RESUMEN
CFAP58 is a testis-enriched gene that plays an important role in the sperm flagellogenesis of humans and mice. However, the effect of CFAP58 on bull semen quality and the underlying molecular mechanisms involved in spermatogenesis remain unknown. Here, we identified two single-nucleotide polymorphisms (rs110610797, A>G and rs133760846, G>T) and one indel (g.-1811_ g.-1810 ins147bp) in the promoter of CFAP58 that were significantly associated with semen quality of bulls, including sperm deformity rate and ejaculate volume. Moreover, by generating gene knockout mice, we found for the first time that the loss of Cfap58 not only causes severe defects in the sperm tail, but also affects the manchette structure, resulting in abnormal sperm head shaping. Cfap58 deficiency causes an increase in spermatozoa apoptosis. Further experiments confirmed that CFAP58 interacts with IFT88 and CCDC42. Moreover, it may be a transported cargo protein that plays a role in stabilizing other cargo proteins, such as CCDC42, in the intra-manchette transport/intra-flagellar transport pathway. Collectively, our findings reveal that CFAP58 is required for spermatogenesis and provide genetic markers for evaluating semen quality in cattle.
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Análisis de Semen , Semen , Humanos , Bovinos , Masculino , Animales , Ratones , Cabeza del Espermatozoide , Espermatozoides , Ratones NoqueadosRESUMEN
Feeder cells play important roles in In-vitro culture of stem cells. However, the preparation protocol of feeder cells produced by bovine embryonic fibroblast cells (bEFs) is still lack. In this study, the preparation of bEF-feeder by Mitomycin C was optimized with different concentrations and treatment time. The cell viability of bEFs was detected by CCK8 and 5-Ethynyl-2'-deoxyuridine. The growth of bESCs in each bEFs-feeder group was assessed by alkaline phosphatase staining and CCK8. Quantitative real time PCR was used to detect the mRNA expression of pluripotency-related genes of bESCs. Results showed that the proliferation of bEFs was significantly repressed while bEFs were treated with 14 ug/mL or 16 ug/mL Mitomycin C for 3 h, and the cell viability within 2-4 days after treatment was consistent with the 1st day. The numbers of bESCs clones in bEF-feeder treated with 14 µg/mL Mitomycin C for 3 h or 16 µg/mL Mitomycin C for 3 h were significantly higher than that in bEF-feeder treated with 8 µg/mL Mitomycin C for 8 h or bEFs treated with 6 µg/mL Mitomycin C for 9 h. The mRNA expression of pluripotency-related genes in bESCs cultured by bEF-feeder were higher than the MEF-feeder, the clone morphology of bESCs cultured in bEF-feeder was rounder and sharper than the MEF-feeder. In conclusion, the bEF-feeder prepared with 14 µg/mL Mitomycin C for 3 h or 16 µg/mL Mitomycin C for 3 h could effectively maintains the growth of bESCs, and bEF-feeder is more suitable for bESCs culture than the MEF-feeder.
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Técnicas de Cultivo de Célula , Células Nutrientes , Fibroblastos , Mitomicina , Células Madre Pluripotentes , Bovinos , Supervivencia Celular/efectos de los fármacos , Mitomicina/farmacología , Células Madre Pluripotentes/citología , AnimalesRESUMEN
Genetic improvement of milk fatty acid content traits in dairy cattle is of great significance. However, chromatography-based methods to measure milk fatty acid content have several disadvantages. Thus, quick and accurate predictions of various milk fatty acid contents based on the mid-infrared spectrum (MIRS) from dairy herd improvement (DHI) data are essential and meaningful to expand the amount of phenotypic data available. In this study, 24 kinds of milk fatty acid concentrations were measured from the milk samples of 336 Holstein cows in Shandong Province, China, using the gas chromatography (GC) technique, which simultaneously produced MIRS values for the prediction of fatty acids. After quantification by the GC technique, milk fatty acid contents expressed as g/100 g of milk (milk-basis) and g/100 g of fat (fat-basis) were processed by five spectral pre-processing algorithms: first-order derivative (DER1), second-order derivative (DER2), multiple scattering correction (MSC), standard normal transform (SNV), and Savitzky-Golsy convolution smoothing (SG), and four regression models: random forest regression (RFR), partial least square regression (PLSR), least absolute shrinkage and selection operator regression (LassoR), and ridge regression (RidgeR). Two ranges of wavebands (4000~400 cm-1 and 3017~2823 cm-1/1805~1734 cm-1) were also used in the above analysis. The prediction accuracy was evaluated using a 10-fold cross validation procedure, with the ratio of the training set and the test set as 3:1, where the determination coefficient (R2) and residual predictive deviation (RPD) were used for evaluations. The results showed that 17 out of 31 milk fatty acids were accurately predicted using MIRS, with RPD values higher than 2 and R2 values higher than 0.75. In addition, 16 out of 31 fatty acids were accurately predicted by RFR, indicating that the ensemble learning model potentially resulted in a higher prediction accuracy. Meanwhile, DER1, DER2 and SG pre-processing algorithms led to high prediction accuracy for most fatty acids. In summary, these results imply that the application of MIRS to predict the fatty acid contents of milk is feasible.
