scholarly journals The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences

2020 ◽  
Vol 12 (8) ◽  
pp. 1444-1458
Author(s):  
Isaac Adeyemi Babarinde ◽  
Naruya Saitou
Keyword(s):  
Litter Size ◽  
Evolutionary Rate ◽  
Expression Patterns ◽  
Draft Genome ◽  
Evolutionary Rates ◽  
Gestation Length ◽  
Generation Interval ◽  
Rate Acceleration ◽  
Mammalian Genomes ◽  
Taxonomic Order

Abstract Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae–Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.

scholarly journals The impact of maternal genetic merit and country of origin on ewe reproductive performance, lambing performance and ewe survival

2021 ◽  
Author(s):  
N Fetherstone ◽  
N McHugh ◽  
T M Boland ◽  
F M McGovern
Keyword(s):  
New Zealand ◽  
Birth Weight ◽  
Litter Size ◽  
Country Of Origin ◽  
Reproductive Traits ◽  
Gestation Length ◽  
Genetic Merit ◽  
Genetic Groups ◽  
One Year ◽  
The Impact

Abstract The objective of this study was to investigate the impact of the ewe’s maternal genetic merit and country of origin (New Zealand or Ireland) on ewe reproductive, lambing and productivity traits. The study was performed over a four year period (2016 to 2019) and consisted of three genetic groups: high maternal genetic merit New Zealand (NZ), high maternal genetic merit Irish (High Irish) and low maternal genetic merit Irish (Low Irish) ewes. Each group contained 30 Suffolk and 30 Texel ewes, selected based on the respective national maternal genetic indexes; i.e. either the New Zealand Maternal Worth (New Zealand group) or the €uro-star Replacement index (Irish groups). The impact of maternal genetic merit on reproductive traits such as litter size; lambing traits such as gestation length, birth weight, lambing difficulty, mothering ability, and productivity traits such as the number of lambs born and weaned were analyzed using linear mixed models. For binary traits, the impact of maternal genetic merit on reproductive traits such as conception to first AI service; lambing traits such as dystocia, perinatal lamb mortality and productivity traits such as ewe survival were analyzed using logistic regression. New Zealand ewes outperformed Low Irish ewes for conception to first AI (P<0.05) and litter size (P=0.05). Irish ewes were more likely to suffer from dystocia (6.84 (High Irish) and 8.25 (Low Irish) times) compared to NZ ewes (P<0.001); birth weight and perinatal mortality did not differ between groups (P>0.05). Lambs born from NZ ewes were 4.67 (95% CI: 1.89 to 11.55; P<0.001) and 6.54 (95% CI: 2.56 to 16.71; P<0.001) times more likely to stand up and suckle unassisted relative to lambs born from High or Low Irish ewes, respectively. New Zealand and High Irish ewes had a greater number of lambs born and weaned throughout the duration of the study compared to their Low Irish counterparts (P<0.001). New Zealand ewes tended to be more likely to survive from one year to the next compared to Low Irish ewes (P=0.07). Irish ewes of high maternal genetic merit outperformed their Low counterparts in total number of lambs born and weaned per ewe, but performance did not differ across other traits investigated. This highlights the importance of continuous development of the Irish maternal sheep index to ensure favourable improvements in reproductive, lambing and productivity traits at farm level. Overall, results demonstrate the suitability of NZ genetics in an Irish production system.

scholarly journals Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates

PLoS ONE ◽  
2008 ◽  
Vol 3 (10) ◽  
pp. e3599 ◽  
Author(s):  
Aleksey Y. Ogurtsov ◽  
Leonardo Mariño-Ramírez ◽  
Gibbes R. Johnson ◽  
David Landsman ◽  
Svetlana A. Shabalina ◽  
...  
Keyword(s):  
Protein Kinases ◽  
Expression Patterns ◽  
Evolutionary Rates ◽  
Gene Architecture

scholarly journals Large-Scale Metadata Analysis of Ovary Based Multi-Omics Datasets for Understanding the Genes Regulating Litter Size

2020 ◽  
Author(s):  
Ayyappa Kumar Sista Kameshwar ◽  
Julang Li
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Litter Size ◽  
Large Scale ◽  
Expression Patterns ◽  
Genetic Selection ◽  
Follicular Development ◽  
Oocyte Quality ◽  
Differentially Expressed ◽  
Metadata Analysis

