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https://www.readbyqxmd.com/read/28334050/improving-transcriptome-de-novo-assembly-by-using-a-reference-genome-of-a-related-species-translational-genomics-from-oil-palm-to-coconut
#1
Alix Armero, Luc Baudouin, Stéphanie Bocs, Dominique This
The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions...
2017: PloS One
https://www.readbyqxmd.com/read/28333248/the-evolutionary-dynamics-of-orthologs-that-shift-in-gene-body-methylation-between-arabidopsis-species
#2
Shohei Takuno, Danelle K Seymour, Brandon S Gaut
DNA methylation labels a specific subset of genes in plant genomes. Recent work has shown that this gene-body methylation (gbM) is a conserved feature of orthologs, because highly methylated genes in one species tend to be highly methylated in another. In this study, we examined the exceptions to that rule by identifying genes that differ in gbM status between two plant species - Arabidopsis thaliana and Arabidopsis lyrata. Using Capsella grandiflora as an outgroup, we polarized the loss and gain of gbM for orthologs in Arabidopsis lineages...
March 2, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28296592/ethanol-extract-of-capsella-bursa-pastoris-improves-hepatic-steatosis-through-inhibition-of-histone-acetyltransferase-activity
#3
Hyo-Kyoung Choi, Eun Ju Shin, Su Jin Park, Haeng Jeon Hur, Jae Ho Park, Min-Yu Chung, Myung Sunny Kim, Jin-Taek Hwang
Histone lysine acetylation is thought to play a role in regulating the balance between energy storage and energy expenditure. However, the epigenetic mechanisms by which food phytochemicals influence metabolic processes in the liver have not been thoroughly investigated. In this study, we investigated the effect of an ethanol extract of Capsella bursa-pastoris (ECB) on histone acetyltransferase (HAT) inhibition, and whether it could thereby attenuate lipid accumulation in vitro and in vivo. We observed that ECB inhibits HAT activity as assessed by colorimetric and autoradiography assay systems...
March 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28285128/using-mustard-genomes-to-explore-the-genetic-basis-of-evolutionary-change
#4
REVIEW
Lachezar A Nikolov, Miltos Tsiantis
Recent advances in sequencing technologies and gene manipulation tools have driven mustard species into the spotlight of comparative research and have offered powerful insight how phenotypic space is explored during evolution. Evidence emerged for genome-wide signal of transcription factors and gene duplication contributing to trait divergence, e.g., PLETHORA5/7 in leaf complexity. Trait divergence is often manifested in differential expression due to cis-regulatory divergence, as in KNOX genes and REDUCED COMPLEXITY, and can be coupled with protein divergence...
March 8, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28131821/the-fate-of-retrotransposed-processed-genes-in-arabidopsis-thaliana
#5
Basma T M Abdelkarim, Vincent Maranda, Guy Drouin
Processed genes are functional genes that have arisen as a result of the retrotransposition of mRNA molecules. We found 6 genes that generated processed genes in the common ancestor of five Brassicaceae species (Arabidopsis thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula). These processed genes have therefore been kept for at least 30millionyears. Analyses of the Ka/Ks ratio of these genes, and of those having given rise to them, show that they evolve relatively slowly and suggest that the processed genes maintained the same function as that of their parental gene...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28096395/genomic-analysis-reveals-major-determinants-of-cis-regulatory-variation-in-capsella-grandiflora
#6
Kim A Steige, Benjamin Laenen, Johan Reimegård, Douglas G Scofield, Tanja Slotte
Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE)...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27916528/repeated-inactivation-of-the-first-committed-enzyme-underlies-the-loss-of-benzaldehyde-emission-after-the-selfing-transition-in-capsella
#7
Claudia Sas, Frank Müller, Christian Kappel, Tyler V Kent, Stephen I Wright, Monika Hilker, Michael Lenhard
The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]...
December 19, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27916524/gain-and-loss-of-floral-scent-production-through-changes-in-structural-genes-during-pollinator-mediated-speciation
#8
Avichai Amrad, Michel Moser, Therese Mandel, Michel de Vries, Robert C Schuurink, Loreta Freitas, Cris Kuhlemeier
The interactions of plants with their pollinators are thought to be a driving force in the evolution of angiosperms. Adaptation to a new pollinator involves coordinated changes in multiple floral traits controlled by multiple genes. Surprisingly, such complex genetic shifts have happened numerous times during evolution. Here we report on the genetic basis of the changes in one such trait, floral scent emission, in the genus Petunia (Solanaceae). The increase in the quantity and complexity of the volatiles during the shift from bee to hawkmoth pollination was due to de novo expression of the genes encoding benzoic acid/salicylic acid carboxyl methyltransferase (BSMT) and benzoyl-CoA:benzylalcohol/2-phenylethanol benzoyltransferase (BPBT) together with moderately increased transcript levels for most enzymes of the phenylpropanoid/benzenoid pathway...
