DNA Research最新文献

High-altitude hypoxia provides a natural laboratory for studying adaptation in plateau mammals. As an interface for oxygen and nutrient exchange, placenta plays a critical role in fetal development. While high-altitude adaptation in systemic physiological responses and cardiopulmonary tissues has been well-studied, a comprehensive landscape of porcine placental transcriptomic diversity and alternative splicing (AS) complexity across altitudes remains lacking. Here, we integrated Iso-Seq and RNA-Seq to profile placental transcriptomes from placentas of 3 pig breeds across altitudes: the Diannan small-ear pig (DSE ~500 m), the Baoshan pig (BS ~1500 m), and the Changdu Tibetan Pig (CT ~3500 m). We identified 39,776 full-length transcripts, including 25,471 novel ones, significantly enhancing pig genome annotation. Additionally, 24,879 AS events from 8,390 AS genes were detected, with skipping exon (SE) as the most prevalent AS type. Differential expression (DE) and differential alternative splicing (DAS) analyses highlighted key DEGs (IGF1, GHR, RASGRP4, MECOM, SPP1), as well as DAS genes (HIF1A, HSPA8, RHOA, HMGCR, PLAGL1), which may be implicated in placental adaptation to high-altitude conditions. This study provides a comprehensive analysis of the transcriptomic diversity and AS complexity in porcine placentas across altitudes, laying a foundation for future investigations into the molecular mechanisms underlying high-altitude adaptation in plateau mammals.

The New World Ampullariids, encompassing the ecologically important genera Pomacea and Marisa, are gastropods with dual attributes-serving as model systems for evolutionary and environmental research while posing severe threats as globally invasive species. Here, we present chromosome-scale genomes of four key species-Pomacea canaliculata, P. maculata, P. diffusa, and Marisa cornuarietis-generated through PacBio HiFi sequencing and Hi-C scaffolding. These assemblies exhibit exceptional continuity and completeness (BUSCO scores > 95%) with genome sizes ranging 450-540 Mb, while high-quality annotations predicting 21,687-22,481 protein-coding genes per genome. Comparative analysis reveals divergent genome architectures: the invasive P. canaliculata and P. maculata harbour lower LINE (5.7-5.8%) and LTR (0.7-0.8%) content compared to non-invasive P. diffusa (LINE: 7.7%; LTR: 0.8%) and M. cornuarietis (LINE: 9.5%; LTR: 1.1%), suggesting repeat dynamics linked to ecological plasticity. Macrosynteny analyses identify five dynamic but conserved ancestral chromosomal fusions across species but with limited rearrangements among species. These resources, integrating chromosomal resolution with functional annotation, provide a foundation for comparative studies on molluscan karyotype evolution and adaptive radiation research, as well as possible targets for CRISPR-cas9-driven biocontrol strategies.

Bats are known reservoirs for many viruses of zoonotic potential and can tolerate or clear infections efficiently. They are important hosts for multiple coronaviruses and harbour ancestral lineages of coronaviruses known to cause diseases in both humans and animals. In this study, we describe a high-quality hybrid genome assembly of the Blyth's horseshoe bat Rhinolophus lepidus. It is a widespread species and an important cell-line model system for studying virus entry and replication. We used a combination of short Illumina reads and long reads from Oxford Nanopore to assemble the genome, with N50 of 5.3 Mb and Benchmarking Universial Single-Copy Orthologs (BUSCO) score of ~94%. The Angiotensin-converting enzyme 2 receptor responsible for the entry of severe acute respiratory syndrome coronaviruses (SARS and SARS-CoV-2) was highly conserved within bats, especially the region responsible for virus entry into the cell. In total, 50% of the amino acids necessary for virus entry were conserved between humans and R. lepidus. We observed an effect of past climatic conditions on the effective population size with drastic population size reduction in the past 50,000 years. This study adds to the growing list of bat genomes which are important resources to understand the co-evolution of bats and viruses and the mechanism by which bats can tolerate and clear infections effectively.

