Abstract Background Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, it is not well studied in livestock, including cattle. Results To investigate their distributions in the cattle sperm genome, we sequenced 143 single sperms from two Holstein bulls. We mapped meiotic recombination events at high resolution based on phased heterozygous single nucleotide polymorphism (SNP). In the absence of evolutionary selection pressure in fertilization and survival, recombination events in sperm are enriched near distal chromosomal ends, revealing that such a pattern is intrinsic to the molecular mechanism of meiosis. Furthermore, we further validated these findings in single sperms with results derived from sequencing its family trio of diploid genomes and our previous studies of recombination in cattle. Conclusions To our knowledge, this is the first large-scale single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of recombination, genome instability, and male infertility.
Tobacco (Nicotiana tabacum L.) is an important cash crop in China, with an estimated production of 2.2 million tons every year (Berbeć and Matyka, 2020). In June 2020, a root rot disease was observed on tobacco (cv. Zhongyan 100) in four surveyed counties (Mianchi, Lushi, Duguan and Lingbao) in Sanmenxia. Diseased plants exhibited leaf chlorosis and purplish to brown vascular discoloration of stem, taproot and lateral roots. The disease incidence ranged from 15% to 40% in 11 surveyed fields, 36.7 ha in total. Twenty five diseased tissues were surface sterilized in 75% ethanol and placed on potato dextrose agar (PDA) medium. Fifteen single-spore isolates were obtained from 25 diseased tissue samples. All cultures growing on PDA had white colonies with abundant aerial mycelia initially, turning into yellow to orange in the center and produced red pigmentation after seven days of growth. The 7-day-old cultures grown on carnation leaf agar (CLA) produced macroconidia that were curved with 3-5 septa, had wide central cells, slightly pointy apex, and measured 17.0-45.9 μm long×3.0-4.6 μm wide (n=50). The microconidia formed on CLA were slightly curved, ovoid with zero to two septa, measuring 5.4-15.5 μm long×2.0-3.2 μm wide (n=50). Spherical chlamydospores (7.58-13.52 μm; n=50) were terminal or intercalary, single or in chains. Such characteristics were typical of Fuarium brachygibbosum (Tirado-Ramírez et al. 2018). DNA from one representative single-spore isolate (MC1) was extracted, and the translation elongation factor 1-alpha (EF1-α), RNA polymerase I largest subunit (RPB1) and second largest subunit (RPB2) genes were amplified with primers EF1/EF2, F5/G2R and RPB2F/R respectively (O'Donnell et al. 1998, 2010), and sequenced. Sequences were submitted to GenBank under accession numbers MT947796 (EF1-α), MW679536 (RPB1) and MW430664 (RPB2). The consensus sequences showed 99.70%, 99.94% and 100% identity to the sequences of F. brachygibbosum strain NRRL 34033 (accession no. GQ505418.1, HM347172.1 and GQ505482.1, Wang et al 2021). Morphological and molecular results confirmed this species as F. brachygibbosum (Al-Mahmooli, et al., 2013, Rentería -Martínez, et al., 2018). Pathogenicity tests were performed on tobacco seedlings grown on autoclaved tobacco specific substrate (Tobacco specific matrix, Ainong Biotechnology Co. Ltd, China). Healthy six-leaf stage tobacco seedlings (n=30; Zhongyan 100) were inoculated by placing 7-days old wheat seed (15 seeds per plant) infested with MC1 around the root. Thirty seedlings inoculated with sterile wheat seeds served as controls. All the plants were maintained in a growth chamber at 25±0.5℃ and 70% relative humidity. The assay was conducted three times. Typical symptoms of foliage chlorosis and root browning were observed 7-14 days after inoculation. The pathogen was reisolated from the necrotic tissue from all inoculated seedlings and was identified by sequencing partial EF1-α and RPB2 genes. Control plants remained asymptomatic and no pathogen was recovered from the control plants. Fusarium brachygibbosum is known as a pathogen of grains and cash crops in China (Shan, et al., 2017, Xia, et al., 2018). To our knowledge, this is the first report of F. brachygibbosum causing root rot on tobacco. We believe that our results will help to better understand rhizome fungal diseases affecting tobacco production in China. Acknowledgements: Funding was provided by the Science and Technology Project of Henan Provincial Tobacco Company (2020410000270012), Independent Innovation Project of Hennan Academy of Agricultural Sciences (2020ZC18) and Research and Development project of Henan Academy of Agricultural Sciences (2020CY010). References: Al-Mahmooli, I. H., et al. 2013. Plant Dis. 97:687; https://doi.org/10.1094/PDIS-09-12-0828-PDN Berbeć A. K. and Matyka M. 2020. Agric. 10(11), 551; https://doi.org/10.3390/agriculture10110551 O'Donnell, K., et al. 1998. P. Natl. Acad. Sci. USA. 95(5):2044-2049; https://doi.org/10.1073/pnas.95.5.2044 O'Donnell, K., et al. 2010. J. Clin. Microbiol. 48(10)3708-3718; https://doi.org/10.1128/JCM.00989-10 Rentería -Martínez M.E., et al. 2018. Mex. J. of Phytopathol. 36(2):1-23; https://doi.org/10.18781/R.MEX.FIT.1710-1 Shan, L. Y., et al. 2017. Plant Dis. 101:837; https://doi.org/10.1094/PDIS-10-16-1465-PDN Tirado-Ramírez, M. A., et al. 2018. Plant Dis. 103; https://doi.org/10.1094/PDIS-04-18-0710-PDN Wang, S., et al. 2021. Plant Dis. 2021 Jan 6. doi: 10.1094/PDIS-05-20-0941-PDN. Epub ahead of print. PMID: 33406862. Xia, B., et al. 2018. Plant Dis. 102(11):2372; https://doi.org/10.1094/PDIS-12-17-1939-PDN The author(s) declare no conflict of interest.
