallescens</i> polyketide synthase (PKS) genes and other fungal PKSs.

<p>The KS domain of deduced PKS proteins were aligned with fungal PKS sequences retrieved from GenBank. Sequences were aligned using Clustal W and analyzed according to the minimum evolution method. A phylogenetic tree with 1000 bootstrap replicates was generated, with a branch support threshold of 70%. PKSs from the <i>N</i>. <i>pallescens</i> clade are marked in bold.</p

Detection of usnic acid in extracts of different <i>N</i>. <i>pallescens</i> cultures.

<p>Cultures maintained on each of the following media each resulted in different extracts, respectively: MY (1.5% malt-yeast, Difco, Lawrence, USA); MYM (MY+2% mannitol); PDB (2.5% potato dextrose broth, Difco, Lawrence, USA); MS (0.5% Murashige and Skoog medium (Chembase, Shanghai, China); 5 g/L glucose); CMG (10g/L casein peptone; 5g/L maltose, 10g/L glucose); SMG (10g/L soya peptone, 5g/L maltose, 10g/L glucose); and TMG (10g/L tomato extract, 5g/L maltose, 10g/L glucose). The culture media were collected by filtration and extracted with 100 mL ethyl acetate. The crude extracts were redissolved in 2 mL of methanol. The SIM (single ion monitoring) mode of three ions, 345.0932 ([M+H]+), 709.1534 ([2M-H]-), and 343.0827 ([M-H]-) are presented as the main ions in the mass spectra for usnic acid. These three ions were used as monitoring ions in the LCMS analyses.</p

The length distribution of unigenes, the horizontal coordinates are unigene lengths and the vertical coordinates are numbers of unigenes.

<p>The length distribution of unigenes, the horizontal coordinates are unigene lengths and the vertical coordinates are numbers of unigenes.</p

Transcriptome Analysis Reveals the Putative Polyketide Synthase Gene Involved in Hispidin Biosynthesis in <i>Sanghuangporus sanghuang</i>

Hispidin is an important styrylpyrone produced by Sanghuangporus sanghuang. To analyze hispidin biosynthesis in S. sanghuang, the transcriptomes of hispidin-producing and non-producing S. sanghuang were determined by Illumina sequencing. Five PKSs were identified using genome annotation. Comparative analysis with the reference transcriptome showed that two PKSs (ShPKS3 and ShPKS4) had low expression levels in four types of media. The gene expression pattern of only ShPKS1 was consistent with the yield variation of hispidin. The combined analyses of gene expression with qPCR and hispidin detection by liquid chromatography-mass spectrometry coupled with ion-trap and time-of-flight technologies (LCMS-IT-TOF) showed that ShPKS1 was involved in hispidin biosynthesis in S. sanghuang. ShPKS1 is a partially reducing PKS gene with extra AMP and ACP domains before the KS domain. The domain architecture of ShPKS1 was AMP-ACP-KS-AT-DH-KR-ACP-ACP. Phylogenetic analysis shows that ShPKS1 and other PKS genes from Hymenochaetaceae form a unique monophyletic clade closely related to the clade containing Agaricales hispidin synthase. Taken together, our data indicate that ShPKS1 is a novel PKS of S. sanghuang involved in hispidin biosynthesis.</p

Comparison of genotype imputation strategies from SNP-chip to sequence with a combined reference panel

<div>Materials <br></div>The SNP data of reference panel and target panel on chromosomes 6.<br><div><p>Supplementary material</p> <p>Table S1. Summary of WGS data per chicken from public datasets </p> <p>Table S2. Summary statistics of chromosome 6 per sequenced individual</p> <p>Table S3. The Hamming distances matrix among 289 chickens based on chromosome 6</p><p>Table S4. The computational consuming of Beagle 4.1 for different reference panel.<br></p></div

Additional file 1: of Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Table S1. A pedigree-based genetic relationship matrix among the 24 key individuals. Table S2 A summary of the sequencing and assembly of 24 key individuals. Table S3 Number of identified variants in the chicken genome with GATK. Table S4 The results of the SNP calling for chromosomes (chr1, chr3, chr6, and chr28) with different sequencing depth under the different total cost of genotyping, respectively. (XLSX 25 kb

Image_1_Distributions and controlling processes of the carbonate system in the Eastern Indian Ocean during autumn and spring.pdf

The Eastern Indian Ocean (EIO) is an ideal region to explore the variability and controlling mechanisms of the seawater carbonate system and their potential influence on global climate change due to the distinctive environmental features, while studies in the EIO is far from sufficient. The spatiotemporal distributions of pH, dissolved inorganic carbon (DIC), alkalinity (Alk), and partial pressure of carbon dioxide (pCO2) were investigated in the EIO during autumn 2020 and spring 2021. The respective quantitative contributions of different controlling processes to DIC were further delineated. Significant seasonal variations were observed in the study area. Overall, the surface pH was lower and DIC, Alk, and pCO2 were higher during spring 2021 than during autumn 2020. The pH generally decreased from east to west during autumn 2020, whereas it decreased from north to south during spring 2021. The low values of DIC and Alk that were detected in the Bay of Bengal in these two seasons were mainly attributed to the influence of river inputs. Coastal upwelling during monsoon periods led to higher pCO2 and DIC values near Sumatra and Sri Lanka during spring 2021. The relationships of carbonate system parameters with different types of nutrients and different sized chlorophyll-a in the two seasons indicated the shifts of nutrients utilized by the phytoplankton, and phytoplankton species dominated the carbonate system variabilities. In vertical profiles, carbonate system parameters showed strong correlations with other physical and biogeochemical parameters, and these correlations were more robust during spring 2021 than during autumn 2020. The average sea–air flux of CO2 was 10.00 mmol m−2 d−1 during autumn 2020 and was 16.00 mmol m−2 d−1 during spring 2021, which revealed that the EIO served as a CO2 source during the study period. In addition, the separation of different controlling processes of DIC indicated stronger mixing processes, less CaCO3 precipitation, more intensive sea–air exchange, and weaker photosynthesis during spring 2021 than during autumn 2020.</p

Additional file 2: of Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Figure S1. Imputation accuracy in different total X obtained with FImpute and Beagle against 4 chromosomes (chr1, chr3, chr6, and chr28) among 5 replications, respectively. Figure S2 Imputation accuracy in different X with fixed N (N = 24) obtained with FImpute and Beagle against 4 chromosomes (chr1, chr3, chr6, and chr28) among 5 replications, respectively. Figure S3 The average imputation accuracy of direct imputation from 600 K to WGS data obtained with FImpute, Beagle v.3.3.2, Beagle v.4.0, and Beagle v.4.1 against four chromosomes (chr1, chr3, chr6 and chr28) among 5 replications. (DOCX 1755 kb