Animal Gene最新文献

{"title":"Estimation of cell type proportions from bulk RNA-Seq of porcine whole blood samples using partial reference-free deconvolution","authors":"Brittney N. Keel,&nbsp;Amanda K. Lindholm-Perry,&nbsp;Gary A. Rohrer,&nbsp;William T. Oliver","doi":"10.1016/j.angen.2023.200159","DOIUrl":"https://doi.org/10.1016/j.angen.2023.200159","url":null,"abstract":"<div><p>Whole blood has become increasingly utilized in transcriptomic studies because it is easily accessible and can be collected from live animals with minimal invasiveness. However, whole blood represents an extremely complex mixture of cell types, and cell type proportions can confound downstream statistical analyses. Information on cell type proportions may be missing from blood transcriptome studies for a variety of reasons. Experimental approaches for cell counting, such as cell sorting, are arduous and expensive, and therefore may not feasible for studies conducted on a limited budget. Statistical deconvolution can be applied directly to transcriptomic data sets to estimate cell type proportions. In addition to being financially advantageous, computational deconvolution can readily be applied to old datasets, where it may be difficult or impossible to re-analyze for cell type information. In an effort to assist researchers in recovering cell type proportions from porcine whole blood transcriptome samples, we present a manually curated set of porcine blood cell markers that can be utilized in a partial reference-free deconvolution framework to obtain estimates of cell types measured in a standard complete blood count (CBC) panel, which includes neutrophils, lymphocytes, monocytes, eosinophils, basophils, and red blood cells.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"30 ","pages":"Article 200159"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50194484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl","authors":"Ashutosh Sharma ,&nbsp;Sagar Sharad Shinde ,&nbsp;Nagarjun Vijay","doi":"10.1016/j.angen.2023.200157","DOIUrl":"https://doi.org/10.1016/j.angen.2023.200157","url":null,"abstract":"<div><p><span>Small and midsize deletions and insertions<span><span> (InDels) are major events that play a crucial role in the evolution of genome size and contribute to the </span>genetic<span><span> and phenotypic diversity of species. In recent years, considerable attention has been given to studying small indels associated with various developmental, growth, and production traits in domestic chicken breeds. Additionally, small and midsize indels have been studied between chicken and phylogenetically more distant species such as duck, turkey, </span>rock pigeon, and other passerine birds. However, the investigation of small and midsize deletions in the wild relatives of chickens has been relatively overlooked until now. To address this gap, our study aimed to identify the presence and distribution of midsize deletions (&gt; 1 Kb) in the wild relatives of chickens. We conducted a comparative genomic analysis using high-quality genomic data from four species belonging to the </span></span></span><span><em>Gallus</em></span> genus. Our analysis revealed the existence of &gt;125 midsize deletions in the three other species compared to <span><em>Gallus gallus</em></span><span> (red junglefowl). These midsize deletions were found to be distributed in intergenic regions<span> and within introns of various protein-coding genes but not in the exonic regions of protein-coding genes. Furthermore, we observed a trend between the number of midsize deletions and the phylogenetic distance in the phylogeny of the </span></span><em>Gallus</em> genus. The most ancestral species, <em>Gallus varius</em> (green junglefowl), exhibited the highest deletions, followed by <em>Gallus lafayettii</em> (Ceylon junglefowl) and <em>Gallus sonneratii</em><span> (grey junglefowl). Some protein-coding genes harboring deletions in their introns and upstream regions were associated with body development, production, growth traits<span><span>, abdominal fat<span> deposition, behavioral patterns such as stress, fear, anxiety, plumage color, and adaptation to extreme climatic conditions. Our study finds that the midsize deletions identified in wild relatives of red junglefowl contribute &lt;1% of </span></span>DNA loss with a rate of 8–44 Kb/My during the evolution of the </span></span><em>Gallus</em> genus.