Abstract Background : Litter size is a very important production index in the livestock industry, which is controlled by various complex physiological processes. To understand and reveal the common gene expression patterns involved in controlling prolificacy, we have performed a large-scale metadata analysis of five genome-wide transcriptome datasets of pig and sheep ovary samples obtained from high and low litter groups, respectively. We analyzed separately each transcriptome dataset using GeneSpring v14.8 software by implementing standard, generic analysis pipelines and further compared the list of most significant and differentially expressed genes obtained from each dataset to identify genes that are found to be common and significant across all the studies. Results : We have observed a total of 62 differentially expressed genes common among more than two gene expression datasets. The KEGG pathway analysis of most significant genes has shown that they are involved in metabolism, the biosynthesis of lipids, cholesterol and steroid hormones, immune system, cell growth and death, cancer-related pathways and signal transduction pathways. Of these 62 genes, we further narrowed the list to the 25 most significant genes by focusing on the ones with fold change >1.5 and p<0.05. These genes are CYP11A1, HSD17B2, STAR, SCARB1, IGSF8, MSMB, SERPINA1 , FAM46C, HEXA, PTTG1, TIMP1, FAM167B, CCNG1, FAXDC2, HMGCS1, L2HGDH, Lipin1, MME, MSMO1, PARM1, PTGFR, SLC22A4, SLC35F5, CCNA2, CENPU, CEP55, RASSF2, and SLC16A3 . Conclusions : Interestingly, comparing the list of genes with the list of genes obtained from our literature search analysis, we found only three genes in common. These genes are HEXA, PTTG1, and TIMP1. Our finding points to the potential of a few genes that may be important for ovarian follicular development and oocyte quality. Future studies revealing the function of these genes will further our understanding of how litter size is controlled in the ovary while also providing insight on genetic selection of high litter gilts.

scholarly journals Selective modes determine evolutionary rates, gene compactness and expression patterns inBrassica

2017 ◽  
Vol 91 (1) ◽  
pp. 34-44 ◽  
Author(s):  
Yue Guo ◽  
Jing Liu ◽  
Jiefu Zhang ◽  
Shengyi Liu ◽  
Jianchang Du
Keyword(s):  
Expression Patterns ◽  
Evolutionary Rates ◽  
Gene Compactness

Gene Duplication of Zebrafish JAK2 Homologs Is Accompanied by Divergent Embryonic Expression Patterns: Only jak2a Is Expressed During Erythropoiesis

Blood ◽  
1999 ◽  
Vol 94 (8) ◽  
pp. 2622-2636 ◽  
Author(s):  
Andrew C. Oates ◽  
Alison Brownlie ◽  
Stephen J. Pratt ◽  
Danielle V. Irvine ◽  
Eric C. Liao ◽  
...  
Keyword(s):  
Protein Tyrosine Kinase ◽  
Gene Knockout ◽  
Expression Patterns ◽  
Zebrafish Genome ◽  
Hematopoietic Tissue ◽  
Orthologous Genes ◽  
Surface Receptors ◽  
Mammalian Genomes ◽  
Chromosome Segments ◽  
Receptor Family

Members of the JAK family of protein tyrosine kinase (PTK) proteins are required for the transmission of signals from a variety of cell surface receptors, particularly those of the cytokine receptor family. JAK function has been implicated in hematopoiesis and regulation of the immune system, and recent data suggest that the vertebrate JAK2gene may play a role in leukemia. We have isolated and characterizedjak cDNAs from the zebrafish Danio rerio. The zebrafish genome possesses 2 jak2 genes that occupy paralogous chromosome segments in the zebrafish genome, and these segments conserve syntenic relationships with orthologous genes in mammalian genomes, suggesting an ancient duplication in the zebrafish lineage. The jak2a gene is expressed at high levels in erythroid precursors of primitive and definitive waves and at a lower level in early central nervous system and developing fin buds. jak2b is expressed in the developing lens and nephritic ducts, but not in hematopoietic tissue. The expression of jak2a was examined in hematopoietic mutants and found to be disrupted in clocheand spadetail, suggesting an early role in hematopoiesis. Taken together with recent gene knockout data in the mouse, we suggest that jak2a may be functionally equivalent to mammalianJak2, with a role in early erythropoiesis.