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Lactancia , Leche , Animales , Femenino , Bovinos , Leche/química , Ácidos Grasos/análisis , Espectrofotometría Infrarroja/métodos , Análisis de los Mínimos CuadradosRESUMEN
BACKGROUND: Bulbus Fritillariae Cirrhosae (BFC) is an endangered high-altitude medicine and food homology plant with anti-tumor, anti-asthmatic, and antitussive activities as it contains a variety of active ingredients, especially steroidal alkaloids. Bulbus Fritillariae Thunbergia (BFT) is another species of Fritillaria that grows at lower altitude areas. Production of plant-derived active ingredients through a synthetic biology strategy is one of the current hot topics in biological research, which requires a complete understanding of the related molecular pathways. Our knowledge of the steroidal alkaloid biosynthesis in Fritillaria species is still very limited. RESULTS: To promote our understanding of these pathways, we performed non-target metabolomics and transcriptome analysis of BFC and BFT. Metabolomics analysis identified 1288 metabolites in BFC and BFT in total. Steroidal alkaloids, including the proposed active ingredients of Fritillaria species peimine, peimisine, peiminine, etc., were the most abundant alkaloids detected. Our metabolomics data also showed that the contents of the majority of the steroidal alkaloids in BFC were higher than in BFT. Further, our comparative transcriptome analyses between BFC and BFT identified differentially expressed gene sets among these species, which are potentially involved in the alkaloids biosynthesis of BFC. CONCLUSION: These findings promote our understanding of the mechanism of steroidal alkaloids biosynthesis in Fritillaria species.
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Alcaloides , Fritillaria , Fritillaria/genética , Perfilación de la Expresión Génica , Metaboloma , Raíces de PlantasRESUMEN
BACKGROUND: Gram-negative bacteria are important pathogens in cattle, causing severe infectious diseases, including mastitis. Lipopolysaccharides (LPS) are components of the outer membrane of Gram-negative bacteria and crucial mediators of chronic inflammation in cattle. LPS modulations of bovine immune responses have been studied before. However, the single-cell transcriptomic and chromatin accessibility analyses of bovine peripheral blood mononuclear cells (PBMCs) and their responses to LPS stimulation were never reported. RESULTS: We performed single-cell RNA sequencing (scRNA-seq) and single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) in bovine PBMCs before and after LPS treatment and demonstrated that seven major cell types, which included CD4 T cells, CD8 T cells, and B cells, monocytes, natural killer cells, innate lymphoid cells, and dendritic cells. Bioinformatic analyses indicated that LPS could increase PBMC cell cycle progression, cellular differentiation, and chromatin accessibility. Gene analyses further showed significant changes in differential expression, transcription factor binding site, gene ontology, and regulatory interactions during the PBMC responses to LPS. Consistent with the findings of previous studies, LPS induced activation of monocytes and dendritic cells, likely through their upregulated TLR4 receptor. NF-κB was observed to be activated by LPS and an increased transcription of an array of pro-inflammatory cytokines, in agreement that NF-κB is an LPS-responsive regulator of innate immune responses. In addition, by integrating LPS-induced differentially expressed genes (DEGs) with large-scale GWAS of 45 complex traits in Holstein, we detected trait-relevant cell types. We found that selected DEGs were significantly associated with immune-relevant health, milk production, and body conformation traits. CONCLUSION: This study provided the first scRNAseq and scATAC-seq data for cattle PBMCs and their responses to the LPS stimulation to the best of our knowledge. These results should also serve as valuable resources for the future study of the bovine immune system and open the door for discoveries about immune cell roles in complex traits like mastitis at single-cell resolution.
