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https://www.readbyqxmd.com/read/28334286/differences-in-the-photosynthetic-plasticity-of-ferns-and-ginkgo-grown-in-experimentally-controlled-low-o2-co2-atmospheres-may-explain-their-contrasting-ecological-fate-across-the-triassic-jurassic-mass-extinction-boundary
#1
C Yiotis, C Evans-Fitz Gerald, J C McElwain
Background and Aims: Fluctuations in [CO 2 ] have been widely studied as a potential driver of plant evolution; however, the role of a fluctuating [O 2 ]:[CO 2 ] ratio is often overlooked. The present study aimed to investigate the inherent physiological plasticity of early diverging, extant species following acclimation to an atmosphere similar to that across the Triassic-Jurassic mass extinction interval (TJB, approx. 200 Mya), a time of major ecological change. Methods: Mature plants from two angiosperm ( Drimys winteri and Chloranthus oldhamii ), two monilophyte ( Osmunda claytoniana and Cyathea australis ) and one gymnosperm ( Ginkgo biloba ) species were grown for 2 months in replicated walk-in Conviron BDW40 chambers running at TJB treatment conditions of 16 % [O 2 ]-1900 ppm [CO 2 ] and ambient conditions of 21 % [O 2 ]-400 ppm [CO 2 ], and their physiological plasticity was assessed using gas exchange and chlorophyll fluorescence methods...
March 11, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334206/polyploid-species-rely-on-vegetative-reproduction-more-than-diploids-a-re-examination-of-the-old-hypothesis
#2
Tomáš Herben, Jan Suda, Jitka Klimešová
Background and Aims: Polyploidy is arguably the single most important genetic mechanism in plant speciation and diversification. It has been repeatedly suggested that polyploids show higher vegetative reproduction than diploids (to by-pass low fertility after the polyploidization), but there are no rigorous tests of it. Methods: Data were analysed by phylogenetic regressions of clonal growth parameters, and vegetative reproduction in culture on the ploidy status of a large set of species (approx...
February 27, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28333233/contrasting-rates-of-molecular-evolution-and-patterns-of-selection-among-gymnosperms-and-flowering-plants
#3
Amanda R De La Torre, Zhen Li, Yves Van de Peer, Pär K Ingvarsson
The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28331573/evolution-of-the-spatula-alcatraz-gene-lineage-and-expression-analyses-in-the-basal-eudicot-bocconia-frutescens-l-papaveraceae
#4
Cecilia Zumajo-Cardona, Barbara Ann Ambrose, Natalia Pabón-Mora
BACKGROUND: SPATULA (SPT) and ALCATRAZ (ALC) are recent paralogs that belong to the large bHLH transcription factor family. Orthologs of these genes have been found in all core eudicots, whereas pre-duplication genes, named paleoSPATULA/ALCATRAZ, have been found in basal eudicots, monocots, basal angiosperms and gymnosperms. Nevertheless, functional studies have only been performed in Arabidopsis thaliana, where SPT and ALC are partially redundant in carpel and valve margin development and ALC has a unique role in the dehiscence zone...
2017: EvoDevo
https://www.readbyqxmd.com/read/28328971/mapping-the-n-linked-glycosites-of-rice-oryza-sativa-l-germinating-embryos
#5
Jiezheng Ying, Juan Zhao, Yuxuan Hou, Yifeng Wang, Jiehua Qiu, Zhiyong Li, Xiaohong Tong, Zhaomei Shi, Jun Zhu, Jian Zhang
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered...
2017: PloS One
https://www.readbyqxmd.com/read/28326093/the-complete-chloroplast-genome-of-wild-rice-oryza-minuta-and-its-comparison-to-related-species
#6
Sajjad Asaf, Muhammad Waqas, Abdul L Khan, Muhammad A Khan, Sang-Mo Kang, Qari M Imran, Raheem Shahzad, Saqib Bilal, Byung-Wook Yun, In-Jung Lee
Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28321577/hiding-in-plain-sight-the-f-segment-and-other-conserved-features-of-seed-plant-skn-dehydrins
#7
G Richard Strimbeck
An 11-residue amino acid sequence, DRGLFDFLGKK, is highly conserved in a subset of dehydrins found across the full spectrum of seed plants and here given the name F-segment. An 11-residue amino acid sequence, DRGLFDFLGKK, is highly conserved in identity and polarity in 130 non-redundant dehydrin sequences representing conifers and all major angiosperm groups. This newly described motif is here given the name F segment based on the pair of hydrophobic F residues at the core of the sequence. The majority of dehydrins previously classified as SKn dehydrins contain one F segment N terminal to the S and K segments and can accordingly be reclassified as FSKn dehydrins...
