Benchmarking gene set of gymnosperms for assessing genome and annotation completeness in BUSCO

Chromosome-level genome assembly of the butterfly hillstream loach Beaufortia pingi

The Butterfly hillstream loach (Beaufortia pingi), an aquatic benthic fish species inhabiting mountain rapids, exhibits exceptional capabilities in movement, adsorption, and desorption processes, enabling it to adhere to smooth and contaminated surfaces in turbulent streams. These attributes make it a significant subject for genetic and evolutionary research. In this study, the genomic sequences of this species were acquired utilizing PacBio sequencing and Hi-C methods. The genome assembly is 459.8 Mb in size with a contig N50 of 5.35 Mb, and the assembled contigs were anchored into 25 chromosomes. BUSCO analysis confirmed a high completeness level with 97.0% gene coverage. A total of 111.47 Mb repetitive sequences (24.25% of the assembled genome), and 22,906 protein-coding genes were identified in the genome. This study represents the first investigation of the species' genome. The establishment of this genome assembly provides valuable resources for future genetic research and facilitates the study of genetic changes during evolution.

Physiological responses to drought stress of three pine species and comparative transcriptome analysis of Pinus yunnanensis var. pygmaea

Drought stress can significantly affect plant growth, development, and yield. Fewer comparative studies have been conducted between different species of pines, particularly involving Pinus yunnanensis var. pygmaea (P. pygmaea). In this study, the physiological indices, photosynthetic pigment and related antioxidant enzyme changes in needles from P. pygmaea, P. elliottii and P. massoniana under drought at 0, 7, 14, 21, 28 and 35 d, as well as 7 days after rehydration, were measured. The PacBio single-molecule real-time (SMRT) and Illumina RNA sequencing were used to uncover the gene expression differences in P. pygmaea under drought and rehydration conditions. The results showed that the total antioxidant capacity (TAOC) of P. pygmaea was significantly higher than P. massoniana and P. elliottii. TAOC showed a continuous increase trend across all species. Soluble sugar (SS), starch content and non-structural carbohydrate (NSC) of all three pines displayed a "W" pattern, declining initially, increasing, and then decreasing again. P. pygmaea exhibits stronger drought tolerance and greater recovery ability under prolonged drought conditions. Through the PacBio SMRT-seq, a total of 50,979 high-quality transcripts were generated, and 6,521 SSR and 5,561 long non-coding RNAs (LncRNAs) were identified. A total of 2310, 1849, 5271, 5947, 7710, and 6854 differentially expressed genes (DEGs) were identified compared to the control (Pp0D) in six pair-wise comparisons of treatment versus control. bHLH, NAC, ERF, MYB_related, C3H transcription factors (TFs) play an important role in drought tolerance of P. pygmaea. KEGG enrichment analysis and Gene set enrichment analysis (GSEA) analysis showed that P. pygmaea may respond to drought by enhancing metabolic processes such as ABA signaling pathway, alpha-linolenic acid. Weighted gene co-expression network analysis (WGCNA) revealed GST, CAT, LEC14B, SEC23 were associated with antioxidant enzyme activity and TAOC. This study provides a basis for further research on drought tolerance differences among coniferous species.