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Plant chromosomes

Julia Pezarini Baptista, Paula Pinheiro Sanches, Gustavo Manoel Teixeira, Alexandre Tadachi Morey, Eliandro Reis Tavares, Sueli Fumie Yamada-Ogatta, Sérgio Paulo Dejato da Rocha, Mariangela Hungria, Renan Augusto Ribeiro, Maria Isabel Balbi-Peña, Roberta Torres Chideroli, Ulisses de Padua Pereira, Admilton Gonçalves de Oliveira
Bacillus velezensis strain LABIM40 holds high potential for biological control of plant pathogens. Its complete genome contains one chromosome of 3,972,310 bp with 3,777 DNA coding sequences and displays 33 gene clusters potentially involved in the suppression of fungal pathogens.
June 21, 2018: Genome Announcements
Chunhua Zhang, Ruijuan Ma, Jianlan Xu, Juan Yan, Lei Guo, Juan Song, Ruchao Feng, Mingliang Yu
The MYB transcription factor superfamily is one of the largest superfamilies modulating various biological processes in plants. Over the past few decades, many MYB superfamily genes have been identified and characterized in some plant species. However, genes belonging to the MYB superfamily in peach (Prunus persica) have not been comprehensively identified and characterized although the genome sequences of peach were released several years ago. In total, this study yielded a set of 256 MYB superfamily genes that was divided into five subfamilies: the R2R3-MYB (2R-MYB), R1R2R3-MYB (3R-MYB), MYB-related (1R-MYB), 4R-MYB, and Atypical-MYB subfamilies...
2018: PloS One
Min Liu, Jie Ran, Jun Zhou
Kinesins are widely expressed, microtubule-dependent motors that play vital roles in microtubule-associated cellular activities, such as cell division and intracellular transport. Eg5, also known as kinesin-5 or kinesin spindle protein, is a member of the kinesin family that contributes to the formation and maintenance of the bipolar mitotic spindle during cell division. Small-molecule compounds that inhibit Eg5 activity have been shown to impair spindle assembly, block mitotic progression, and possess anti-cancer activity...
June 21, 2018: Thoracic Cancer
Xiaojian Zhou, Xiaozhu Wu, Tongjian Li, Mingliang Jia, Xinshen Liu, Yulan Zou, Zixia Liu, Feng Wen
Auxin response factors (ARFs) are one type of essential family of transcription factors that bind with auxin response elements (AuxRE), and play vital roles in variety of plant development and physiological processes. Brachypodium distachyon, related to the major cereal grain species, were recently developed to be a good model organism for functional genomics research. So far, genome-wide overview of the ARF gene family in B. distachyon was not available. Here, a systemic analysis of ARF gene family members in B...
June 20, 2018: Functional & Integrative Genomics
Kurtis L Dluge, Zhongbang Song, Bingwu Wang, W Tyler Steede, Bingguang Xiao, Yong Liu, Ralph E Dewey
BACKGROUND: Advances in genomics technologies are making it increasingly feasible to characterize breeding lines that carry traits of agronomic interest. Tobacco germplasm lines that carry loci designated VAM and va have been extensively investigated due to their association with potyvirus resistance (both VAM and va) and defects in leaf surface compounds originating from glandular trichomes (VAM only). Molecular studies and classical genetic analyses are consistent with the model that VAM and va represent deletion mutations in the same chromosomal region...
June 20, 2018: BMC Genomics
Paul A Saunders, Samuel Neuenschwander, Nicolas Perrin
The recent advances of new genomic technologies has enabled to identify and characterize sex chromosomes in an increasing number of non-model species, revealing that many plants and animals undergo frequent sex chromosome turnovers. What evolutionary forces drive these turnovers remains poorly understood, but it was recently proposed that drift might play a more important role than generally assumed. We analyzed the dynamics of different types of turnovers using individual-based simulations, and show that when mediated by genetic drift, turnovers are usually easier to achieve than substitutions at neutral markers, but that their dynamics and relative likelihoods vary with the type of the resident and emergent sex chromosome system (XY and/or ZW), and the dominance relationships among the sex-determining factors...
