Semi-supervised learning advances species recognition for aquatic biodiversity monitoring

Aquatic biodiversity monitoring relies on species recognition from images. While deep learning (DL) streamlines the recognition process, the performance of these method is closely linked to the large-scale labeled datasets, necessitating manual processing with expert knowledge and consume substantial time, labor, and financial resources. Semi-supervised learning (SSL) offers a promising avenue to improve the performance of DL models by utilizing the extensive unlabeled samples. However, the complex collection environments and the long-tailed class imbalance of aquatic species make SSL difficult to implement effectively. To address these challenges in aquatic species recognition within the SSL scheme, we propose a Wavelet Fusion Network and the Consistency Equilibrium Loss function. The former mitigates the influence of data collection environment by fusing image information at different frequencies decomposed through wavelet transform. The latter improves the SSL scheme by refining the consistency loss function and adaptively adjusting the margin for each class. Extensive experiments are conducted on the large-scale FishNet dataset. As expected, our method improves the existing SSL scheme by up to 9.34% in overall classification accuracy. With the accumulation of image data, the improved SSL method with limited labeled data, shows the potential to advance species recognition for aquatic biodiversity monitoring and conservation

Identification and characterization of multiple novel picornaviruses in fecal samples of bar-headed goose

IntroductionThe bar-headed goose (Anser indicus), one of the most well-known high-altitude birds, is renowned for its adaptation to high-altitude environments. Previous studies have shown that they can be infected with highly pathogenic avian influenza; however, there is currently limited research on other viruses in bar-headed geese.MethodsIn this study, 10 fecal samples of healthy bar-headed geese were collected, and viral metagenomics method was conducted to identify novel picornaviruses.ResultsSeven novel picornaviruses were identified in the fecal samples of bar-headed geese. Most of these picornaviruses were genetically different from other currently known viruses in the NCBI dataset. Among them, PICV4 was determined to be a new species belonging to the Anativirus genus, PICV5 and PICV13 were classified as novel species belonging to the Hepatovirus genus, and the remaining four picornaviruses (PICV1, PICV19, PICV21, and PICV22) were identified as part of the Megrivirus A species of the Megrivirus genus. Recombinant analysis indicates that PICV21 was a potential recombinant, and the major and minor parents were PICV1 and PICV22, respectively.ConclusionThe findings of this study increase our understanding of the diversity of picornaviruses in bar-headed geese and provide practical viral genome information for the prevention and treatment of potential viral diseases affecting this species

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded similar to 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of similar to 81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

DATA AVAILABILITY : The raw sequencing data generated in this study have been deposited in the NCBI under accession PRJNA796762 and PRJNA895586 The chloroplast andmitochondrial genome were also available at GenBank under the accession number OP104251 and OP104742 respectively. The assembled genome sequences and annotations are available at Figshare [https://doi.org/10.6084/m9.figshare.21655364.v2]. The Arabidopsis ABCE and chrysanthemum CYC2 genes were used as query sequences for gene family identification, which are available at Figshare [https://doi.org/10.6084/m9.figshare.21610305]. Source data are provided with this paper.Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement.The National Natural Science Foundation of China, the Natural Science Fund of Jiangsu Province, China Agriculture Research System, the National Key Research and Development Program of China, the “JBGS” Project of Seed Industry Revitalisation in Jiangsu Province, the European Union’s Horizon 2020 research and innovation program from European Research Council, the Methusalem funding from Ghent University, and a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institution.https://www.nature.com/ncomms/am2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan