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https://www.readbyqxmd.com/read/29764984/parallel-evolution-of-common-allelic-variants-confers-flowering-diversity-in-capsella-rubella
#1
Li Yang, Hui-Na Wang, Xing-Hui Hou, Yu-Pan Zou, Ting-Shen Han, Xiao-Min Niu, Jie Zhang, Zhong Zhao, Marco Todesco, Sureshkumar Balasubramanian, Ya-Long Guo
Flowering time is an adaptive life history trait. Capsella rubella, a close relative of Arabidopsis thaliana and a young species, displays extensive variation for flowering time but low standing genetic variation due to an extreme bottleneck event, providing an excellent opportunity to understand how phenotypic diversity can occur with a limited initial gene pool. Here, we demonstrate that common allelic variation and parallel evolution at the FLC locus confer variation in flowering time in C. rubella. We show that two overlapping deletions in the 5' UTR region of C...
May 15, 2018: Plant Cell
https://www.readbyqxmd.com/read/29691226/successive-duplication-divergence-mechanisms-at-the-rco-locus-contributed-to-leaf-shape-diversity-in-the-brassicaceae
#2
Susanna Streubel, Michael André Fritz, Melanie Teltow, Christian Kappel, Adrien Sicard
Gene duplication is a major driver for the increase of biological complexity. The divergence of newly duplicated paralogs may allow novel functions to evolve, while maintaining the ancestral one. Alternatively, partitioning the ancestral function among paralogs may allow parts of that role to follow independent evolutionary trajectories. We studied the REDUCED COMPLEXITY ( RCO ) locus, which contains three paralogs that have evolved through two independent events of gene duplication, and which underlies repeated events of leaf shape evolution within the Brassicaceae ...
April 24, 2018: Development
https://www.readbyqxmd.com/read/29643859/major-co-localized-qtl-for-plant-height-branch-initiation-height-stem-diameter-and-flowering-time-in-an-alien-introgression-derived-brassica-napus-dh-population
#3
Yusen Shen, Yang Xiang, Ensheng Xu, Xianhong Ge, Zaiyun Li
Plant height (PH), branch initiation height (BIH), and stem diameter (SD) are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH) population obtained from a cross between Y689 (one Capsella bursa - pastoris derived Brassica napus intertribal introgression) and Westar ( B . napus cultivar) that these traits were significantly positively correlated with one another and with flowering time (FT). Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL) were identified across six environments...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29608724/higher-rates-of-protein-evolution-in-the-self-fertilizing-plant-arabidopsis-thaliana-than-in-the-out-crossers-arabidopsis-lyrata-and-arabidopsis-halleri
#4
Bryan L Payne, David Alvarez-Ponce
The common transition from out-crossing to self-fertilization in plants decreases effective population size. This is expected to result in a reduced efficacy of natural selection and in increased rates of protein evolution in selfing plants compared with their outcrossing congeners. Prior analyses, based on a very limited number of genes, detected no differences between the rates of protein evolution in the selfing Arabidopsis thaliana compared with the out-crosser Arabidopsis lyrata. Here, we reevaluate this trend using the complete genomes of A...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29532337/sequence-and-functional-characterization-of-mirna164-promoters-from-brassica-shows-copy-number-dependent-regulatory-diversification-among-homeologs
#5
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
https://www.readbyqxmd.com/read/29479407/the-role-of-ecotypic-variation-in-driving-worldwide-colonization-by-a-cosmopolitan-plant
#6
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
https://www.readbyqxmd.com/read/29476024/targeted-long-read-sequencing-of-a-locus-under-long-term-balancing-selection-in-capsella
#7
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...
March 28, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29471370/competitive-ability-of-capsella-species-with-different-mating-systems-and-ploidy-levels
#8
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
https://www.readbyqxmd.com/read/29275992/variation-in-splicing-efficiency-underlies-morphological-evolution-in-capsella
#9
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...
January 22, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29275166/functional-divergence-between-subgenomes-and-gene-pairs-after-whole-genome-duplications
#10
REVIEW
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 raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes...
March 5, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29183598/tribenuron-methyl-resistance-and-mutation-diversity-of-the-ahas-gene-in-shepherd-s-purse-capsella-bursa-pastoris-l-medik-in-henan-province-china
#11
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
https://www.readbyqxmd.com/read/29141655/long-term-balancing-selection-contributes-to-adaptation-in-arabidopsis-and-its-relatives
#12
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
https://www.readbyqxmd.com/read/29109411/structural-basis-for-receptor-recognition-of-pollen-tube-attraction-peptides
#13
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
https://www.readbyqxmd.com/read/29036316/the-role-of-small-rna-based-epigenetic-silencing-for-purifying-selection-on-transposable-elements-in-capsella-grandiflora
#14
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
https://www.readbyqxmd.com/read/28942459/novel-and-major-qtl-for-branch-angle-detected-by-using-dh-population-from-an-exotic-introgression-in-rapeseed-brassica-napus-l
#15
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...
January 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28859098/a-comparative-transcriptomic-analysis-reveals-the-core-genetic-components-of-salt-and-osmotic-stress-responses-in-braya-humilis
#16
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
https://www.readbyqxmd.com/read/28855910/perspective-research-progress-in-cold-responses-of-capsella-bursa-pastoris
#17
REVIEW
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
https://www.readbyqxmd.com/read/28808021/kinetic-and-high-throughput-profiling-of-epigenetic-interactions-by-3d-carbene-chip-based-surface-plasmon-resonance-imaging-technology
#18
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
https://www.readbyqxmd.com/read/28674753/regulation-of-fatty-acid-elongation1-expression-and-production-in-brassica-oleracea-and-capsella-rubella
#19
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
https://www.readbyqxmd.com/read/28673978/unearthing-a-sesterterpene-biosynthetic-repertoire-in-the-brassicaceae-through-genome-mining-reveals-convergent-evolution
#20
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
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