Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0%, 34.8%, and 21.4% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

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Isolation and characterization of the rat chromosomal gene for a polypeptide (pS1) antigenically related to statin

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)99243-4 ◽

1991 ◽

Vol 266 (16) ◽

pp. 10429-10437 ◽

Cited By ~ 2

Author(s):

D.K. Ann ◽

I.K. Moutsatsos ◽

T. Nakamura ◽

H.H. Lin ◽

P.L. Mao ◽

...

Keyword(s):

Chromosomal Gene ◽

Isolation And Characterization

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A comparative study on the reproductive success of two rewarding Habenaria species (Orchidaceae) occurring in roadside verge habitats

BMC Plant Biology ◽

10.1186/s12870-021-02968-w ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Wenliu Zhang ◽

Jiangyun Gao

Keyword(s):

Reproductive Success ◽

Fruit Set ◽

Plant Density ◽

Flowering Plant ◽

Floral Display ◽

Pollinator Behaviour ◽

Factors Affecting ◽

Nectar Sugar ◽

Viable Seeds ◽

Viable Embryo

Abstract Background Most orchid species have been shown to be severely pollination limited, and the factors affecting reproductive success have been widely studied. However, the factors determining the reproductive success vary from species to species. Habenaria species typically produce nectar but exhibit variable fruit set and reproductive success among species. Here, we investigated the influence of the flowering plant density, inflorescence size, breeding system, and pollinator behaviour on the reproductive success of two rewarding Habenaria species. Results Our observations indicated that Habenaria limprichtii and H. petelotii co-occur in roadside verge habitats and present overlapping flowering periods. Both species were pollination limited, although H. limprichtii produced more fruits than H. petelotii under natural conditions during the 3-year investigation. H. petelotii individuals formed distinct patches along roadsides, while nearly all H. limprichtii individuals clustered together. The bigger floral display and higher nectar sugar concentration in H. limprichtii resulted in increased attraction and visits from pollinators. Three species of effective moths pollinated for H. limprichtii, while Thinopteryx delectans (Geometridae) was the exclusive pollinator of H. petelotii. The percentage of viable seeds was significantly lower for hand geitonogamy than for hand cross-pollination in both species. However, H. limprichtii may often be geitonogamously pollinated based on the behaviours of the pollinators and viable embryo assessment. Conclusions In anthropogenic interference habitats, the behaviours and abundance of pollinators influence the fruit set of the two studied species. The different pollinator assemblages in H. limprichtii can alleviate pollinator specificity and ensure reproductive success, whereas the more viable embryos of natural fruit seeds in H. petelotii suggested reducing geitonogamy by pollinators in the field. Our results indicate that a quantity-quality trade-off must occur between species with different breeding strategies so that they can fully exploit the existing given resources.

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EXTRACHROMOSOMAL ELEMENT DELTA IN DROSOPHILA MELANOGASTER. IX. INDUCTION OF DELTA-RETAINING CHROMOSOME LINES BY MUTATION AND GENE MAPPING

Genetics ◽

10.1093/genetics/74.3.477 ◽

1973 ◽

Vol 74 (3) ◽

pp. 477-487

Author(s):

Sumio Minamori ◽

Kinue Sugimoto

Keyword(s):

Drosophila Melanogaster ◽

Crossing Over ◽

Chromosomal Gene ◽

Ethyl Methane Sulfonate ◽

Methane Sulfonate ◽

Multiple Alleles ◽

Ethyl Methane ◽

Extrachromosomal Element ◽

Polygenic System ◽

Killing Action

ABSTRACT [Delta b], symbolized as [δb], is retained by Sb chromosome lines and transmitted through the females to their progeny. Transmission through the males is not directly demonstrable (Minamori 1969a). [delta r], symbolized as [δr], is retained by Sr chromosome lines and transmitted biparentally (Minamori 1971). The multiplication of delta is suppressed at low temperature. All descendant lines derived from Sb-carrying or Sr-carrying flies in which the presence of delta cannot be demonstrated gradually accumulate their specific delta factors over many generations (Minamori 1969b, 1972). The delta factors and the sensitive chromosomes are inseparably associated. This observation led to the assumption that delta may be a copy of a chromosomal gene or a certain agent integrated into the chromosome (Minamori 1972). This assumption was examined in the present study by experiments designed to induce delta-retaining sensitive chromosomes, and to map the gene(s) responsible for delta-retention and/or for sensitivity to the killing action of delta factor. One sensitive chromosome which retained [δb] (Sb chromosome) was obtained in the presence of [δb] out of 2492 insensitive chromosomes which retained no delta; in addition one Sb chromosome was obtained in the presence of [δr] out of 2131 insensitives. The latter finding suggests that Sb might be induced by a mutation caused by [δb] or [δr], but not by integration of either delta into the chromosome. Four Sb chromosomes and one sensitive chromosome which retained [δr] (Sr chromosome) were obtained out of 1970 insensitives when males carrying the chromosome were fed an alkylating mutagen, ethyl methane sulfonate (EMS). The location of delta-retaining genes was examined by crossing-over experiments employing eight Sb and five Sr chromosomes. The genes on these chromosomes were found to be located in the same region or near one another. The gene for [δb], symbolized as Dab, and the gene for [δr], symbolized as Dar, are assumed to be multiple alleles of a locus at 2-24.9. The sensitivity of the chromosomes was modified appreciably by recombination; hence, the genes controlling this trait are assumed to be a polygenic system. The findings obtained in this study lead to the hypothesis that delta may be produced by a chromosomal gene (Da) and transmitted extrachromosomally.