Annona squamosa, also known as custard apple, is an emerging fruit crop with medicinal significance. We constructed a high-quality genome of A. squamosa along with transcriptome data to gain insights into its phylogeny, evolution, and demographic history. The genome has a size of 730.4 Mb with an N50 value of 93.2 Mb assembled into seven pseudochromosomes. The demographic history showed a continuous decline in the effective population size of A. squamosa. Phylogenetic analysis revealed that magnoliids were sister to eudicots. Genome syntenic and Ks distribution analyses confirmed the absence of a recent whole-genome duplication event in the A. squamosa. Gene families related to photosynthesis, oxidative phosphorylation, and plant thermogenesis were found to be highly expanded in the genome. Comparative analysis with other magnoliids revealed the adaptive evolution in the genes of flavonoid biosynthesis pathway, amino sugar, nucleotide sugar and sucrose metabolism, conferring medicinal value, and enhanced hexose sugar accumulation. In addition, we performed genome-wide identification of SWEET genes. Our high-quality genome and evolutionary insights of this emerging fruit crop, thus, serve as a valuable resource for advancing studies in functional genomics, evolutionary biology, and crop improvement.

The ant Crematogaster osakensis (Hymenoptera: Formicidae: Myrmicinae) serves as a valuable model organism for investigating queen-specific traits, such as reproductive capacity and longevity, at the cellular and molecular levels. To support future research on queen traits using molecular techniques, including genome editing and multi-omics data analyses, we performed whole-genome sequencing of this species. The genome size of C. osakensis was estimated to be 284 Mb, with a heterozygosity of 0.26%. Annotation revealed the presence of 16,053 protein-coding genes. Furthermore, using the coding sequences annotated in this study, we reanalyzed previously obtained transcriptome data to identify highly expressed genes in the reproductive organs of queens and males. This data will contribute to a deeper understanding of the genetic mechanisms underlying reproductive strategies in ants.

Pontederia cordata L. is an aquatic ornamental plant native to the Americas but has been widely distributed in South Asia, Australia, and Europe. The genetic mechanisms behind its rapid adaptation and spread have not yet been well understood. To understand the mechanisms for its rapid adaptation, this study assembled the first chromosome-level genome of P. cordata. The genome assembly, which spans 527.5 Mb, is anchored on 8 pseudochromosomes with a scaffold N50 of 48 Mb and encompasses 29,389 protein-coding genes. Further analyses revealed that P. cordata had experienced 3 whole-genome duplications (WGDs) events. These WGDs are associated with gene family expansion and increased numbers of resistance gene analogs and transcription factors. Positive selection analysis indicated that genes derived from tandem duplication (TD) and proximal duplication were more likely to undergo positive selection, and were enriched in plant defense and disease resistance. These results implied that WGDs, TD, and positive selection enhanced the environmental adaptability of P. cordata. In addition, we found that down-regulation of F3'5'H, DFR, ANS, and UFGT likely caused the flower colour variation for P. cordata from violet to white. The first chromosome-level genome of P. cordata here provides a valuable genomic resource for investigating the rapid adaptation and flower colour variation of the species.

Phyllanthus emblica L. is an edible plant with medicinal properties native to the dry-hot valley of Yunnan, China. Here, we report a de novo chromosome-scale genome of P. emblica wild type 'Yingyu'. 'Yingyu' is an octopoid plant with a total of 104 chromosomes. In total, we assembled and clustered 480 Mb of the genome and constructed 26 pseudochromosomes (haplotypes) of P. emblica wild type 'Yingyu' that encompass 97.9% of the genome and demonstrate to have relatively high integrity. We annotated 31,111 genes found in the genome of P. emblica. We screened 5 different tissues for searching the tissue-specific expression candidate genes. Four unknown function candidate genes were expressed at high levels in the flowers while genes relating to the biosynthesis of gibberellins and cellulose were specifically expressed in the fruits. The ascorbate biosynthesis-related genes were screened on P. emblica 'Yingyu' genome. The high expression level of 2 GDP-mannose epimerases and one L-galactono-1,4- lactone dehydrogenases in the fruit may be related to the activity of absorbate biosynthesis in the fruit. The chromosome-level genomic data for P. emblica we report will be important for the development of molecular markers to facilitate the selection of superior cultivars for processing and pharmaceuticals.