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Cromatina , Leucocitos Mononucleares , Lipopolisacáridos , Transcriptoma , Animales , Bovinos/inmunología , Cromatina/genética , Cromatina/metabolismo , Femenino , Inmunidad Innata , Leucocitos Mononucleares/metabolismo , Lipopolisacáridos/farmacología , Linfocitos/metabolismo , FN-kappa B/metabolismoRESUMEN
Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.
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Altitud , Polimorfismo de Nucleótido Simple , Aclimatación/genética , Alelos , Animales , Bovinos/genética , Genotipo , Selección GenéticaRESUMEN
PREMISE: Evolutionary transitions among floral morphologies, many of which provide evidence for adaptation to novel pollinators, are common. Some trumpet-shaped flowers are among the largest flowers in angiosperms, occurring in different lineages. Our goal was to investigate the role of pollinators in the evolution of these flowers using Lilium. METHODS: We investigated floral traits and pollinators of L. primulinum var. ochraceum and L. brownii var. viridulum and reviewed reports of visitors to huge trumpet-shaped flowers. Using a published phylogeny of Lilium, we reconstructed ancestral floral morphological states in Lilium to elucidate the origins of trumpet-shaped lilies. RESULTS: Both lilies are largely self-incompatible and show floral syndromes indicative of hawkmoth pollination. The short trumpet-shaped lily can be pollinated by short-tongued (<40 mm) but not long-tongued hawkmoths (>65 mm), while the huge trumpet-shaped lily can be pollinated by both. A literature review including 22 species of trumpet-shaped flowers suggests that their pollinator guilds commonly include both short- and long-tongued moths. A phylogenetic reconstruction indicates that trumpet-shaped lilies possibly have multiple origins from tepal-reflexed ancestors, at least six of which have evolved huge flowers (>50 mm). CONCLUSIONS: Adaptation to short-tongued hawkmoths may have initiated the evolution of trumpet-shaped lilies. Huge trumpet-shaped lilies may have evolved as a response to selection by long-tongued hawkmoths, without excluding the short-tongued ones. This evolutionary pathway leads to a functionally more generalized pollination system instead of an increasingly specialized one and is not necessarily associated with pollinator shifts.
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Flores/anatomía & histología , Lilium/anatomía & histología , Lilium/fisiología , Polinización , Animales , Cadena Alimentaria , Mariposas Nocturnas/fisiología , Filogenia , Especificidad de la EspecieRESUMEN
Explaining how plants from eastern Asia migrated to other Northern Hemisphere regions is still challenging. The genus Sorbus sensu stricto (including c. 88 species) is considered as a good example to illuminate this scenario, due to the wide distribution in the temperate zone and high diversity in the Himalayas and Hengduan Mountains. Based on four nuclear markers (LEAFY-2, GBSSI-1, SBEI and WD) and one chloroplast marker (rps16-trnK), we reconstructed the phylogenetic relationship of Sorbus using 54 taxa (60% of the genus representing all subgenera, sections, or series and geographical areas in the previous classifications), and estimated divergence time and historical biogeography of the genus. Phylogenetic analyses supported that the subgenera Sorbus and Albo-carmesinae, as defined by traditional morphological characters (such as fruit color), are suitable. However, five clades defined by phylogenetic analysis of the genus are not consistent with traditionally defined sections or series. Molecular dating and biogeographic reconstruction showed that the age of the most recent common ancestor was estimated at 41mya (95% HPD: 49-35mya) in eastern Asia. Four dispersal events are assumed to explain the wide distribution of Sorbus in the temperate zone and diversification in the edges of Qinghai-Tibet Plateau (QTP). Species dispersed from eastern Asia to the Tianshan Mountains, North America and Europe during the Oligocene and Miocene period. We found that polyploidization occurred multiple times in the subgenus Albo-carmesinae, in the Tianshan Mountains, Himalayas, and H-D Mountains. Finally, we suggest that apomixis, polyploidization, and hybridization may have combined with the multistage uplifting of Himalayas and H-D Mountains (and the subsequent increases in geologic, ecological and climatic heterogeneity) to drive the striking species diversity of Sorbus in this region.