December 19, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27849572/standing-genetic-variation-in-a-tissue-specific-enhancer-underlies-selfing-syndrome-evolution-in-capsella
#9
Adrien Sicard, Christian Kappel, Young Wha Lee, Natalia Joanna Woźniak, Cindy Marona, John R Stinchcombe, Stephen I Wright, Michael Lenhard
Mating system shifts recurrently drive specific changes in organ dimensions. The shift in mating system from out-breeding to selfing is one of the most frequent evolutionary transitions in flowering plants and is often associated with an organ-specific reduction in flower size. However, the evolutionary paths along which polygenic traits, such as size, evolve are poorly understood. In particular, it is unclear how natural selection can specifically modulate the size of one organ despite the pleiotropic action of most known growth regulators...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27846808/pinpointing-genes-underlying-annual-perennial-transitions-with-comparative-genomics
#10
Andrew J Heidel, Christiane Kiefer, George Coupland, Laura E Rose
BACKGROUND: Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. To identify genes that confer differences between annuals and perennials we compared the gene content of four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata, Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair contains one annual and one perennial, plus one extra annual species (Capsella rubella)...
November 15, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27818675/cbrci35-a-cold-responsive-peroxidase-from-capsella-bursa-pastoris-regulates-reactive-oxygen-species-homeostasis-and-enhances-cold-tolerance-in-tobacco
#11
Mingqi Zhou, Weiwei Li, Ye Zheng, Ping Lin, Xiaohua Yao, Juan Lin
Low temperature affects gene regulatory networks and alters cellular metabolism to inhibit plant growth. Peroxidases are widely distributed in plants and play a large role in adjusting and controlling reactive oxygen species (ROS) homeostasis in response to abiotic stresses such as low temperature. The Rare Cold-Inducible 35 gene from Capsella bursa-pastoris (CbRCI35) belongs to the type III peroxidase family and has been reported to be a cold responsive gene in plants. Here we performed an expressional characterization of CbRCI35 under cold and ionic liquid treatments...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27630652/genome-wide-analysis-of-the-glutathione-s-transferase-gene-family-in-capsella-rubella-identification-expression-and-biochemical-functions
#12
Gang He, Chao-Nan Guan, Qiang-Xin Chen, Xiao-Jun Gou, Wei Liu, Qing-Yin Zeng, Ting Lan
Extensive subfunctionalization might explain why so many genes have been maintained after gene duplication, which provides the engine for gene family expansion. However, it is still a particular challenge to trace the evolutionary dynamics and features of functional divergences in a supergene family over the course of evolution. In this study, we identified 49 Glutathione S-transferase (GST) genes from the Capsella rubella, a close relative of Arabidopsis thaliana and a member of the mustard family. Capsella GSTs can be categorized into eight classes, with tau and phi GSTs being the most numerous...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27624834/fruit-shape-diversity-in-the-brassicaceae-is-generated-by-varying-patterns-of-anisotropy
#13
Tilly Eldridge, Łukasz Łangowski, Nicola Stacey, Friederike Jantzen, Laila Moubayidin, Adrien Sicard, Paul Southam, Richard Kennaway, Michael Lenhard, Enrico S Coen, Lars Østergaard
Fruits exhibit a vast array of different 3D shapes, from simple spheres and cylinders to more complex curved forms; however, the mechanism by which growth is oriented and coordinated to generate this diversity of forms is unclear. Here, we compare the growth patterns and orientations for two very different fruit shapes in the Brassicaceae: the heart-shaped Capsella rubella silicle and the near-cylindrical Arabidopsis thaliana silique. We show, through a combination of clonal and morphological analyses, that the different shapes involve different patterns of anisotropic growth during three phases...
September 15, 2016: Development
https://www.readbyqxmd.com/read/27592229/patterns-of-substitution-rate-variation-at-many-nuclear-loci-in-two-species-trios-in-the-brassicaceae-partitioned-with-anova
#14
John M Braverman, Matthew B Hamilton, Brent A Johnson
There are marked variations among loci and among lineages in rates of nucleotide substitution. The generation time hypothesis (GTH) is a neutral explanation for substitution rate heterogeneity that has genomewide application, predicting that species with shorter generation times accumulate DNA sequence substitutions faster than species with longer generation times do since faster genome replication provides more opportunities for mutations to occur and reach fixation by genetic drift. Relatively few studies have rigorously evaluated the GTH in plants, and there are numerous alternative hypotheses for plant substitution rate variation...