Type 2 diabetes (T2D) is a multifactorial disease caused by insulin resistance and impaired insulin secretion from pancreatic β-cells, but the precise mechanisms remain to be elucidated. To identify primary genetic factors of T2D in a rat model, we performed comparative transcriptome and mutation analyses of the pancreatic islets between the obese Zucker fatty rat and the Zucker fatty rat-derived T2D model Zucker fatty diabetes mellitus (ZFDM) rat. Among differentially expressed genes irrespective of obesity and glucose intolerance states, we identified a nonsense mutation, c.409C > T (p.Gln137X), in the lipocalin 2 (Lcn2) gene which encodes a secreted protein called neutrophil gelatinase-associated lipocalin, a well-known biomarker for inflammation. We examined the relevance of the Lcn2 mutation with T2D in the ZFDM rat by using genome editing and genetic linkage analysis and confirmed that the Lcn2 mutation exhibits no significant association with the onset of T2D. Interestingly, we found that the Lcn2 mutation is distributed widely in rat species, such as commonly used DA and F344 strains. Our data indicate that several rat strains would serve as Lcn2 deficient models, contributing to elucidate the pathophysiological roles of Lcn2 in a wide variety of phenotypes.

Polyrhachis lamellidens is a temporary socially parasitic ant. The newly mated P. lamellidens queen takes over a colony of several Camponotus ant species and uses the labour of the host workers in the early stages of social parasitism. To facilitate genomic resources for these species, we assembled and annotated the chromosomal genome of P. lamellidens using the 10× Genomics linked-read and Hi-C sequencing, and the draft genome of its host, Camponotus japonicus, using long-read sequencing with the Revio system. The P. lamellidens chromosomal genome assembly is 214.1 Mb, 95.5% BUSCO completeness, and contains 13,703 protein-coding genes. The C. japonicus draft genome assembly is 314.2 Mb, 99.0% BUSCO completeness, and contains 11,207 protein-coding genes. Genome-wide phylogeny and synteny analysis confirmed the phylogenetic position of P. lamellidens and C. japonicus, and a high level of synteny with the genome of both ant species. In addition, P. lamellidens possesses nearly identical chemosensory proteins to its host, C. japonicus, and these genes tended to exhibit higher expression levels in the newly mated queen. The genome assemblies of P. lamellidens and its host C. japonicus provide a valuable resource for the molecular biological and bioinformatic basis for studying the strategy of social parasitism in ants.

Bud dormancy is a vital physiological process in woody perennials, facilitating their adaptation to seasonal environmental changes. Satisfying genotype-specific chilling requirements (CR) and heat requirements (HR) through exposure to specific chilling and warm temperatures is essential for dormancy release and the subsequent resumption of growth. The genetic mechanisms regulating bud dormancy traits in Prunus mume remain unclear. In this study, we first assembled the genome of 'Nanko', the leading P. mume cultivar in Japan, in a haplotype-resolved manner. Using an F1 segregating population from a cross between 'Nanko' (high-chill) and 'SC' (low-chill), a cultivar adapted to subtropical conditions, we identified quantitative trait loci (QTLs) for vegetative bud dormancy traits on chromosome 4 (LG4 QTLs) in the 'Nanko' genome and for CR and HR on chromosome 7 (LG7 QTL) in the 'SC' genome. A notable 5.6 Mb chromosome inversion was overlapped with LG4 QTL interval in one of the 'Nanko' haplotypes. We also identified candidate genes based on haplotyping, differential expression between the parents or the presence of trait-correlated variants in coding regions. Notably, genes such as PmuMAIN, PmuNAC2, PmuDOG1, PmuSUI1, PmuATG8CL, PmubZIP44, and PmuSAUR50 were identified. This study provides valuable insights into the genetic regulation of vegetative bud dormancy in Prunus species.