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Filogenia , Filogeografía , Sorbus/clasificación , Teorema de Bayes , Núcleo Celular/genética , ADN de Cloroplastos/genética , Fósiles , Funciones de Verosimilitud , Análisis de Secuencia de ADN , Sorbus/genética , Factores de TiempoRESUMEN
The respective roles that the Hengduan Mountains Region (HMR) uplift around 4-3 Ma and Quaternary climatic oscillations played in causing the environmental changes in the Qinghai-Tibet Plateau (QTP) remain unknown. Here, we reconstruct the evolutionary history of two varieties of Allium cyathophorum and A. spicatum of subgenus Cyathophora, restricted to the HMR and the western QTP, respectively. Forty-five populations were surveyed for chloroplast and nuclear sequence variation to evaluate phylogenetic relationships, dates of divergence and ancestral area/inflorescence reconstructions. In addition, analyses were conducted on discernable micromorphologies, cytotypes and seed size variation. Our results indicated that two varieties of A. cyathophorum are separate species, i.e. A. farreri and A. cyathophorum, and the initial split of Cyathophora was triggered by the HMR uplift around 4-3 Ma. Subsequently, A. spicatum originated through the strengthened aridification in the western QTP induced vicariance of the ancestral populations in the HMR during the early Pleistocene. A self-sustaining allotetraploid species from A. farreri and A. cyathophorum was established during an interglacial period of penultimate glaciation of the QTP. Seed size variation also supports these by the colonization-competition tradeoff among small and large seeds. Our findings appear to suggest that the HMR uplift could have strengthened the development of the Asian monsoon regimes in this region and aridification in the western QTP, while the Quaternary climatic oscillations spurred the allopatric species' range shifts and created new open microhabitat for the alloploid species.
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Allium/clasificación , Allium/genética , Evolución Biológica , ADN de Cloroplastos , Ambiente , Variación Genética , Filogenia , Filogeografía , TibetRESUMEN
BACKGROUND: Several previous studies have shown that some morphologically distinctive, small genera of vascular plants that are endemic to the Qinghai-Tibetan Plateau and adjacent Hengduan Mountains appear to have unexpected and complex phylogenetic relationships with their putative sisters, which are typically more widespread and more species rich. In particular, the endemic genera may form one or more poorly resolved paraphyletic clades within the sister group despite distinctive morphology. Plausible explanations for this evolutionary and biogeographic pattern include extreme habitat specialization and hybridization. One genus consistent with this pattern is Nomocharis Franchet. Nomocharis comprises 7-15 species bearing showy-flowers that are endemic to the H-D Mountains. Nomocharis has long been treated as sister to Lilium L., which is comprised of more than 120 species distributed throughout the temperate Northern Hemisphere. Although Nomocharis appears morphologically distinctive, recent molecular studies have shown that it is nested within Lilium, from which is exhibits very little sequence divergence. In this study, we have used a dated molecular phylogenetic framework to gain insight into the timing of morphological and ecological divergence in Lilium-Nomocharis and to preliminarily explore possible hybridization events. We accomplished our objectives using dated phylogenies reconstructed from nuclear internal transcribed spacers (ITS) and six chloroplast markers. RESULTS: Our phylogenetic reconstruction revealed several Lilium species nested within a clade of Nomocharis, which evolved ca. 12 million years ago and is itself nested within the rest of Lilium. Flat/open and horizon oriented flowers are ancestral in Nomocharis. Species of Lilium nested within Nomocharis diverged from Nomocharis ca. 6.5 million years ago. These Lilium evolved recurved and campanifolium flowers as well as the nodding habit by at least 3.5 million years ago. Nomocharis and the nested Lilium species had relatively low elevation ancestors (<1000 m) and underwent diversification into new, higher elevational habitats 3.5 and 5.5 million years ago, respectively. Our phylogeny reveals signatures of hybridization including incongruence between the plastid and nuclear gene trees, geographic clustering of the maternal (i.e., plastid) lineages, and divergence ages of the nuclear gene trees consistent with speciation and secondary contact, respectively. CONCLUSIONS: The timing of speciation and ecological and morphological evolutionary events in Nomocharis are temporally consistent with uplift in the Qinghai-Tibetan Plateau and of the Hengduan Mountains 7 and 3-4 million years ago, respectively. Thus, we speculate that the mountain building may have provided new habitats that led to specialization of morphological and ecological features in Nomocharis and the nested Lilium along ecological gradients. Additionally, we suspect that the mountain building may have led to secondary contact events that enabled hybridization in Lilium-Nomocharis. Both the habitat specialization and hybridization have probably played a role in generating the striking morphological differences between Lilium and Nomocharis.