June 20, 2018: Journal of Evolutionary Biology
Jana Dluhošová, Jan Ištvánek, Jan Nedělník, Jana Řepková
The genus clover ( Trifolium sp.) is one of the most economically important genera in the Fabaceae family. More than 10 species are grown as manure plants or forage legumes. Red clover's ( T. pratense ) genome size is one of the smallest in the Trifolium genus, while many clovers with potential breeding value have much larger genomes. Zigzag clover ( T. medium ) is closely related to the sequenced red clover; however, its genome is approximately 7.5x larger. Currently, almost nothing is known about the architecture of this large genome and differences between these two clover species...
2018: Frontiers in Plant Science
Panfeng Guan, Lahu Lu, Lijia Jia, Muhammad Rezaul Kabir, Jinbo Zhang, Tianyu Lan, Yue Zhao, Mingming Xin, Zhaorong Hu, Yingyin Yao, Zhongfu Ni, Qixin Sun, Huiru Peng
Major advances in wheat production are needed to address global food insecurity under future climate conditions, such as high temperatures. The grain yield of bread wheat ( Triticum aestivum L.) is a quantitatively inherited complex trait that is strongly influenced by interacting genetic and environmental factors. Here, we conducted global QTL analysis for five yield-related traits, including spike yield, yield components and plant height (PH), in the Nongda3338/Jingdong6 doubled haploid (DH) population using a high-density SNP and SSR-based genetic map...
2018: Frontiers in Plant Science
Koen Hoogendoorn, Lena Barra, Cees Waalwijk, Jeroen S Dickschat, Theo A J van der Lee, Marnix H Medema
Plant pathogenic fungi in the Fusarium genus cause severe damage to crops, resulting in great financial losses and health hazards. Specialized metabolites synthesized by these fungi are known to play key roles in the infection process, and to provide survival advantages inside and outside the host. However, systematic studies of the evolution of specialized metabolite-coding potential across Fusarium have been scarce. Here, we apply a combination of bioinformatic approaches to identify biosynthetic gene clusters (BGCs) across publicly available genomes from Fusarium , to group them into annotated families and to study gain/loss events of BGC families throughout the history of the genus...
2018: Frontiers in Microbiology
Susan D Lawrence, Nicole G Novak
OBJECTIVE: Q-type C2H2 transcription factors (TF) play crucial roles in the plant response to stress, often leading to regulation of downstream genes required for tolerance to these challenges. An infestation-responsive Q-type C2H2 TF (StZFP2) is induced by wounding and infestation in potato. While mining the Solanum tuberosum Group Phureja genome for additional members of this family of proteins, five StZFP2-like genes were found on a portion of chromosome 11. The objective of this work was to differentiate these genes in tissue specificity and expression upon infestation...
June 19, 2018: BMC Research Notes
Yao Bian, Chunwu Yang, Xiufang Ou, Zhibin Zhang, Bin Wang, Weiwei Ma, Lei Gong, Huakun Zhang, Bao Liu
Polyploidy is a prominent route to speciation in plants; however, this entails resolving the challenges of meiotic instability facing abrupt doubling of chromosome complement. This issue remains poorly understood. We subjected progenies of a synthetic hexaploid wheat, analogous to natural common wheat, but exhibiting extensive meiotic chromosome instability, to heat or salt stress. We selected stress-tolerant cohorts and generated their progenies under normal condition. We conducted fluorescent in situ hybridization/genomic in situ hybridization-based meiotic/mitotic analysis, RNA-Seq and virus-induced gene silencing (VIGS)-mediated assay of meiosis candidate genes...
June 19, 2018: New Phytologist
Zexun Huai, Lishun Peng, Sheliang Wang, Hua Zhao, Lei Shi, Fangsen Xu
Boron (B) is an essential micronutrient of plants. In the present study, we characterized an Arabidopsis mutant lbt with significant l ow -b oron t olerance that was identified based on our previous mapping of QTL for B efficiency in Arabidopsis . Multiple nutrient-deficiency analyses point out that lbt mutant is insensitive to only B-limitation stress. Compared with wild-type Col-0, the fresh weight, leaf area, root length and root elongation rate of lbt mutant were significantly improved under B deficiency during vegetative growth...