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"30 ","pages":"Article 200157"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50194485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “Biosafety assessment of lactic acid probiotic isolates obtained from the gastrointestinal tract of livestock, poultry and bees native to Iran” [Animal Gene volume 27 (March 2023) 200140]","authors":"Ramin Seighalani,&nbsp;Maryam Royan,&nbsp;Morteza Fardi","doi":"10.1016/j.angen.2023.200160","DOIUrl":"https://doi.org/10.1016/j.angen.2023.200160","url":null,"abstract":"","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"30 ","pages":"Article 200160"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50194486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"K-ras proto-oncogene (KRAS): Evolutionary dissection on the indispensable predictive and prognostic cancer biomarker across 32 primates","authors":"Leonard Whye Kit Lim","doi":"10.1016/j.angen.2023.200158","DOIUrl":"10.1016/j.angen.2023.200158","url":null,"abstract":"<div><p>The Kirsten rat sarcoma (KRAS) gene is one of the most critical proto-oncogene to target in combating various cancers as its mutation is one of the major cancer-causing causes in most cancers. In this study, we investigated all 32 primate KRAS nucleotide and protein sequences<span><span><span> found within the public GenBank database. The Tibetan macaque KRAS protein supersedes the others in terms of amino acid length, molecular weight and </span>isoelectric point. The motif distribution of the Tibetan macaque was also found to vary significantly from the other KRAS proteins examined. Nevertheless, the predicted protein three-dimensional structure of Tibetan macaque did not differ much from that of human and Ugandan red </span>colobus<span>. Fascinatingly, the Coquerel’s sifaka KRAS protein structure and conformation is distinctive from all other 31 primate KRAS proteins. The maximum likelihood phylogenetic tree revealed several potential candidates that are closely related to that of the human KRAS protein to aid future human personalised therapy studies.</span></span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"30 ","pages":"Article 200158"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49466769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative mitogenomic analysis confirms that the southern African long-snout pipefish Syngnathus temminckii is distinct from the northern hemisphere Syngnathus acus","authors":"Arsalan Emami-Khoyi","doi":"10.1016/j.angen.2023.200163","DOIUrl":"https://doi.org/10.1016/j.angen.2023.200163","url":null,"abstract":"<div><p>Sequencing of mitochondrial genomes is a powerful tool to resolve taxonomic relationships between closely related taxa with high confidence. <em>Syngnathus temminckii</em> is a pipefish species endemic to Southern Africa. The taxonomic status of this species and the phylogenetic relationship with its widely distributed northern hemisphere congener <em>Syngnathus acus</em> has been subject to uncertainty. The current study is the first to assemble, annotate and describe the complete mitochondrial genome of this species, and investigate phylogenetic relationships with its northern hemisphere sister taxa. The mitogenome assembly pipeline reconstructed a circular contig 16,452 bp in length, with an average GC content of 44.8%. A total of 37 mitogenomic features, including 13 protein-coding genes, 22 tRNAs, two rRNAs and a putative control region, were annotated. A Bayesian phylogenetic analysis confirmed that <em>S. temminckii</em> is a distinct southern African species that diverged from a northern hemisphere clade of pipefishes that includes its congener <em>S. acus</em> approximately seven million years ago.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"30 ","pages":"Article 200163"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2352406523000192/pdfft?md5=86b9e9e548ec8ffdcec4df55e3cac261&pid=1-s2.0-S2352406523000192-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138548835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of miRNAs in regulating virus replication","authors":"Sakshi Pandita ,&nbsp;Assim Verma ,&nbsp;Naveen Kumar","doi":"10.1016/j.angen.2023.200162","DOIUrl":"https://doi.org/10.1016/j.angen.2023.200162","url":null,"abstract":"<div><p><span><span>MicroRNAs (miRNAs) are short non-coding RNAs that play an important role in the regulation of gene expression. In addition to being encoded by the host cells, miRNAs are also encoded by certain DNA and </span>RNA viruses, blurring the lines between host and </span>viral genetic<span><span> regulation. This duality allows miRNAs to assume both antiviral and proviral roles in the viral life cycle. Furthermore, miRNAs exert profound influence over immune responses, viral latency, host susceptibility<span> to infections, cellular differentiations and pathways governing </span></span>programmed cell death<span>. In this comprehensive discussion, we delve into the current state of knowledge regarding miRNAs, including the diverse types of miRNAs, such as canonical and viral miRNAs, and explore their multifaceted roles in virus replication, pathogenesis, and immune modulation<span>. This exploration enhances our understanding of the intricate interplay between viruses and their host organisms and encompasses various other RNA molecules that contribute to this dynamic landscape.