Smooth muscle cell-specific TMEM16A deletion does not alter Ca2+ signaling, uterine contraction, gestation length, or litter size in mice†

2019 ◽  
Vol 101 (2) ◽  
pp. 318-327 ◽  
Author(s):  
Mingzi Qu ◽  
Ping Lu ◽  
Karl Bellve ◽  
Kevin Fogarty ◽  
Lawrence Lifshitz ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Ion Channels ◽  
Smooth Muscle Cell ◽  
Litter Size ◽  
Muscle Cell ◽  
Uterine Contraction ◽  
Gestation Length ◽  
Specific Marker ◽  
Myometrial Cells

Abstract Ion channels in myometrial cells play critical roles in spontaneous and agonist-induced uterine contraction during the menstrual cycle, pregnancy maintenance, and parturition; thus, identifying the genes of ion channels in these cells and determining their roles are essential to understanding the biology of reproduction. Previous studies with in vitro functional and pharmacological approaches have produced controversial results regarding the presence and role of TMEM16A Ca2+-activated Cl− channels in myometrial cells. To unambiguously determine the function of this channel in these cells, we employed a genetic approach by using smooth muscle cell-specific TMEM16A deletion (i.e. TMEM16ASMKO) mice. We found that myometrial cells from TMEM16ASMKO mice generated the same pattern and magnitude in Ca2+ signals upon stimulation with KCl, oxytocin, and PGF2α compared to the isogenic control myometrial cells. At the uterine tissue level, TMEM16A deletion also did not cause detectable changes in either spontaneous or agonist (i.e. KCl, oxytocin, and PGF2α)-induced contractions. Moreover, in vivo the TMEM16ASMKO mice gave birth at full term with the same litter size as genetically identical control mice. Finally, TMEM16A immunostaining in both control and TMEM16ASMKO mice revealed that this protein was highly expressed in the endometrial stroma, but did not co-localize with a smooth muscle specific marker MYH11. Collectively, these results unequivocally demonstrate that TMEM16A does not serve as a pacemaking channel for spontaneous uterine contraction, neither does it function as a depolarizing channel for agonist-evoked uterine contraction. Yet these two functions could underlie the normal gestation length and litter size in the TMEM16ASMKO mice.

Serial transvaginal ultrasound-guided biopsy of the porcine corpus luteum in vivo

2017 ◽  
Vol 29 (5) ◽  
pp. 931 ◽  
Author(s):  
S. Björkman ◽  
J. Yun ◽  
M. Niku ◽  
C. Oliviero ◽  
N. M. Soede ◽  
...  
Keyword(s):  
Corpus Luteum ◽  
Pregnancy Rate ◽  
Litter Size ◽  
Reproductive Tract ◽  
Transvaginal Ultrasound ◽  
Gestation Length ◽  
Ultrasound Guided ◽  
Guided Biopsy ◽  
Biopsy Method ◽  
Ultrasound Guided Biopsy

The aims of the present study was to develop and describe a transvaginal ultrasound-guided biopsy method for luteal tissue in the porcine and to evaluate the effects of the method on the reproductive tract, ovarian status and pregnancy status. Biopsies were performed in four multiparous sows on Days 9 and 15 of three consecutive oestrous cycles; the size and histological composition of the samples obtained were evaluated and the reproductive tract of the sows was monitored. Furthermore, biopsies were performed in 26 multiparous sows on Days 10 and 13 after insemination, and the pregnancy rate, gestation length and subsequent litter size were evaluated. RNA was extracted from the samples obtained and the quality and quantity were determined. Altogether, 76 biopsies were performed and 38 samples were obtained. Compared with sows from which no samples were obtained (n = 6), sows from which one or more samples were obtained (n = 24) were older (parity 5.0 ± 2.8 vs 2.2 ± 0.4, mean ± s.d.), heavier (290 ± 26 vs 244 ± 27 kg) and had higher back fat (11.4 ± 2.7 vs 6.4 ± 2.5 mm; P < 0.05 for all). No effect of the biopsies (P > 0.05) was observed on the cyclicity and reproductive organs of the sows, or on corpus luteum diameter on Day 13 (8.9 ± 1.0 vs 9.2 ± 1.1 mm), pregnancy rate (95% vs 96%), gestation length (115 ± 1 vs 115 ± 1 days) and subsequent litter size (12.7 ± 2.5 vs 13.3 ± 2.8) between sows from which samples were obtained and those from which no samples were obtained. The samples obtained had a diameter of 1 mm and contained heterogeneous tissue with various cell types. The RNA quantity was 520 ± 160 µg per sample and the RNA integrity number was 8.5 ± 1.0. In conclusion, an ultrasound-guided biopsy method for ovarian tissue, which can be used for gene expression studies, was established in the porcine. No effect on corpus luteum function was found.

