BMC Genomics

Peralta-Sánchez, Juan Manuel; Rabelo-Ruiz, Miguel; Martín-Platero, Antonio Manuel; Vizcaíno, Antonio Jesús; Flores-Moreno, Sara; Macías-Vidal, Judit; Martos-Sitcha, Juan Antonio; Alarcón-López, Francisco Javier; Baños, Alberto; Valdivia, Eva; Martínez-Bueno, Manuel

doi: 10.1186/s12864-024-10760-xpmid: 39242559

Fishmeal and fish oil have been the main sources of protein and fatty acid for aquaculture fish. However, their increasing price and low sustainability have led the aquafeed industry to seek sustainable alternative feedstuffs to meet the nutritional requirements of fish and improve their health and performance. Plant proteins have been successfully used to replace fishery derivatives in aquafeeds, but the presence of anti-nutritional substances is a potential drawback of this approach. Thus, it has been reported that phytate breakdown can be caused by feed supplementation with exogenous phytase. The inclusion of microalgae has been proposed to improve gut functionality in fish fed diets with a high vegetable protein content. The aim of this study was to evaluate the effect on the growth and gut microbiota of European seabass (Dicentrarchus labrax) juveniles of a diet containing a blend of microalgae (Arthrospira platensis and Nannochloropsis gaditana) and different concentrations of phytase. An 83-day feeding trial was conducted, comprising four experimental diets with 2.5% microalgae and 500, 1,000, 2,000, or 10,000 phytase units (FTU)/kg feed and a microalgae- and phytase-free control diet. At the end of the trial, a significantly increased body weight was observed in fish fed the diet with the highest phytase concentration (10,000 FTU/kg) versus controls, although the gut bacterial composition did not differ from controls in alpha or beta diversity with either majority (Weighted UniFrac) or minority bacterial strains (Unweighted UniFrac). In comparison to the control group, the groups fed diets with 1,000 or 2,000 FTU/kg diets had a lower alpha diversity (Shannon’s diversity index), while those fed diets with 500 FTU/kg or 1,000 FTU/kg showed distinct clusters in beta diversity (involving minority ASVs). According to these findings, the diet containing the 2.5% microalgae blend with 10,000 FTU/kg may be useful to increase the aquafeed quality and sustain the growth performance of juvenile European seabass.

Cuevas-Diaz Duran, Raquel; Wei, Haichao; Wu, Jiaqian

doi: 10.1186/s12864-024-10364-5pmid: 38711017

BackgroundNormalization is a critical step in the analysis of single-cell RNA-sequencing (scRNA-seq) datasets. Its main goal is to make gene counts comparable within and between cells. To do so, normalization methods must account for technical and biological variability. Numerous normalization methods have been developed addressing different sources of dispersion and making specific assumptions about the count data.Main bodyThe selection of a normalization method has a direct impact on downstream analysis, for example differential gene expression and cluster identification. Thus, the objective of this review is to guide the reader in making an informed decision on the most appropriate normalization method to use. To this aim, we first give an overview of the different single cell sequencing platforms and methods commonly used including isolation and library preparation protocols. Next, we discuss the inherent sources of variability of scRNA-seq datasets. We describe the categories of normalization methods and include examples of each. We also delineate imputation and batch-effect correction methods. Furthermore, we describe data-driven metrics commonly used to evaluate the performance of normalization methods. We also discuss common scRNA-seq methods and toolkits used for integrated data analysis.ConclusionsAccording to the correction performed, normalization methods can be broadly classified as within and between-sample algorithms. Moreover, with respect to the mathematical model used, normalization methods can further be classified into: global scaling methods, generalized linear models, mixed methods, and machine learning-based methods. Each of these methods depict pros and cons and make different statistical assumptions. However, there is no better performing normalization method. Instead, metrics such as silhouette width, K-nearest neighbor batch-effect test, or Highly Variable Genes are recommended to assess the performance of normalization methods.