</span></span></span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"30 ","pages":"Article 200162"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50194482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Does atp8 exist in the mitochondrial genome of Proseriata (Metazoa: Platyhelminthes)?","authors":"Daisuke Shimada ,&nbsp;Shimpei F. Hiruta ,&nbsp;Kazuhiro Takahoshi ,&nbsp;Hiroshi Kajihara","doi":"10.1016/j.angen.2023.200161","DOIUrl":"https://doi.org/10.1016/j.angen.2023.200161","url":null,"abstract":"<div><p><span>The adenosine triphosphate (ATP) synthase F</span>₀ subunit 8 gene (<em>atp8</em><span><span><span>) had been believed to be absent in mitochondrial genomes<span> of platyhelminths until the late 2010s, since when multiple lines of emergent evidence have suggested that this gene is actually present, albeit in highly derived forms, throughout the entire phylum except for the parasitic </span></span>Neodermata (tapeworms, </span>flukes, and their kin). Of about 11 non-parasitic (turbellarian) major platyhelminth subtaxa, the existence of </span><em>atp8</em><span><span> has hitherto been documented in five (Catenulida, Macrostomorpha, Polycladida, </span>Rhabdocoela, and Tricladida), while it remains open in the remaining six (Prorhynchida, Gnosonesmida, Proseriata, Fecampiida, Prolecithophora, and Bothrioplanida). Here we report the mitochondrial genome sequence of an undetermined marine interstitial turbellarian species in the genus </span><em>Nematoplana</em> <span>Meixner, 1938</span><span><span> as the first representative of Proseriata. This circular genome comprises 16,106 bp (but potentially 18,812–19,277 bp when unresolved, non-coding tandem repeats are considered) and includes 38 genes, viz. 23 transfer </span>RNA genes, 13 protein-coding genes (including the putative </span><em>atp8</em>), and two ribosomal RNA genes. The putative <em>atp8</em> in <em>Nematoplana</em> sp. was not annotated by a standard automated procedure but was detected by manual inspection. If it encodes a translated product, it consists of 156 bp, with the potential 52-amino-acid-residue product beginning with MPHV, instead of the metazoan-canonical MPQL, and containing a single putative transmembrane region expanding from the 7th to the 29th amino-acid positions. While our finding seemingly strengthens the hypothesis that <em>atp8</em> is in the ground pattern of flatworm mitochondrial genomes, whether the putative <em>atp8</em> in flatworms is actually transcribed and translated to form a functional ATP synthetase F₀ subunit should be tested in future studies.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"30 ","pages":"Article 200161"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50194483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide signature of positive selection in Ethiopian indigenous and European beef cattle breeds","authors":"Dejenie Mengistie ,&nbsp;Zewdu Edea ,&nbsp;Tesfaye Sisay Tesema ,&nbsp;Genet Dejene ,&nbsp;Tadelle Dessie ,&nbsp;Jeilu Jemal ,&nbsp;Ermias Asefa ,&nbsp;Kwan Suk Kim ,&nbsp;Behailu Samuel ,&nbsp;Hailu Dadi","doi":"10.1016/j.angen.2023.200151","DOIUrl":"10.1016/j.angen.2023.200151","url":null,"abstract":"<div><h3>Background</h3><p><span>Despite the availability of genome-wide SNPs to uncover the origin and divergence of Ethiopian cattle population, knowledge regarding their genetic adaptability and divergence remain limited. To investigate signature of selection, three Ethiopian </span>cattle breeds<span> were genotyped with 80 K SNP array and three European beef cattle breeds were also used for comparison purposes.</span></p></div><div><h3>Results</h3><p><span><span>Across Ethiopian cattle populations, the mean observed and expected heterozygosity<span> were 0.403 and 0.400, respectively, and for European beef cattle breeds observed and expected heterozygosity were 0.25 and 0.26 respectively. PCA and NJ-tree grouped the study cattle according to their breed group with close clustering of Ethiopian cattle breeds. The top 1% values were considered to delimit genomic regions under positive selection. Some of the candidate genes involved in </span></span>biological processes and pathways linked to meat quality attributes. Furthermore, some of the candidate genes associated with tropical adaptation like </span>heat tolerance and resistance to disease.