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Lilium/anatomía & histología , Lilium/clasificación , Evolución Biológica , ADN de Plantas/genética , Ecosistema , Flores/anatomía & histología , Hibridación Genética , Lilium/genética , Filogenia , Plastidios/genética , TibetRESUMEN
BACKGROUND: The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS: In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characterized by the retention of a 48 bp sequence from intron 8 of the bovine CD46 gene, which encodes a putative protein enlarged by 16 amino acids. CD46-TV mRNA was found to be over expressed in mastitis-infected mammary gland tissues relative to healthy tissues. A single nucleotide polymorphism (c. 1033 + 2184 C > T) in the exonic splicing enhancer (ESE) motif region was shown to result in the CD46-TV aberrant splice variant through constructing alternative alleles using the pSPL3 exon capturing vector and transfecting these into 293 T cells. Allelic frequency in 56,682 individuals belonging to 112 Bos taurus, Bos indicus, Bos javanicus, Bos grunniens and Bos mutus, etc. suggests that the C allele (80.09%) is the ancestral allele. Association analysis found that the mean genomic estimated breeding values (gEBV) for milk somatic cell score and the occurrence of clinical mastitis, as well as the milk somatic cell score of Chinese Holsteins with the CT genotype was lower than those of individuals with either the CC or TT genotypes. The mean gEBV for udder health synthesis for the TT genotype was greater than those for the CC or CT genotypes. CONCLUSIONS: Our findings suggest that the CD46 gene likely plays a critical role in the risk of mastitis caused by Streptococcus in dairy cows via an alternative splicing mechanism caused by a functional mutation in intron 8. Our data also underline the importance of variation within ESEs in regulating transcript processing.
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Intrones/genética , Mastitis Bovina/genética , Proteína Cofactora de Membrana/genética , Polimorfismo de Nucleótido Simple , Alelos , Empalme Alternativo , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Cruzamiento , Bovinos , Exones/genética , Femenino , Regulación de la Expresión Génica , Genotipo , Glándulas Mamarias Animales/metabolismo , Mastitis Bovina/patología , Proteína Cofactora de Membrana/química , Leche , Mutación , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , ARN Mensajero/genética , ARN Mensajero/metabolismoRESUMEN
The former genus Nomocharis, which has been merged as a clade within the genus Lilium (Liliaceae), represents one of the most complicated and unclear groups included in the latter. Research on members of the Nomocharis clade has been quite limited due to the sampling difficulties caused by its selective environmental preferences. In this study, we propose a new species within this clade, Lilium liangiae, as a further bridge connecting the former genus Nomocharis with other members of the genus Lilium. We conducted morphological clustering, phylogenetic, and comparative genomics analyses of nuclear internal spacers and the newly generated complete chloroplast genome, in conjunction with previously published sequences, and performed ancestral state reconstruction to clarify the evolutionary pattern of important traits in Lilium. The clustering results of 38 morphological traits indicated that the new species is allied to Nomocharis, further increasing the morphological polymorphism in the latter. The phylogenetic results and morphological clustering both supported L. liangiae belonging to the subclade Ecristata in Nomocharis, its closest affinity being Lilium gongshanense. Inconsistencies in phylogenetic relationships were detected between nuclear and plastid datasets, possibly due to ancient hybridization and ongoing introgression. Comparative genomics revealed the conservation and similarity of their chloroplast genomes, with variations observed in the expansion and contraction of the IR regions. A/T and palindromic repeat sequences were the most abundant. Seven highly variable regions (Pi≥0.015) were identified as potential molecular markers based on the chloroplast genomes of 47 species within Lilium. Both nuclear and plastid genes exhibited very low variability within the Nomocharis clade, contrasting with their highly variable morphological appearance. The ancestral state reconstruction analysis suggests that the campanulate flower form, as in L. liangiae, arose at least three times within the genus Lilium, revealing parallel evolution in the latter. Overall, this study adds important genetic and morphological evidence for understanding the phylogenetic relationships and parallel evolution patterns of species within the genus Lilium.