March 20, 2017: Planta
https://www.readbyqxmd.com/read/28321576/two-distinct-cinnamoyl-coa-reductases-in-selaginella-moellendorffii-offer-insight-into-the-divergence-of-ccrs-in-plants
#8
Nan Chao, Shuang Li, Ning Li, Qi Qi, Wen-Ting Jiang, Xiang-Ning Jiang, Ying Gai
Two distinct cinnamoyl-coenzyme A reductases (CCRs) from Selaginella moellendorffii were evaluated, and of these, SmCCR2-1, which has both distinct sequence motifs and catalytic properties, was clustered into a new CCR subgroup. Cinnamoyl-coenzyme A reductases (CCRs) have been reported in many land plants to have critical functions in monolignol biosynthesis. In this study, we performed a genome-wide screen and obtained two distinct SmCCRs from S. moellendorffii. Phylogenetic analysis indicated that SmCCR2 (both SmCCR2-1 and 2-2) and SmCCR3 together with PpaCCR belong to a distinct subgroup of genuine CCRs with variations in the NAD(P)H-binding motif...
March 20, 2017: Planta
https://www.readbyqxmd.com/read/28316149/detecting-alternatively-spliced-transcript-isoforms-from-single-molecule-long-read-sequences-without-a-reference-genome
#9
Xiaoxian Liu, Wenbin Mei, Pamela S Soltis, Douglas E Soltis, W Brad Barbazuk
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq(™) data for isoform-level transcriptome analysis, including the study of AS and gene fusion. We applied Iso-Seq(™) to investigate AS in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living angiosperms. Our data show that, compared with RNA-Seq data, the Iso-Seq(™) platform provides better recovery on large transcripts, new gene locus identification, and gene model correction...
March 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28314936/distribution-of-divo-in-coffea-genomes-a-poorly-described-family-of-angiosperm-ltr-retrotransposons
#10
Mathilde Dupeyron, Rogerio Fernandes de Souza, Perla Hamon, Alexandre de Kochko, Dominique Crouzillat, Emmanuel Couturon, Douglas Silva Domingues, Romain Guyot
Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains...
March 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28304126/transcript-profiling-of-a-novel-plant-meristem-the-monocot-cambium
#11
Matthew Zinkgraf, Suzanne Gerttula, Andrew Groover
While monocots lack the ability to produce a vascular cambium or woody growth, some monocot lineages evolved a novel lateral meristem, the monocot cambium, which supports secondary radial growth of stems. In contrast to the vascular cambium found in woody angiosperm and gymnosperm species, the monocot cambium produces secondary vascular bundles, which have an amphivasal organization of tracheids encircling a central strand of phloem. Currently there is no information concerning the molecular genetic basis of the development or evolution of the monocot cambium...
March 17, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28304077/alternative-electron-transport-mediated-by-flavodiiron-proteins-is-operational-in-organisms-from-cyanobacteria-up-to-gymnosperms
#12
Petr Ilík, Andrej Pavlovič, Roman Kouřil, Alessandro Alboresi, Tomas Morosinotto, Yagut Allahverdiyeva, Eva-Mari Aro, Hiroshi Yamamoto, Toshiharu Shikanai
Photo-reduction of O2 to water mediated by flavodiiron proteins (FDPs) represents a safety valve for the photosynthetic electron transport chain in fluctuating light. So far, the FDP-mediated O2 photo-reduction has been evidenced only in cyanobacteria and the moss Physcomitrella; however, a recent phylogenetic analysis of transcriptomes of photosynthetic organisms has also revealed the presence of FDP genes in several nonflowering plant groups. What remains to be clarified is whether the FDP-dependent O2 photo-reduction is actually operational in these organisms...
March 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28303145/evolutionary-analyses-of-gras-transcription-factors-in-angiosperms
#13
Alberto Cenci, Mathieu Rouard
GRAS transcription factors (TFs) play critical roles in plant growth and development such as gibberellin and mycorrhizal signaling. Proteins belonging to this gene family contain a typical GRAS domain in the C-terminal sequence, whereas the N-terminal region is highly variable. Although, GRAS genes have been characterized in a number of plant species, their classification is still not completely resolved. Based on a panel of eight representative species of angiosperms, we identified 29 orthologous groups or orthogroups (OGs) for the GRAS gene family, suggesting that at least 29 ancestor genes were present in the angiosperm lineage before the "Amborella" evolutionary split...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28299594/dissecting-pistil-responses-to-incompatible-and-compatible-pollen-in-self-incompatibility-brassica-oleracea-using-comparative-proteomics
#14
Jing Zeng, Qiguo Gao, Songmei Shi, Xiaoping Lian, Richard Converse, Hecui Zhang, Xiaohong Yang, Xuesong Ren, Song Chen, Liquan Zhu
Angiosperms have developed self-incompatibility (SI) systems to reject self-pollen, thereby promoting outcrossing. The Brassicaceae belongs to typical sporophytic system, having a single S-locus controlled SI response, and was chosen as a model system to study SI-related intercellular signal transduction. In this regard, the downstream factor of EXO70A1 was unknown. Here, protein two-dimensional electrophoresis (2-DE) method and coupled with matrix-assisted laser desorption ionization/time of flight of flight mass spectrometry (MALDI-TOF -MS) and peptide mass fingerprinting (PMF) was used to further explore the mechanism of SI responses in Brassica oleracea L...