Shi, Jia; Zhao, Yuqian; Zhao, Peng; Yang, Hongmei; Wang, Chunsheng; Xia, Jianqiang; Zhao, Zhun; Wang, Zhenlong; Yang, Zhenyu; Wang, Zhong; Xu, Shengbao; Zhang, Yueqiang

doi: 10.1186/s12864-024-10713-4pmid: 39174916

BackgroundBread wheat (Triticum aestivum L.) endosperm contains starch and proteins, which determine the final yield, quality, and nutritional value of wheat grain. The preferentially expressed endosperm genes can precisely provide targets in the endosperm for improving wheat grain quality and nutrition using modern bioengineering technologies. However, the genes specifically expressed in developing endosperms remain largely unknown.ResultsIn this study, 315 preferentially expressed endosperm genes (PEEGs) in the spring wheat landrace, Chinese Spring, were screened using data obtained from an open bioinformatics database, which reveals a unique grain reserve deposition process and special signal transduction in a developing wheat endosperm. Furthermore, transcription and accumulation of storage proteins in the wheat cultivar, XC26 were evaluated. The results revealed that 315 PEEG plays a critical role in storage protein fragment deposition and is a potential candidate for modifying grain quality and nutrition.ConclusionThese results provide new insights into endosperm development and candidate genes and promoters for improving wheat grain quality through genetic engineering and plant breeding techniques.

Tribhuvan, Kishor U.; Shivakumaraswamy, M.; Mishra, Twinkle; Kaur, Simardeep; Sarkar, Biplab; Pattanayak, A.; Singh, Binay K.

doi: 10.1186/s12864-024-10964-1pmid: 39567864

Indian Mustard (Brassica juncea L.) is a globally cultivated winter oilseed crop of the rapeseed-mustard group. It is predominantly grown in the semi-arid northwest agroclimatic zone of India, characterized by high soil salinity. Enhancing tolerance to salt stress in B. juncea is therefore crucial for sustaining its production in this region. Long non-coding RNAs (lncRNAs) play critical roles in coordinating gene expression under various abiotic stresses, including salt stress, but their involvement in the salt stress response in B. juncea remains largely unknown. In this study, we conducted RNA-seq analysis on control, salt-stressed, and salt-shocked young leaves of the salt-tolerant B. juncea cv CS-52. We identified a total of 3,602 differentially expressed transcripts between stress versus control and shock versus control samples. Among these, 61 were identified as potential lncRNAs, with 21 specific to salt stress and 40 specific to salt shock. Of the 21 lncRNAs specific to salt stress, 15 were upregulated and six were downregulated, while all 40 lncRNAs unique to salt shock were downregulated. Chromosomal distribution analysis of the lncRNAs revealed their uneven placement across 18 chromosomes in B. juncea. RNA-RNA interaction analysis between salt stress-upregulated lncRNAs and salt stress-related miRNAs identified 26 interactions between 10 lncRNAs and 23 miRNAs and predicted 13 interactions between six miRNAs and 13 mRNAs. Finally, six lncRNA-miRNA-mRNA interaction networks were established, involving five lncRNAs, 13 miRNAs, and 23 mRNAs. RT-qPCR analysis revealed the upregulation of four out of five lncRNAs, along with their target mRNAs, supporting their involvement in the salt stress response in B. juncea.

Rork, Adam M.; Bala, Arthi S.; Renner, Tanya

doi: 10.1186/s12864-024-10159-8pmid: 38693486

BackgroundThe folate cycle of one-carbon (C1) metabolism, which plays a central role in the biosynthesis of nucleotides and amino acids, demonstrates the significance of metabolic adaptation. We investigated the evolutionary history of the methylenetetrahydrofolate dehydrogenase (mTHF) gene family, one of the main drivers of the folate cycle, across life.ResultsThrough comparative genomic and phylogenetic analyses, we found that several lineages of Archaea lacked domains vital for folate cycle function such as the mTHF catalytic and NAD(P)-binding domains of FolD. Within eukaryotes, the mTHF gene family diversified rapidly. For example, several duplications have been observed in lineages including the Amoebozoa, Opisthokonta, and Viridiplantae. In a common ancestor of Opisthokonta, FolD and FTHFS underwent fusion giving rise to the gene MTHFD1, possessing the domains of both genes.ConclusionsOur evolutionary reconstruction of the mTHF gene family associated with a primary metabolic pathway reveals dynamic evolution, including gene birth-and-death, gene fusion, and potential horizontal gene transfer events and/or amino acid convergence.