RESUMEN
The elite bull plays an extremely important role in the genetic progression of the dairy cow population. The previous results indicated the potential positive relationship of large scrotal circumference (SC) with improved semen volume, concentration, and motility. In order to improve bull's semen quantity and quality by selection, it is necessary to estimate the genetic parameters of semen traits and their correlations with other conformation traits such as SC that could be used for an indirect selection. In this study, the genetic parameters of seven semen traits (n = 66,260) and nine conformation traits (n = 3,642) of Holstein bulls (n = 453) were estimated by using the bivariate repeatability animal model with the average information-restricted maximum likelihood (AI-REML) approach. The results showed that the estimated heritabilities of semen traits ranged from 0.06 (total number of motile sperm, TNMS) to 0.37 (percentage of abnormal sperm, PAS) and conformation traits ranged from 0.23 (pin width, PW) to 0.69 (hip height, HH). The highest genetic correlations were found between semen volume per ejaculation (SVPE), semen concentration per ejaculation (SCPE), total number of sperm (TNS), and TNMS traits that were 0.97, 0.98, 1.00, and 0.99, respectively. Phenotypic correlations between SC and SVPE, SCPE, TNS, and TNMS were 0.35, 0.35, 0.48, and 0.42, respectively. In summary, the moderate or high heritability of semen traits indicates that genetic improvement of semen quality by selection is feasible, where SC could be a useful trait for indirect selection or as correlated information to improve semen quantity and production in the practical bull breeding programs.
RESUMEN
The Hengduan Mountains (H-D Mountains) in China flank the eastern edge of the Qinghai-Tibet Plateau (Q-T Plateau) and are a center of great temperate plant diversity. The geological history and complex topography of these mountains may have prompted the in situ evolution of many diverse and narrowly endemic species. Despite the importance of the H-D Mountains to biodiversity, many uncertainties remain regarding the timing and tempo of their uplift. One hypothesis is that the Q-T Plateau underwent a final, rapid phase of uplift 8-7 million years ago (Mya) and that the H-D Mountains orogeny was a separate event occurring 4-3 Mya. To evaluate this hypothesis, we performed phylogenetic, biogeographic, divergence time dating, and diversification rate analyses of the horticulturally important genus Lilium, including Nomocharis. The Lilium-Nomocharis complex is distributed throughout the temperate Northern Hemisphere but is most diverse within the H-D Mountains and Q-T Plateau. Our matK and ITS phylogenies support previous studies showing that Nomocharis is nested within Lilium. However, we detected incongruence between the two gene trees which may result from hybridization. Dating analyses performed using the ITS dataset showed that the evolution of major lineages within Lilium-Nomocharis may be temporally coincident with Q-T Plateau uplift occurring 8-7 Mya and H-D Mountains uplift approximately 4-3 Mya. Our analyses of diversification times and rates among Lilium-Nomocharis clades are less conclusive. However, these do suggest high extinction rates among H-D Mountains lineages.