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Antitumor Potential of Lippia citriodora Essential Oil in Breast Tumor-Bearing Mice

Antioxidants ◽

10.3390/antiox10060875 ◽

2021 ◽

Vol 10 (6) ◽

pp. 875

Author(s):

Katerina Spyridopoulou ◽

Tamara Aravidou ◽

Evangeli Lampri ◽

Eleni Effraimidou ◽

Aglaia Pappa ◽

...

Keyword(s):

Breast Cancer ◽

Antiproliferative Activity ◽

Folk Medicine ◽

Tumor Model ◽

Flowering Plant ◽

Antitumor Effects ◽

Lippia Citriodora ◽

Antitumor Potential ◽

Apoptotic Marker

Lippia citriodora is a flowering plant cultivated for its lemon-scented leaves and used in folk medicine for the preparation of tea for the alleviation of symptoms of gastrointestinal disorders, cold, and asthma. The oil extracted from the plant leaves was shown to possess antioxidant potential and to exert antiproliferative activity against breast cancer. The aim of this study was to further investigate potential antitumor effects of L. citriodora oil (LCO) on breast cancer. The in vitro antiproliferative activity of LCO was examined against murine DA3 breast cancer cells by the sulforhodamine B assay. We further explored the LCO’s pro-apoptotic potential with the Annexin-PI method. The LCO’s anti-migratory effect was assessed by the wound-healing assay. LCO was found to inhibit the growth of DA3 cells in vitro, attenuate their migration, and induce apoptosis. Finally, oral administration of LCO for 14 days in mice inhibited by 55% the size of developing tumors in the DA3 murine tumor model. Noteworthy, in the tumor tissue of LCO-treated mice the apoptotic marker cleaved caspase-3 was elevated, while a reduced protein expression of survivin was observed. These results indicate that LCO, as a source of bioactive compounds, has a very interesting nutraceutical potential.

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Insulin-like growth factor binding protein-3. Organization of the human chromosomal gene and demonstration of promoter activity.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)38392-9 ◽

1990 ◽

Vol 265 (21) ◽

pp. 12642-12649

Author(s):

M L Cubbage ◽

A Suwanichkul ◽

D R Powell

Keyword(s):

Growth Factor ◽

Promoter Activity ◽

Binding Protein ◽

Insulin Like Growth Factor ◽

Chromosomal Gene ◽

Factor Binding

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Estimation of technical efficiency of black cumin (Nigella sativa L.) farming in northwest Ethiopia: a stochastic frontier approach

Journal of Economic Structures ◽

10.1186/s40008-020-00198-1 ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Abebe Birara Dessie ◽

Tadie Mirie Abate ◽

Betelhem Tsedalu Adane ◽

Tiru Tesfa ◽

Shegaw Getu

Keyword(s):

Technical Efficiency ◽

Nigella Sativa ◽

Stochastic Frontier ◽

Market Price ◽

Northwest Ethiopia ◽

Flowering Plant ◽

Yield Potential ◽

Stochastic Frontier Model ◽

Black Cumin ◽

The Mean

Abstract Ethiopia is one of the east African countries which produce and exports various spices to other countries. Black cumin (Nigella sativa L.) is an important stiff annual flowering plant which mainly grows by producers for its seeds. An increasing demand of black cumin seed and oil in local, national and international market for medicinal, consumption and commercial purpose makes the best alternative crop for small holder farmers in Ethiopia. In spite of its importance, not much has been done to improve its production and productivity in Ethiopia. Therefore, this research was designed to examining efficiency variations and factors influencing technical inefficiency levels of producers on black cumin production in northwest Ethiopia. Primary data were collected using a semi-structured questionnaire administered on 188 black cumin producers selected using systematic random sampling technique. Moreover, various data analysis methods such as descriptive statistics and stochastic frontier model were used for analyzing the data. The empirical result obtained by applying maximum likelihood estimate of stochastic frontier model revealed that seed (p < 0.01) labor (p < 0.05), chemical (p < 0.01) and land (p < 0.05) were significant input variables in determining black cumin production. The mean technical efficiency level of black cumin producer was generally low, about 53.1%. The mean value of actual yield, potential yield and yield gap was 3.131, 5.832 and 2.701 quintals, respectively. Moreover, the result of stochastic frontier model together with the inefficiency parameters revealed that market price of black cumin (p < 0.01) and access of extension service (p < 0.1) were significant variables and positively influenced the efficiency levels of black cumin producers. Whereas age of producers (p < 0.05) and distance to farm plot (p < 0.01) negatively influenced the technical efficiency levels of black cumin producers. Therefore, the study recommends that adoption of latest agricultural technologies; development of institutions, agricultural extension services and infrastructure are advisable to improve the efficiency and commercial value of black cumin production.

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