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Aditi Jain, Saurabh Anand, Neer K Singh, Sandip Das
The impact of polyploidy on functional diversification of cis-regulatory elements is poorly understood. This is primarily on account of lack of well-defined structure of cis-elements and a universal regulatory code. To the best of our knowledge, this is the first report on characterization of sequence and functional diversification of paralogous and homeologous promoter elements associated with MIR164 from Brassica. The availability of whole genome sequence allowed us to identify and isolate a total of 42 homologous copies of MIR164 from diploid species-Brassica rapa (A-genome), Brassica nigra (B-genome), Brassica oleracea (C-genome), and allopolyploids-Brassica juncea (AB-genome), Brassica carinata (BC-genome) and Brassica napus (AC-genome)...
March 12, 2018: Functional & Integrative Genomics
Barbara Neuffer, Christina Wesse, Ingo Voss, Renate Scheibe
For almost 100 years now, ecotypic differentiation of plant species has been a major topic of research. In changing environments, the question needs to be answered as to how long it takes to adapt, and which parameters are subject to this fast adaptation. Short-living colonizing plant species are excellent examples, especially when they are selfing. Shepherd's Purse Capsella bursa-pastoris (Brassicaceae) is one of the most wide-spread flowering species on earth and avoids only the hot and humid tropics. Many studies demonstrated the ecotypic differentiation of C...
February 2018: AoB Plants
Jörg A Bachmann, Andrew Tedder, Benjamin Laenen, Kim A Steige, Tanja Slotte
Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection...
February 23, 2018: G3: Genes—Genomes—Genetics
Sandra Petrone Mendoza, Martin Lascoux, Sylvain Glémin
Background and Aims: Capsella is a model genus for studying the transition from outcrossing to selfing, with or without change in ploidy levels. The genomic consequences and changes in reproductive traits (selfing syndrome) associated with these shifts have been studied in depth. However, potential ecological divergence among species of the genus has not been determined. Among ecological traits, competitive ability could be relevant for selfing evolution, as selfing has been shown to be statistically associated with reduced competitiveness in a recent meta-analysis...
February 17, 2018: Annals of Botany
Ushio Fujikura, Runchun Jing, Atsushi Hanada, Yumiko Takebayashi, Hitoshi Sakakibara, Shinjiro Yamaguchi, Christian Kappel, Michael Lenhard
Understanding the molecular basis of morphological change remains a central challenge in evolutionary-developmental biology. The transition from outbreeding to selfing is often associated with a dramatic reduction in reproductive structures and functions, such as the loss of attractive pheromones in hermaphroditic Caenorhabditis elegans and a reduced flower size in plants. Here, we demonstrate that variation in the level of the brassinosteroid-biosynthesis enzyme CYP724A1 contributes to the reduced flower size of selfing Capsella rubella compared with its outbreeding ancestor Capsella grandiflora...
December 20, 2017: Developmental Cell
Zhikai Liang, James C Schnable
Gene loss following whole genome duplication (WGD) is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this shifts the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin markers and epigenetic signals between subgenomes in several model species are now being identified that may provide an explanation for bias in expression between subgenomes...
December 21, 2017: Molecular Plant
Lele Zhang, Wenlei Guo, Qi Li, Cuixia Wu, Ning Zhao, Weitang Liu, Jinxin Wang
Shepherd's purse is a troublesome dicot weed that occurs in the major wheat-producing areas in China. Twenty-eight shepherd's purse populations were collected from winter wheat-planting areas in Henan Province and used to evaluate tribenuron-methyl resistance and acetohydroxyacid synthase (AHAS) gene-mutation diversity. The results indicate that all 28 shepherd's purse populations were resistant to tribenuron-methyl at different levels compared with the susceptible population. Mutation of the 197 codon (CCT) changed proline (Pro) into tyrosine (Tyr), histidine (His), leucine (Leu), serine (Ser), arginine (Arg), alanine (Ala) and threonine (Thr), whereas mutation of the 574 codon (TGG) changed tryptophan (Trp) into leucine (Leu)...
November 2017: Pesticide Biochemistry and Physiology
Qiong Wu, Ting-Shen Han, Xi Chen, Jia-Fu Chen, Yu-Pan Zou, Zi-Wen Li, Yong-Chao Xu, Ya-Long Guo
BACKGROUND: In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adaptation in diverse organisms. However, which genes, genome-wide, are under balancing selection and the extent to which these genes are involved in adaptation are largely unknown. RESULTS: We performed a genome-wide scan for genes under balancing selection across two plant species, Arabidopsis thaliana and its relative Capsella rubella, which diverged about 8 million generations ago...
November 15, 2017: Genome Biology
Xiaoxiao Zhang, Weijia Liu, Takuya T Nagae, Hidenori Takeuchi, Heqiao Zhang, Zhifu Han, Tetsuya Higashiyama, Jijie Chai
Transportation of the immobile sperms directed by pollen tubes to the ovule-enclosed female gametophytes is important for plant sexual reproduction. The defensin-like (DEFL) cysteine-rich peptides (CRPs) LUREs play an essential role in pollen tube attraction to the ovule, though their receptors still remain controversial. Here we provide several lines of biochemical evidence showing that the extracellular domain of the leucine-rich repeat receptor kinase (LRR-RK) PRK6 from Arabidopsis thaliana directly interacts with AtLURE1 peptides...
November 6, 2017: Nature Communications
Robert Horvath, Tanja Slotte
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population...