March 16, 2017: Protein Journal
https://www.readbyqxmd.com/read/28298915/transcriptomic-analysis-reveals-mechanisms-of-sterile-and-fertile-flower-differentiation-and-development-in-viburnum-macrocephalum-f-keteleeri
#15
Zhaogeng Lu, Jing Xu, Weixing Li, Li Zhang, Jiawen Cui, Qingsong He, Li Wang, Biao Jin
Sterile and fertile flowers are an important evolutionary developmental (evo-devo) phenotype in angiosperm flowers, playing important roles in pollinator attraction and sexual reproductive success. However, the gene regulatory mechanisms underlying fertile and sterile flower differentiation and development remain largely unknown. Viburnum macrocephalum f. keteleeri, which possesses fertile and sterile flowers in a single inflorescence, is a useful candidate species for investigating the regulatory networks in differentiation and development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28298518/evidence-for-ancient-origins-of-bowman-birk-inhibitors-from-selaginella-moellendorffii
#16
Amy Midori James, Achala S Jayasena, Jingjing Zhang, Oliver Berkowitz, David Secco, Gavin J Knott, James Whelan, Charles Bond, Joshua S Mylne
Bowman-Birk Inhibitors (BBIs) are a well-known family of plant protease inhibitors first described 70 years ago. BBIs are known only in the legume (Fabaceae) and cereal (Poaceae) families, but peptides that mimic their trypsin inhibitory loops exist in sunflowers and frogs. The disparate biosynthetic origins and distant phylogenetic distribution implies these loops evolved independently, but their structural similarity suggests a common ancestor. Targeted bioinformatic searches for the BBI inhibitory loop discovered highly divergent BBI like sequences in the seedless, vascular spikemoss Selaginella moellendorffii...
March 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28295874/is-the-diversification-of-mediterranean-basin-plant-lineages-coupled-to-karyotypic-changes
#17
Marcial Escudero, Francisco Balao, Santiago Martín-Bravo, Luis Valente, Virginia Valcárcel
The Mediterranean Basin region, home to 25,000 species of plants, is included in the worldwide list of hotspots of biodiversity. Despite the indisputably important role of chromosome transitions in plant evolution and diversification, no reference study to date has dealt with the possible relationship between chromosome evolution and lineage diversification in the Mediterranean Basin. Here we study patterns of diversification, patterns of chromosome number transition (either polyploidy or dysploidy), and the relationship between both for 14 Mediterranean Basin angiosperm lineages using previously published phylogenies...
March 13, 2017: Plant Biology
https://www.readbyqxmd.com/read/28295410/diversity-of-strategies-for-escaping-reactive-oxygen-species-production-within-photosystem-i-among-land-plants-p700-oxidation-system-is-prerequisite-for-alleviating-photoinhibition-in-photosystem-i
#18
Daisuke Takagi, Kimitsune Ishizaki, Hitomi Hanawa, Tomohito Mabuchi, Ginga Shimakawa, Hiroshi Yamamoto, Chikahiro Miyake
In land plants, photosystem (PS) I photoinhibition limits carbon fixation and causes growth defects. In addition, recovery from PSI photoinhibition takes much longer than PSII photoinhibition when the PSI core-complex is degraded by oxidative damage. Accordingly, PSI photoinhibition should be avoided in land plants, and land plants should have evolved mechanisms to prevent PSI photoinhibition. However, such protection mechanisms have not yet been identified, and it remains unclear whether all land plants suffer from PSI photoinhibition in the same way...
March 10, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28293248/a-strategy-for-screening-monoclonal-antibodies-for-arabidopsis-flowers
#19
Qian Shi, Lian Zhou, Yingxiang Wang, Hong Ma
The flower is one of the most complex structures of angiosperms and is essential for sexual reproduction. Current studies using molecular genetic tools have made great advances in understanding flower development. Due to the lack of available antibodies, studies investigating the localization of proteins required for flower development have been restricted to use commercial antibodies against known antigens such as GFP, YFP, and FLAG. Thus, knowledge about cellular structures in the floral organs is limited due to the scarcity of antibodies that can label cellular components...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28289426/transcriptome-wide-identification-classification-and-characterization-of-ap2-erf-family-genes-in-the-desert-moss-syntrichia-caninervis
#20
Xiaoshuang Li, Daoyuan Zhang, Bei Gao, Yuqing Liang, Honglan Yang, Yucheng Wang, Andrew J Wood
APETALA2/Ethylene Responsive Factor (AP2/ERF) is a large family of plant transcription factors which play important roles in the control of plant metabolism and development as well as responses to various biotic and abiotic stresses. The desert moss Syntrichia caninervis, due to its robust and comprehensive stress tolerance, is a promising organism for the identification of stress-related genes. Using S. caninervis transcriptome data, 80 AP2/ERF unigenes were identified by HMM modeling and BLASTP searching...
2017: Frontiers in Plant Science
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