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Altitud , Evolución Biológica , Lilium/genética , Biodiversidad , China , ADN Espaciador Ribosómico/genética , Evolución Molecular , Filogenia , Filogeografía , ARN Ribosómico 5.8S/genética , Análisis de Secuencia de ADNRESUMEN
Rubus L. (Rosaceae, Rosoideae) contains around 700 species distributed on all continents except Antarctica, with the highest species diversity in temperate to subtropical regions of the northern hemisphere. The taxonomy of Rubus is challenging due to the frequency of polyploidy, hybridization and apomixis. Previous studies mostly sampled sparsely and used limited DNA sequence data. The evolutionary relationships between infrageneric taxa, therefore, remain to be further clarified. In the present study, genotyping by sequencing (GBS) reduced-representation genome sequencing data from 186 accessions representing 65 species, 1 subspecies and 17 varieties of Rubus, with emphasis on diploid species, were used to infer a phylogeny using maximum likelihood and maximum parsimony methods. The major results were as follows: (1) we confirmed or reconfirmed the polyphyly or paraphyly of some traditionally circumscribed subgenera, sections and subsections; (2) 19 well-supported clades, which differed from one another on molecular, morphological and geographical grounds, were identified for the species sampled; (3) characteristics such as plants with dense bristles or not, leaves leathery or papyraceous, number of carpels, instead of inflorescences paniculate or not, aggregate fruits and leaves abaxially tomentose or not, may be of some use in classifying taxa whose drupelets are united into a thimble-shaped aggregate fruit that falls in its entirety from the dry receptacle; and (4) a preliminary classification scheme of diploid species of Rubus is proposed based on our results combined with those from previous phylogenetic analyses.
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Rubus , Filogenia , Diploidia , Evolución Biológica , PoliploidíaRESUMEN
DNA methylation and gene alternative splicing drive spermatogenesis. In screening DNA methylation markers and transcripts related to sperm motility, semen from three pairs of full-sibling Holstein bulls with high and low motility was subjected to reduced representation bisulphite sequencing. A total of 948 DMRs were found in 874 genes (gDMRs). Approximately 89% of gDMR-related genes harboured alternative splicing events, including SMAD2, KIF17, and PBRM1. One DMR in exon 29 of PBRM1 with the highest 5mC ratio was found, and hypermethylation in this region was related to bull sperm motility. Furthermore, alternative splicing events at exon 29 of PBRM1 were found in bull testis, including PBRM1-complete, PBRM1-SV1 (exon 28 deletion), and PBRM1-SV2 (exons 28-29 deletion). PBRM1-SV2 exhibited significantly higher expression in adult bull testes than in newborn bull testes. In addition, PBRM1 was localized to the redundant nuclear membrane of bull sperm, which might be related to sperm motility caused by sperm tail breakage. Therefore, the hypermethylation of exon 29 may be associated with the production of PBRM1-SV2 in spermatogenesis. These findings indicated that DNA methylation alteration at specific loci could regulate gene splicing and expression and synergistically alter sperm structure and motility.
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Metilación de ADN , Semen , Masculino , Bovinos , Animales , Empalme Alternativo , Motilidad Espermática/genética , EspermatozoidesRESUMEN
OBJECTIVES: This study was performed in the frame of a more extensive study dedicated to the integrated analysis of the single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells (PBMCs) with a large-scale GWAS of 45 complex traits in Chinese Holstein cattle. Lipopolysaccharide (LPS) is a crucial mediator of chronic inflammation to modulate immune responses. PBMCs include primary T and B cells, natural killer (NK) cells, monocytes (Mono), and dendritic cells (DC). How LPS stimulates PBMCs at the single-cell level in dairy cattle remains largely unknown. DATA DESCRIPTION: We sequenced 30,756 estimated single cells and mapped 26,141 of them (96.05%) with approximately 60,075 mapped reads per cell after quality control for four whole-blood treatments (no, 2 h, 4 h, and 8 h LPS) by single-cell RNA sequencing (scRNA-seq) and single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq). Finally, 7,107 (no), 9,174 (2 h), 6,741 (4 h), and 3,119 (8 h) cells were generated with ~ 15,000 total genes in the whole population. Therefore, the single-cell transcriptome and chromatin accessibility datasets in this study enable a further understanding of the cell types and functions of PBMCs and their responses to LPS stimulation in vitro.