</p></div><div><h3>Conclusion</h3><p>The genetic divergence of Ethiopian breeds from European beef breeds coincides with existing knowledge that European cattle breeds considered in this study are artificially selected for beef traits, while Ethiopian indigenous breeds are naturally selected.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"29 ","pages":"Article 200151"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48069438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of evolutionary imprints among the gut bacteria in phytobiotic supplemented Gallus gallus domesticus","authors":"Soundararajan Sowmiya ,&nbsp;Ragothaman Prathiviraj ,&nbsp;Joseph Selvin ,&nbsp;R. Jasmine","doi":"10.1016/j.angen.2023.200153","DOIUrl":"10.1016/j.angen.2023.200153","url":null,"abstract":"<div><p><span><span>The gut microbiota<span> is an essential part of metabolism, assists in the breakdown of complex carbohydrates, proteins and lipids that enter into the </span></span>digestive tract. Numerous microbial metabolites thus produced can have local and systemic effects which may influence health positively or negatively. The microbial population's dominance in the gut depends on the number of compounds present in the organ. Hence we have focused on analyzing the role of </span><span><em>Moringa oleifera</em></span><span><span> as phytobiotic supplementation in enhancing the beneficial gut microbiota in chicken models. Probiotics improve gut health in chickens through several mechanisms, including tight junction enhancement, </span>nutrient uptake<span>, niche colonization and co-aggregation with enteropathogens. The bacteria from the gut samples obtained from </span></span><em>M.oleifera</em><span> treated chickens were analyzed for various standard morphological and biochemical tests<span>, genotypic classification using 16S rRNA gene sequencing and evaluation of evolutionary marks among the gut bacteria to determine whether they fit the criteria for probiotic traits. A variety of the consequences of beneficial gut microorganisms for hosts could attribute to bacterial communities' processes and the host's capacity for influencing the same processes. According to our study, phylogenetic analysis and taxonomy of the host significantly shape the intestinal flora across a range of host taxonomic levels. However, host ecology (</span></span><em>i.e.</em>, diet) can further alter these gut flora, particularly in the case of many closely related host species.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"29 ","pages":"Article 200153"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46634181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete mitogenome of blue sheep (Pseudois nayaur) from the Indian Himalayan Region and its comparative phylogenetic relationship with other related species","authors":"Deepesh Saini,&nbsp;Prabhaker Yadav,&nbsp;Vishnupriya Kolipakam,&nbsp;Sambandam Sathyakumar,&nbsp;Sandeep Kumar Gupta","doi":"10.1016/j.angen.2023.200155","DOIUrl":"10.1016/j.angen.2023.200155","url":null,"abstract":"<div><p>The ‘<em>Bharal</em>’ or ‘Himalayan Blue Sheep’ (<span><em>Pseudois nayaur</em></span><span><span><span>) is endemic to the Himalayan and Tibetan Regions. There are gaps in the available database for the blue sheep mitogenome sequencing from the Indian region. We sequenced and characterized the whole mitogenome of one blue sheep individual using the Illumina Nova-seq 6000 platform, which was 16,718 bp in length. It included 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding control region (D loop). It was compared with other complete mitochondrial </span>DNA sequences<span> of blue sheep from the NCBI database. The whole mitogenome of blue sheep was found to be highly AT-biased (60%) and had a positive AT skew (0.121) and a negative GC skew (−0.341). In 13 PCGs of blue sheep, Leucine (15.58%) and </span></span>tryptophan<span><span> (2.72%) occurred most frequently. A typical secondary cloverleaf structure was observed for all tRNA genes except for tRNA-Ser, where a stable structure of dihydrouridine did not develop. The </span>phylogenetic analysis showed Indian blue sheep population formed a separate clade with a genetic distance of 3.7 to 4.1% from the Chinese blue sheep population, suggesting it to be of a different lineage and genetically qualifies the status of distinct subspecies. The results of this study will help in further phylogenetic analysis of Indian blue sheep populations in the Western and Eastern Himalayan regions and in understanding lineage identification and evolution for further research.</span></span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"29 ","pages":"Article 200155"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47597066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}