October 1, 2017: Genome Biology and Evolution
Yusen Shen, Yi Yang, Ensheng Xu, Xianhong Ge, Yang Xiang, Zaiyun Li
A high-density SNP map was constructed and several novel QTL for branch angle across six environments in Brassica napus were identified. Branch angle is a major determinant for the ideotype of a plant, while the mechanisms underlying this trait in Brassica napus remain elusive. Herein, we developed one doubled haploid population from a cross involving one Capsella bursa-pastoris derived B. napus intertribal introgression line with the compressed branches and wooden stems, and constructed a high-density SNP map covering the genetic distance of 2242...
September 23, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Pengshan Zhao, Lirong Wang, Xin Zhao, Guoxiong Chen, Xiao-Fei Ma
Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai-Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78...
2017: PloS One
Ali Noman, Hina Kanwal, Noreen Khalid, Tayyaba Sanaullah, Aasma Tufail, Atifa Masood, Sabeeh-Ur-Rasool Sabir, Muhammad Aqeel, Shuilin He
Plants respond to cold stress by modulating biochemical pathways and array of molecular events. Plant morphology is also affected by the onset of cold conditions culminating at repression in growth as well as yield reduction. As a preventive measure, cascades of complex signal transduction pathways are employed that permit plants to endure freezing or chilling periods. The signaling pathways and related events are regulated by the plant hormonal activity. Recent investigations have provided a prospective understanding about plant response to cold stress by means of developmental pathways e...
2017: Frontiers in Plant Science
Shuai Zhao, Mo Yang, Wenfei Zhou, Baichao Zhang, Zhiqiang Cheng, Jiaxin Huang, Min Zhang, Zhiyou Wang, Rui Wang, Zhonglei Chen, Jinsong Zhu, Haitao Li
Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chip-based surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e...
August 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
Dinghong Li, Zhao Lei, Jiayu Xue, Guangcan Zhou, Yueyu Hang, Xiaoqin Sun
The contribution of variations in coding regions or promoters to the changes in FAE1 expression levels have be quantified and compared in parallel by specifically designed swapping constructs. FATTY ACID ELONGATION1 (FAE1) is a key gene in control of erucic acid synthesis in plant seeds. The expression of FAE1 genes in Brassica oleracea and Capsella rubella, representatives of high and low erucic acid species, respectively, was characterized to provide insight into the regulation of very long-chain fatty-acid biosynthesis in seeds...
July 3, 2017: Planta
Ancheng C Huang, Satria A Kautsar, Young J Hong, Marnix H Medema, Andrew D Bond, Dean J Tantillo, Anne Osbourn
Sesterterpenoids are a rare terpene class harboring untapped chemodiversity and bioactivities. Their structural diversity originates primarily from the scaffold-generating sesterterpene synthases (STSs). In fungi, all six known STSs are bifunctional, containing C-terminal trans-prenyltransferase (PT) and N-terminal terpene synthase (TPS) domains. In plants, two colocalized PT and TPS gene pairs from Arabidopsis thaliana were recently reported to synthesize sesterterpenes. However, the landscape of PT and TPS genes in plant genomes is unclear...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
Joon Min Cha, Won Se Suh, Tae Hyun Lee, Lalita Subedi, Sun Yeou Kim, Kang Ro Lee
A new sesquilignan glycoside 1, together with seven known phenolic glycosides 2-8 were isolated from the aerial parts of Capsella bursa-pastoris. The chemical structure of the new compound 1 was elucidated by extensive nuclear magnetic resonance (NMR) data (¹H- and (13)C-NMR, ¹H-¹H correlation spectroscopy (¹H-¹H COSY), heteronuclear single-quantum correlation (HSQC), heteronuclear multiple bond correlation (HMBC), and nuclear overhauser effect spectroscopy (NOESY)) and HR-FABMS analysis. The anti-inflammatory effects of 1-8 were evaluated in lipopolysaccharide (LPS)-stimulated murine microglia BV-2 cells...
June 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Sahar Ghalandari, Nourossadat Kariman, Zohre Sheikhan, Faraz Mojab, Moghadameh Mirzaei, Hadis Shahrahmani
OBJECTIVES: Postpartum hemorrhage (PPH) is one of three main causes of maternal mortality and a life-threatening condition throughout the world. PPH can have irreversible complications for the mother even if it does not lead to death. This study was conducted to determine the effect of hydroalcoholic extract of Capsella bursa pastoris on early PPH. DESIGN: The present study was a single-blinded, randomized, clinical trial. SETTING: The study was conducted in Afzalipour Hospital of Kerman in 2015...
October 2017: Journal of Alternative and Complementary Medicine: Research on Paradigm, Practice, and Policy
Humira Sonah, Rupesh K Deshmukh, Caroline Labbé, Richard R Bélanger
Aquaporins (AQPs) are of vital importance in the cellular transport system of all living organisms. In this study, genome-wide identification, distribution, and characterization of AQPs were determined in Arabidopsis lyrata, Capsella grandiflora, C. rubella, Eutrema salsugineum, Brassica rapa, B. oleracea, and B. napus (canola). Classification and phylogeny of AQPs revealed the loss of XIPs and NIP-IIIs in all species. Characterization of distinctive AQP features showed a high level of conservation in spacing between NPA-domains, and selectivity filters...
June 5, 2017: Scientific Reports
Cheng-Yu Yu, Jun-Gang Dong, Sheng-Wu Hu, Ai-Xia Xu
BACKGROUND: For most cruciferous plants, which are known as important crops and a number of weeds, hybrid breeding is hampered by the unavailability of a pollination control system. Male sterility induced by a gametocide can be useful for the utilization of plant heterosis. RESULTS: The gametocidal effect of sulfonylurea herbicide tribenuron-methyl was tested across seventeen cruciferous species or subspecies including Brassica juncea, B. carinata, B. oleracea ssp...
June 1, 2017: BMC Plant Biology
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