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Cromatina , Transcriptoma , Bovinos , Animales , Transcriptoma/genética , Cromatina/genética , Leucocitos Mononucleares , Lipopolisacáridos/farmacología , Secuencia de BasesRESUMEN
In this paper, karyotype data of the tribe Lilieae in China were analyzed and been superimposed onto a phylogenetic framework constructed by the internal transcribed spacer to investigate the karyotype evolution. Ten parameters for analyzing karyotype asymmetry were assessed and karyotypic idiogram of five genera of Lilieae were illustrated. The results showed that, the relationship of genera in Lilieae that inferred from Maximum Parsimony criteria and Bayesian Inference were congruent with previous studies, which focused on higher level of Liliales. The karyotype showed distinctive among genera, mainly expressed on the location and amount of secondary constrictions and intercalary satellites: the genus Notholirion have neither of them, and the genera Cardiocrinum and Fritillaria have the secondary constriction alone; the genera Lilium and Nomocharis showed both features, and the distribute pattern of the intercalary satellites showed similarity among related clades. The asymmetry that assessed by several methods indicated that the evolution trend of Lilieae did not follow a single direction, but different in each genus. On the sectional level of the genus Lilium (including Nomocharis) the karyotype evolution included three major periods. Combining the chromosomal structure variations and karyotype asymmetry, the chromosome diversity and evolution in Lilieae were quite clear in the light of molecular inference.
Asunto(s)
Cromosomas de las Plantas/genética , Evolución Molecular , Variación Genética , Liliaceae/genética , Secuencia de Bases , China , Cariotipificación , Liliaceae/citología , Filogenia , Especificidad de la EspecieRESUMEN
MicroRNAs (miRNAs) play key roles in sperm as the regulatory factors involved in fertility and subsequent early embryonic development. Bta-miR-6531 is specifically a highly enriched miRNA in low-motility sperms in previous study. To investigate the mechanism of bta-miR-6531, 508 shared target genes of bta-miR-6531 were predicted using two miRNA target databases (TargetScan7 and miRWalk). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the calcium and cAMP signaling pathways were the most enriched of the target genes. A dual-luciferase assay indicated that bta-miR-6531 targeted ATP2A2 mRNA by binding to the coding sequence region. In bovine Leydig cells, bta-miR-6531 overexpression affected the intracellular calcium concentration by restraining ATP2A2 expression. Moreover, we observed high calcium concentrations and high ATP2A2 protein levels in high-motility sperm compared with those in low-motility sperms. Furthermore, high-linkage single-nucleotide polymorphisms (SNPs) of the pre-bta-miR-6531 sequence were identified that related to sperm traits. Genotype TCTC of bta-miR-6531 showed high sperm motility and density and low deformity rate in Holstein bulls. However, the mutation in pre-miR-6531 did not significantly affect mature bta-miR-6531 expression in the sperm or cell models. Our results demonstrate that bta-miR-6531 might involve in sperm motility regulation by targeting ATP2A2 of the calcium signaling pathway in bovine spermatozoa.
Asunto(s)
Calcio , MicroARNs , Bovinos , Masculino , Animales , Motilidad Espermática/genética , Células Intersticiales del Testículo/metabolismo , Semen/metabolismo , MicroARNs/genética , MicroARNs/metabolismo , ARN MensajeroRESUMEN
The Hengduan Mountains region is an important hotspot of alpine plant diversity and endemism. Acanthochlamys bracteata is a species of a threatened monotypic genus endemic to the Hengduan Mountains. In this study, we present a high-quality, chromosome-level reference genome for A. bracteata, constructed using long reads, short reads and Hi-C technology. We characterized its genetic diversity, population structure, demographic history and gene flow by resequencing individuals collected across its distribution. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that A. bracteata and Dioscorea rotundata diverged ~104.5 million years ago. Whole-genome resequencing based on population genetic analysis revealed that the division of the 14 populations into 10 distinct clusters reflected geographical divergence, and three separate high levels of gene flow occurred sequentially between isolated populations of the Hengduan Mountains, a finding which is consistent with the turnover between ice ages and interglacial periods. Our findings indicate that Quaternary climatic changes played an important role in shaping the genetic structure and demographic trajectories of A. bracteata, and provide critical insights into the genetic status and evolutionary history of this poorly understood species, and possibly other alpine plants with a similar distribution. This study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes and identifying conservation units for the conservation and management of threatened species. Our high-quality genome represents a valuable resource for future studies of the underlying molecular mechanisms of adaptive evolution and provides insight for further comparative genomic analysis with other Velloziaceae species.