Pan, Zhe; Li, Wentao; Bialobzyski, Sonja; Chen, Yanhong; O’Hara, Eoin; Sun, Hui-zeng; Schwartzkopf-Genswein, Karen; Guan, Le Luo

doi: 10.1186/s12864-024-10807-zpmid: 39695421

BackgroundLameness is a collective term for multiple foot diseases in cattle including, but not limited to, foot rot (FR), digital dermatitis (DD), and toe tip necrosis (TTN), which is a critical welfare concern. The diagnosis of specific phenotypes of lameness in feedlot cattle is challenging and primarily relies on visual assessments. However, different lameness phenotypes share similar clinical symptoms and there is a limited understanding of potential biomarkers relating to such disease for further molecular diagnosis. This study aimed to identify blood miRNA profiles of feedlot cattle with various lameness phenotypes and whether they could be potential diagnostic markers to differentiate lameness phenotypes and predictive lameness recovery.ResultsMicroRNAome profiles were generated for the whole blood samples collected from feedlot cattle at Week 0 (W0) before treatment (n = 106) and longitudinal miRNA expression profiles relating to lameness recovery from W0 to W2 (n = 140) using RNA-seq. Ten miRNAs were selected to verify miRNA sequencing accuracy using stem-loop RT-qPCR. A total of 321 miRNAs were identified to be expressed in bovine blood samples with three (all downregulated, average log2fold change = -1.32), seven (two downregulated with average log2fold change = -1.15, five upregulated with average log2fold change = 1.68), six (three downregulated with average log2fold change = -1.23, three upregulated with average log2fold change = 3.31), and fourteen (eight downregulated with average log2fold change = -1.24, six upregulated with average log2fold change = 1.26) miRNAs differentially expressed (DE) miRNAs in DD, FR, TTN, and FR combined with DD (FRDD) compared to healthy control at W0 (defined as pre-treatment DE miRNAs), respectively. The predicted functions of identified DE miRNAs among different lameness phenotypes were mainly related to Zinc-finger, muscle cell development, and host inflammatory responses. Furthermore, the longitudinal miRNA expression profiles revealed that a total of eight miRNA changed patterns from W0 to W2, with the BTB/POZ-like domain being the most enriched function by longitudinal miRNA expression profiles in both unrecovered and recovered cattle. A total of nine miRNAs (five downregulated with average log2fold change = -2.4, four upregulated with average log2fold change = 3.7) from W0 to W2 were differentially expressed in unrecovered cattle compared to the recovered cattle, with functions associated with transcription regulation and Zinc-finger. Moreover, the area under the receiver operating characteristics (ROC) curve (AUC) revealed that pre-treatment DE miRNAs could serve as good diagnostic markers to differentiate any two of four phenotypes of lameness, with bta-miR-339b being able to differentiate all lameness phenotypes. Moreover, pre-treatment DE miRNAs could also predict the recovery of three lameness phenotypes (DD, FRDD, TTN) with good to excellent predictiveness.ConclusionOur results comprehensively assessed the blood miRNAomes in response to various lameness phenotypes, promoting the understanding of miRNA-regulated mechanisms of lameness in feedlot cattle. The diagnostic miRNA markers were also identified to differentiate within lameness phenotypes and predictive lameness recovery, shedding light on accurate on-farm lameness detection.

Friedrich, Juliane; Liu, Shuli; Fang, Lingzhao; Prendergast, James; Wiener, Pamela

doi: 10.1186/s12864-024-10852-8pmid: 39425030

BackgroundAfrican cattle represent a unique resource of genetic diversity in response to adaptation to numerous environmental challenges. Characterising the genetic landscape of indigenous African cattle and identifying genomic regions and genes of functional importance can contribute to targeted breeding and tackle the loss of genetic diversity. However, pinpointing the adaptive variant and determining underlying functional mechanisms of adaptation remains challenging.ResultsIn this study, we use selection signatures from whole-genome sequence data of eight indigenous African cattle breeds in combination with gene expression and quantitative trait loci (QTL) databases to characterise genomic targets of artificial selection and environmental adaptation and to identify the underlying functional candidate genes. In general, the trait-association analyses of selection signatures suggest the innate and adaptive immune system and production traits as important selection targets. For example, a large genomic region, with selection signatures identified for all breeds except N’Dama, was located on BTA27, including multiple defensin DEFB coding-genes. Out of 22 analysed tissues, genes under putative selection were significantly enriched for those overexpressed in adipose tissue, blood, lung, testis and uterus. Our results further suggest that cis-eQTL are themselves selection targets; for most tissues, we found a positive correlation between allele frequency differences and cis-eQTL effect size, suggesting that positive selection acts directly on regulatory variants.ConclusionsBy combining selection signatures with information on gene expression and QTL, we were able to reveal compelling candidate selection targets that did not stand out from selection signature results alone (e.g. GIMAP8 for tick resistance and NDUFS3 for heat adaptation). Insights from this study will help to inform breeding and maintain diversity of locally adapted, and hence important, breeds.

