Enhanced SWAT calibration through intelligent range-based parameter optimization.

Hydrological models are vital tools in environmental management. Weaknesses in model robustness for hydrological parameters transfer uncertainties to the model outputs. For streamflow, the optimized parameters are the primary source of uncertainty. A reliable calibration approach that reduces prediction uncertainty in model simulations is crucial for enhancing model robustness and reliability. The optimization of parameter ranges is a key aspect of parameter calibration, yet there is a lack of literature addressing the optimization of parameter ranges in hydrological models. In this paper, we introduce a parameter calibration strategy that applies a clustering technique, specifically the Self-Organizing Map (SM), to intelligently navigate the parameter space during the calibration of the Soil and Water Assessment Tool (SWAT) model for monthly streamflow simulation in the Baishan Basin, Jilin Province, China. We selected the representative algorithm, the Sequential Uncertainty Fitting version 2 (SUFI-2), from the commonly used SWAT Calibration and Uncertainty Programs for comparison. We developed three schemes: SUFI-2, SUFI-2-Narrowing Down (SUFI-2-ND), and SM. Multiple diagnostic error metrics were used to compare simulation accuracy and prediction uncertainty. Among all schemes, SM outperformed the others in describing watershed streamflow, particularly excelling in the simulation of spring snowmelt runoff (baseflow period). Additionally, the prediction uncertainty was effectively controlled, demonstrating the SM's adaptability and reliability in the interval optimization process. This provides managers with more credible prediction results, highlighting its potential as a valuable calibration tool in hydrological modeling.

Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly.

Poplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of Populus simonii which is a Chinese native species with many excellent traits. This karyotype was anchored by oligonucleotide (oligo)-based chromosome specific painting probes, a centromere-specific repeat (Ps34), ribosomal DNA, and telomeric DNA. We updated the known karyotype formula for P. simonii to 2n = 2x = 38 = 26m + 8st + 4t and the karyotype was 2C. The fluorescence in situ hybridization (FISH) results revealed some errors in the current P. simonii genome assembly. The 45S rDNA loci were located at the end of the short arm of chromosomes 8 and 14 by FISH. However, they were assembled on pseudochromosomes 8 and 15. In addition, the Ps34 loci were distributed in every centromere of the P. simonii chromosome in the FISH results, but they were only found to be present in pseudochromosomes 1, 3, 6, 10, 16, 17, 18, and 19. Our results reveal that pachytene chromosomes oligo-FISH is a powerful tool for constructing high-resolution karyotypes and improving the quality of genome assembly.

EST-SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb).

The fast advancement and deployment of sequencing technologies after the Human Genome Project have greatly increased our knowledge of the eukaryotic genome sequences. However, due to technological concerns, high-quality genomic data has been confined to a few key organisms. Moreover, our understanding of which portions of genomes make up genes and which transcript isoforms synthesize these genes is scarce. Therefore, the current study has been designed to explore the reliability of the tiger lily (Lilium lancifolium Thunb) transcriptome. The PacBio-SMRT was used for attaining the complete transcriptomic profile. We obtained a total of 815,624 CCS (Circular Consensus Sequence) reads with an average length of 1295 bp. The tiger lily transcriptome has been sequenced for the first time using third-generation long-read technology. Furthermore, unigenes (38,707), lncRNAs (6852), and TF members (768) were determined based on the transcriptome data, followed by evaluating SSRs (3319). It has also been revealed that 105 out of 128 primer pairs effectively amplified PCR products. Around 15,608 transcripts were allocated to 25 distinct KOG Clusters, and 10,706 unigenes were grouped into 52 functional categories in the annotated transcripts. Until now, no tiger lily lncRNAs have been discovered. Results of this study may serve as an extensive set of reference transcripts and help us learn more about the transcriptomes of tiger lilies and pave the path for further research.