The effect of nutrition in mid pregnancy and ewe liveweight change on birth weight and management for lamb survival in highly fecund ewes

1992 ◽  
Vol 32 (1) ◽  
pp. 1 ◽  
Author(s):  
NM Fogarty ◽  
DG Hall ◽  
PJ Holst
Keyword(s):  
Birth Weight ◽  
Treatment Period ◽  
Litter Size ◽  
Late Pregnancy ◽  
Weather Conditions ◽  
Gestation Length ◽  
Nutritional Treatment ◽  
Lamb Survival ◽  
Staple Strength ◽  
Fleece Weight

The effect of moderate undernutrition in mid pregnancy on lamb birth weight and survival of single- and multiple-bearing ewes is reported. A total of 1220 ewes of 3 crossbred types with different fecundity, Booroola Merino x Dorset (BD), Trangie Fertility Merino x Dorset (TD) and Border Leicester x Merino (BLM), were examined over 2 years. The treatments were low (L) and high (H) nutrition at pasture for 4 weeks from about day 75 of pregnancy. Ewe liveweight of the L group at the end of the treatments was 5 kg lower in 1984 and 8 kg lower in 1985 (P<0.01) than the H group. The differences were smaller by late pregnancy and post-lambing. The L treatment increased (P<0.01) birth weight by 0.16 kg in 1984 but had little effect in 1985. Litter size had the greatest effect on birth weight (P<0.01). Ewe crossbred type and lamb sex effects were also significant (P<0.01), although they tended to be reduced for higher order births. Nutritional treatment had no effect on gestation length. Ewe liveweight at joining and weight gains before and after the treatment period significantly affected birth weight and accounted for the large difference in birth weight between years (0.7 kg). Ewe weight gain during the treatment period in mid pregnancy had no significant effect on lamb birth weight. Nutritional treatment in mid pregnancy had no effect on lamb survival. Litter size significantly affected lamb survival, although inclusion of birth weight in the model reduced the effect. Weather conditions, as measured by chill index, significantly (P<0.01) affected lamb survival in 1984 but accounted for less variation in 1985 (P<0.05). Lamb survival for ewes was ranked BLM > TD > BD. Maximum survival was achieved at birth weights of 4-5 kg from BD and TD ewes and 5-6 kg from BLM ewes. The L treatment reduced (P<0.01) ewe greasy fleece weight by 0.15 kg but did not affect staple strength. Plasma glucose concentration at the end of treatment was lower (P<0.01) for L ewes, but there was no difference between L and H ewes in late pregnancy. Glucose declined with increasing fetal number. Plasma B-hydroxybutyrate concentration was lower for the H group than for L, and also for BLM than TD and BD ewes (P<0.01).

scholarly journals Temporal signal and the phylodynamic threshold of SARS-CoV-2

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Sebastian Duchene ◽  
Leo Featherstone ◽  
Melina Haritopoulou-Sinanidou ◽  
Andrew Rambaut ◽  
Philippe Lemey ◽  
...  
Keyword(s):  
Time Scales ◽  
Sequence Variation ◽  
Evolutionary Rate ◽  
Sequence Data ◽  
Genomic Variation ◽  
Evolutionary Rates ◽  
Data Sets ◽  
Genome Sequences ◽  
First Time ◽  
Time Of Origin

Abstract The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real time. Early analyses of these data revealed low sequence variation, a finding that is consistent with a recently emerging outbreak, but which raises the question of whether such data are sufficiently informative for phylogenetic inferences of evolutionary rates and time scales. The phylodynamic threshold is a key concept that refers to the point in time at which sufficient molecular evolutionary change has accumulated in available genome samples to obtain robust phylodynamic estimates. For example, before the phylodynamic threshold is reached, genomic variation is so low that even large amounts of genome sequences may be insufficient to estimate the virus’s evolutionary rate and the time scale of an outbreak. We collected genome sequences of SARS-CoV-2 from public databases at eight different points in time and conducted a range of tests of temporal signal to determine if and when the phylodynamic threshold was reached, and the range of inferences that could be reliably drawn from these data. Our results indicate that by 2 February 2020, estimates of evolutionary rates and time scales had become possible. Analyses of subsequent data sets, that included between 47 and 122 genomes, converged at an evolutionary rate of about 1.1 × 10−3 subs/site/year and a time of origin of around late November 2019. Our study provides guidelines to assess the phylodynamic threshold and demonstrates that establishing this threshold constitutes a fundamental step for understanding the power and limitations of early data in outbreak genome surveillance.

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