September 3, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27485883/evolutionary-fates-and-dynamic-functionalization-of-young-duplicate-genes-in-arabidopsis-genomes
#15
Jun Wang, Feng Tao, Nicholas C Marowsky, Chuanzhu Fan
Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis...
September 2016: Plant Physiology
https://www.readbyqxmd.com/read/27468293/trophic-relationships-between-the-parasitic-plant-species-phelipanche-ramosa-l-and-different-hosts-depending-on-host-phenological-stage-and-host-growth-rate
#16
Delphine Moreau, Stéphanie Gibot-Leclerc, Annette Girardin, Olivia Pointurier, Carole Reibel, Florence Strbik, Mónica Fernández-Aparicio, Nathalie Colbach
Phelipanche ramosa (L.) Pomel (branched broomrape) is a holoparasitic plant that reproduces on crops and also on weeds, which contributes to increase the parasite seed bank in fields. This parasite extracts all its nutrients at the host's expense so that host-parasite trophic relationships are crucial to determine host and parasite growth. This study quantified the intensity with which P. ramosa draws assimilates from its host and analyzed whether it varied with host species, host phenological stage and host growth rate...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27465027/rapid-evolution-of-genomic-imprinting-in-two-species-of-the-brassicaceae
#17
Marcelinus R Hatorangan, Benjamin Laenen, Kim A Steige, Tanja Slotte, Claudia Köhler
Genomic imprinting is an epigenetic phenomenon occurring in mammals and flowering plants that causes genes to adopt a parent-of-origin-specific mode of expression. While the imprinting status of genes is well conserved in mammals, clear estimates for the degree of conservation were lacking in plants. We therefore analyzed the genome-wide imprinting status of Capsella rubella, which shared a common recent ancestor with Arabidopsis thaliana ∼10 to 14 million years ago. However, only ∼14% of maternally expressed genes (MEGs) and ∼29% of paternally expressed genes (PEGs) in C...
August 2016: Plant Cell
https://www.readbyqxmd.com/read/27440791/transposable-element-evolution-in-the-allotetraploid-capsella-bursa-pastoris
#18
J Arvid Ågren, Hui-Run Huang, Stephen I Wright
PREMISE OF THE STUDY: Shifts in ploidy affect the evolutionary dynamics of genomes in a myriad of ways. Population genetic theory predicts that transposable element (TE) proliferation may follow because the genomewide efficacy of selection should be reduced and the increase in gene copies may mask the deleterious effects of TE insertions. Moreover, in allopolyploids, TEs may further accumulate because of hybrid breakdown of TE silencing. However, to date the evidence of TE proliferation following an increase in ploidy is mixed, and the relative importance of relaxed selection vs...
July 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27378621/screening-of-recombinant-glycosyltransferases-reveals-the-broad-acceptor-specificity-of-stevia-ugt-76g1
#19
Griet Dewitte, Maarten Walmagh, Margo Diricks, Alexander Lepak, Alexander Gutmann, Bernd Nidetzky, Tom Desmet
UDP-glycosyltransferases (UGTs) are a promising class of biocatalysts that offer a sustainable alternative for chemical glycosylation of natural products. In this study, we aimed to characterize plant-derived UGTs from the GT-1 family with an emphasis on their acceptor promiscuity and their potential application in glycosylation processes. Recombinant expression in E. coli provided sufficient amounts of enzyme for the in-depth characterization of the salicylic acid UGT from Capsella rubella (UGT-SACr) and the stevia UGT from Stevia rebaudiana (UGT-76G1Sr)...
September 10, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27095398/microsynteny-and-phylogenetic-analysis-of-tandemly-organised-mirna-families-across-five-members-of-brassicaceae-reveals-complex-retention-and-loss-history
#20
Priyanka Rathore, R Geeta, Sandip Das
Plant genomes are characterized by the presence of large miRNA gene families which are few in number. The expansion of miRNA families is thought to be driven by gene and genome duplication. Some members of these miRNA gene families are tandemly arranged and their analysis is of interest because such organisation may indicate origin through tandem duplication and also to investigate whether some such tandem clusters have similar expression patterns, and whether these are regulated through a common set of cis-regulatory elements (eg...
June 2016: Plant Science: An International Journal of Experimental Plant Biology
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