Abstract miRNAs are encoded by eukaryotic genomes and are characterized by tissue-specific and temporal expression, suggesting that miRNAs play multiple roles in different tissues and developmental periods of a species through a variety of regulatory pathways. miR-144 regulates cell development in other species, but its regulatory mechanism in bovine skeletal muscle satellite cells (BSMSCs) is unknown. So, this experiment was designed to elucidate the function of miR-144 in BSMSCs development. It was found that miR-144 promoted the proliferation of BSMSCs, but it plays an inhibitory role in the differentiation process. After transfection of the miR-144 mimic, 476 differentially expressed genes (DEGs) were detected by RNA-seq, and these DEGs mainly regulate adrenergic, MAPK, and PI3K-AKT signaling pathways. Further studies revealed that bta-miR-144 targets binding to the NACC1 gene; whereas NACC1 regulates BSMSCs in a manner opposite to bta-miR-144. These findings suggest that miR-144 negatively regulates BSMSCs development by targeting the NACC1gene.
Additional file 3. Differentially expressed genes (DEGs) between the Resistant and Susceptible lines in the TSF flock. Genes with significantly different abundance between the Resistant and Susceptible lines in response to a primary Haemonchus contortus infection in the Trichostrongylus Selection Flock (TSF) at a False Discovery Rate (FDR)â
Additional file 9. 277 unique differentially expressed genes detected using the STAR-EdgeR pipeline. 185 of the 277 genes, approximately, 67% of the all DEGs identified by the STAR pipeline are also detected using the same stringency cutoff by the Tophat2-Cufflink-Cuffdiff pipeline.
Abstract Deoxyribonucleic acid (DNA) represents an important class of molecular building blocks for the assembly of supramolecular functional systems primarily due to its molecular recognition capability and sequence programmability. Eventually, DNA‐based nanostructures are assembled in a way that their states remain at the thermodynamic minimum of the energy. However, active life‐like functions and their interactive adaption require the integration of energy away from thermodynamic equilibrium. The construction of DNA‐based artificial systems was often inspired by the naturally occurring dissipative assembly processes, which leads to the consumption of energy to maintain the thermodynamically non‐equilibrium state. In this review, the recent progress of the fabrications and properties of DNA‐based dissipative assembly systems toward nanoarchitectonics is summarized. It focuses on the principle of dissipative assembly and shows some pioneering examples of DNA‐based dissipative assembly systems. The latest corresponding perspectives are also proposed.
The rumen bacterial composition of both pre- ruminant dairy calves and cows and beef steers was surveyed using pyrosequencing of the 16S rRNA gene. Sequences were analyzed using taxonomy-dependent and -independent clustering methods. The core rumen microbiome, regardless of the rumen developmental status or breeds, consisted of 8 phyla, 11 classes, 15 families, and 17 genera. Principal component analysis and clustering demonstrated that the bacterial communities in the rumen of pre-ruminant dairy calves, dairy cows, and beef steers were clearly distinguishable. Approximately 66% of phyla and 41% of Operational Taxonomic Units (OTUs) in a typical rumen bacterial community differed in relative abundance between the developing and mature rumen. Greater abundance of Fibrobacteraceae and Ruminococaceae in the rumen of beef steers likely reflected the need for enhanced fiber-digesting capacity in beef cattle. Our results should facilitate understanding of the structural and functional relationships in the rumen microbial ecosystem.
This study aimed to identify long non-coding RNA (lncRNA) from the rumen tissue in dairy cattle, explore their features including expression and conservation levels, and reveal potential links between lncRNA and complex traits that may indicate important functional impacts of rumen lncRNA during the transition to the weaning period.A total of six cattle rumen samples were taken with three replicates from before and after weaning periods, respectively. Total RNAs were extracted and sequenced with lncRNA discovered based on size, coding potential, sequence homology, and known protein domains. As a result, 404 and 234 rumen lncRNAs were identified before and after weaning, respectively. However, only nine of them were shared under two conditions, with 395 lncRNAs found only in pre-weaning tissues and 225 only in post-weaning samples. Interestingly, none of the nine common lncRNAs were differentially expressed between the two weaning conditions. LncRNA averaged shorter length, lower expression, and lower conservation scores than the genome overall, which is consistent with general lncRNA characteristics. By integrating rumen lncRNA before and after weaning with large-scale GWAS results in cattle, we reported significant enrichment of both pre- and after-weaning lncRNA with traits of economic importance including production, reproduction, health, and body conformation phenotypes.The majority of rumen lncRNAs are uniquely expressed in one of the two weaning conditions, indicating a functional role of lncRNA in rumen development and transition of weaning. Notably, both pre- and post-weaning lncRNA showed significant enrichment with a variety of complex traits in dairy cattle, suggesting the importance of rumen lncRNA for cattle performance in the adult stage. These relationships should be further investigated to better understand the specific roles lncRNAs are playing in rumen development and cow performance.
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