2018: Frontiers in Plant Science
A Bouam, N Armstrong, A Levasseur, M Drancourt
Three slowly growing mycobacteria named strain AB308, strain AB215 and strain AB57 were isolated from the tomato plant roots. The 16S rRNA and rpoB gene sequence analyses suggested that each strain was representative of one hitherto unidentified slowly-growing Mycobacterium species of the Mycobacterium simiae complex. Genome sequencing indicated that each strain contained one chromosome of 6.015-6.029 Mbp. A total of 1,197, 1,239 and 1,175 proteins were found to be associated with virulence and 107, 76 and 82 proteins were associated with toxin/antitoxin systems for strains AB308, AB215 and AB57, respectively...
June 18, 2018: Scientific Reports
Pandiyan Muthuramalingam, Subramanian Radhesh Krishnan, Subramani Pandian, Narayanan Mareeswaran, Wilson Aruni, Shunmugiah Karutha Pandian, Manikandan Ramesh
The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) - Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser...
June 18, 2018: Scientific Reports
Zuzanna Kantarek, Piotr Masojć, Anna Bienias, Paweł Milczarski
Shortening rye stems to improve lodging resistance is among the major tasks awaiting breeders of this cereal. The most straightforward way to achieve this goal is the implementation of a dominant dwarfing gene into high yielding cultivars. The choice of dominant dwarfing genes in rye is limited to Ddw1 and Ddw3 loci, which are well characterized with respect to map position and tightly linked molecular markers on the long arms of chromosomes 5RL and 1RL, respectively. This paper reports on the identification and preliminary characterization of a novel dominant dwarfing gene, Ddw4, from line S44...
2018: PloS One
Jianhui Wu, Shuo Huang, Qingdong Zeng, Shengjie Liu, Qilin Wang, Jingmei Mu, Shizhou Yu, Dejun Han, Zhensheng Kang
A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis. CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169 × P10103...
June 16, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Elodie Vandelle, Alessandro Vannozzi, Darren Wong, Davide Danzi, Anne-Marie Digby, Silvia Dal Santo, Alessandra Astegno
Calcium (Ca2+ ) is an ubiquitous key second messenger in plants, where it modulates many developmental and adaptive processes in response to various stimuli. Several proteins containing Ca2+ binding domain have been identified in plants, including calmodulin (CaM) and calmodulin-like (CML) proteins, which play critical roles in translating Ca2+ signals into proper cellular responses. In this work, a genome-wide analysis conducted in Vitis vinifera identified three CaM- and 62 CML-encoding genes. We assigned gene family nomenclature, analyzed gene structure, chromosomal location and gene duplication, as well as protein motif organization...
June 4, 2018: Plant Physiology and Biochemistry: PPB
Ana Luísa Garcia-Oliveira, César Benito, Henrique Guedes-Pinto, Paula Martins-Lopes
Recently, members of MATE family have been implicated in aluminium (Al) tolerance by facilitating citrate efflux in plants. The aim of the present work was to perform a molecular characterisation of the MATE2 gene in bread wheat. Here, we cloned a member of the MATE gene family in bread wheat and named TaMATE2, which showed the typical secondary structure of MATE-type transporters maintaining all the 12 transmembrane domains. The amplification in Chinese Spring nulli-tetrasomic and ditelosomic lines revealed that TaMATE2 is located on the long arm of homoeologous group 1 chromosomes...
June 15, 2018: Plant Biology
Marta Vazquez-Vilar, Diego Orzaez, Nicola Patron
Synthetic Biology is defined as the application of engineering principles to biology. It aims to increase the speed, ease and predictability with which desirable changes and novel traits can be conferred to living cells. The initial steps in this process aim to simplify the encoding of new instructions in DNA by establishing low-level programming languages for biology. Together with advances in the laboratory that allow multiple DNA molecules to be efficiently assembled together into a desired order in a single step, this approach has simplified the design and assembly of multigene constructs and has even facilitated the automated construction of synthetic chromosomes...
August 2018: Plant Science: An International Journal of Experimental Plant Biology
Liang Chen, Jianmin Bian, Shilai Shi, Jianfeng Yu, Hira Khanzada, Ghulam Mustafa Wassan, Changlan Zhu, Xin Luo, Shan Tong, Xiaorong Yang, Xiaosong Peng, Shuang Yong, Qiuying Yu, Xiaopeng He, Junru Fu, Xiaorong Chen, Lifang Hu, Linjuan Ouyang, Haohua He
BACKGROUND: Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy. RESULTS: Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations...
June 15, 2018: Rice
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