Olumakaiye, Richard; Corre, Christophe; Alberti, Fabrizio

doi: 10.1186/s12864-024-11064-wpmid: 39592925

BackgroundFungi are talented producers of secondary metabolites with applications in the pharmaceutical and agrochemical sectors. Aspergillus wentii CBS 141173 has gathered research interest due to its ability to produce high-value norditerpenoid compounds, including anticancer molecules. In this study, we aimed to expand the genomic information available for A. wentii to facilitate the identification of terpenoid biosynthetic genes that may be involved in the production of bioactive molecules.ResultsLong-read genome sequencing of Aspergillus wentii CBS 141173 was conducted using Oxford Nanopore Technologies (ONT) MinION MK1C. In addition, paired-end stranded RNA-seq data from two time points, 7 days and 30 days, was used for functional annotation of the assembled genome. Overall, we assembled a genome of approximately 31.2 Mb and identified 66 biosynthetic gene clusters from the annotated genome. Metabolic extracts of A. wentii were analysed and the production of the bioactive terpenoid asperolide A was confirmed. We further mined the assembled and annotated genome for BGCs involved in terpenoid pathways using a combination of antiSMASH and local BlastP and identified 16 terpene synthases. Phylogenetic analysis was conducted and allowed us to establish relationships with other characterised terpene synthases. We identified two terpene clusters potentially involved in pimarane-like diterpenoid biosynthesis. Finally, the analysis of the 16 terpene synthases in our 7-day and 30-day transcriptomic data suggested that only four of them were constitutively expressed under laboratory conditions.ConclusionThese results provide a scaffold for the future exploration of terpenoid biosynthetic pathways for bioactive molecules in A. wentii. The terpenoid clusters identified in this study are candidates for heterologous gene expression and/or gene disruption experiments. The description and availability of the long-read genome assembly of A. wentii CBS 141173 further provides the basis for downstream genome analysis and biotechnological exploitation of this species.

Strickland, Alyssa; Brown, Bonnie L.

doi: 10.1186/s12864-024-10988-7pmid: 39627704

Eastern oysters, Crassostrea virginica, are historically a keystone species in many of the estuaries in which they reside, providing critical ecosystem services. Because oyster populations have been on the decline for the past century, restoration initiatives currently are underway in many estuarine systems, including Great Bay Estuary (GBE), New Hampshire. Results of prior studies of eastern oyster population genomics cannot be applied directly to GBE, as it is a well-mixed estuarine system that is relatively contained, and the sources of recruits are split among cultivated and native. This study aimed to identify the population genomic structure of eastern oysters in GBE to facilitate determination of effective population size and estimation of genetic differentiation among subpopulations. Results showed moderate genomic differentiation among native, cultivated, and restoration C. virginica subpopulations in the Bay. A small number of breeders (Ne=163–276) was found in all subpopulations except the Lamprey River site (Ne=995). This research provides a contemporary snapshot of eastern oyster subpopulation structure at the genomic level in GBE that will facilitate restoration and enhanced management.

Martineau, Matthieu; Ambroset, Chloé; Lefebvre, Stéphanie; Kokabi, Éléna; Léon, Albertine; Tardy, Florence

doi: 10.1186/s12864-024-10789-ypmid: 39304803

BackgroundMycoplasma spp. are wall-less bacteria with small genomes (usually 0.5–1.5 Mb). Many Mycoplasma (M.) species are known to colonize the respiratory tract of both humans and livestock animals, where they act as primary pathogens or opportunists. M. equirhinis was described for the first time in 1975 in horses but has been poorly studied since, despite regular reports of around 14% prevalence in equine respiratory disorders. We recently showed that M. equirhinis is not a primary pathogen but could play a role in co-infections of the respiratory tract. This study was a set up to propose the first genomic characterization to better our understanding of the M. equirhinis species.ResultsFour circularized genomes, two of which were generated here, were compared in terms of synteny, gene content, and specific features associated with virulence or genome plasticity. An additional 20 scaffold-level genomes were used to analyse intra-species diversity through a pangenome phylogenetic approach. The M. equirhinis species showed consistent genomic homogeneity, pointing to potential clonality of isolates despite their varied geographical origins (UK, Japan and various places in France). Three different classes of mobile genetic elements have been detected: insertion sequences related to the IS1634 family, a putative prophage related to M. arthritidis and integrative conjugative elements related to M. arginini. The core genome harbours the typical putative virulence-associated genes of mycoplasmas mainly involved in cytoadherence and immune escape.ConclusionM. equirhinis is a highly syntenic, homogeneous species with a limited repertoire of mobile genetic elements and putative virulence genes.