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https://www.readbyqxmd.com/read/28542519/characterization-of-the-whole-chloroplast-genome-of-chikusichloa-mutica-and-its-comparison-with-other-rice-tribe-oryzeae-species
#1
Zhiqiang Wu, Cuihua Gu, Luke R Tembrock, Dong Zhang, Song Ge
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B)...
2017: PloS One
https://www.readbyqxmd.com/read/28541477/mitochondrial-retroprocessing-promoted-functional-transfers-of-rpl5-to-the-nucleus-in-grasses
#2
Zhiqiang Wu, Daniel B Sloan, Colin W Brown, Mónica Rosenblueth, Jeffrey D Palmer, Han Chuan Ong
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus...
May 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28540354/data-on-the-exon-intron-organization-of-genes-coding-for-b-cell-receptor-like-proteins
#3
Sergey Y Morozov, Anna V Pankratenko, Anastasia K Atabekova, Andrey G Solovyev
B-cell receptor-associated protein (BAP) family plays important roles in the ER homeostasis and stress responses of eukaryotic cells [1]. We reported the analysis of plant BAP-like (PBL) genes and the encoded proteins of higher land plants [2]. The origin and functional divergence of these genes among all eukaryotes, however, are poorly studied, which impedes our understanding of the functional relationships and diversity among BAP-like proteins. One possible reason for the potential functional diversity may be the differences in the exon-intron structure of PBL genes...
June 2017: Data in Brief
https://www.readbyqxmd.com/read/28535985/recalcitrant-deep-and-shallow-nodes-in-aristolochia-aristolochiaceae-illuminated-using-anchored-hybrid-enrichment
#4
Stefan Wanke, Carolina Granados Mendoza, Sebastian Müller, Anna Paizanni Guillén, Christoph Neinhuis, Alan R Lemmon, Emily Moriarty Lemmon, Marie-Stéphanie Samain
Recalcitrant relationships are characterized by very short internodes that can be found among shallow and deep phylogenetic scales all over the tree of life. Adding large amounts of presumably informative sequences, while decreasing systematic error, has been suggested as a possible approach to increase phylogenetic resolution. The development of enrichment strategies, coupled with next generation sequencing, resulted in a cost-effective way to facilitate the reconstruction of recalcitrant relationships. By applying the anchored hybrid enrichment (AHE) genome partitioning strategy to Aristolochia using an angiosperm probe set, we obtained 231 to 233 out of 517 single or low copy nuclear loci originally contained in the enrichment kit, resulting in a total alignment length of 154,756 bp to 160,150 bp...
May 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28532390/comparative-genomics-of-eucalyptus-and-corymbia-reveals-low-rates-of-genome-structural-rearrangement
#5
J B Butler, R E Vaillancourt, B M Potts, D J Lee, G J King, A Baten, M Shepherd, J S Freeman
BACKGROUND: Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. RESULTS: We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28531314/the-solanum-tuberosum-kst1-partial-promoter-as-a-tool-for-guard-cell-expression-in-multiple-plant-species
#6
Gilor Kelly, Nitsan Lugassi, Eduard Belausov, Dalia Wolf, Belal Khamaisi, Danja Brandsma, Jayaram Kottapalli, Lena Fidel, Batsheva Ben-Zvi, Aiman Egbaria, Atiako Kwame Acheampong, Chuanlin Zheng, Etti Or, Assaf Distelfeld, Rakefet David-Schwartz, Nir Carmi, David Granot
To date, guard cell promoters have been examined in only a few species, primarily annual dicots. A partial segment of the potato (Solanum tuberosum) KST1 promoter (KST1 partial promoter, KST1ppro) has previously been shown to confer guard cell expression in potato, tomato (Solanum lycopersicum), citrus [Troyer citrange (C. sinensis×Poncirus trifoliata)], and Arabidopsis (Arabidopsis thaliana). Here, we describe an extensive analysis of the expression pattern of KST1ppro in eight (previously reported, as well as new) species from five different angiosperm families, including the Solanaceae and the Cucurbitaceae, Arabidopsis, the monocot barley (Hordeum vulgare), and two perennial species: grapevine (Vitis vinifera) and citrus...
May 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28531201/evolutionary-forces-affecting-synonymous-variations-in-plant-genomes
#7
Yves Clément, Gautier Sarah, Yan Holtz, Felix Homa, Stéphanie Pointet, Sandy Contreras, Benoit Nabholz, François Sabot, Laure Sauné, Morgane Ardisson, Roberto Bacilieri, Guillaume Besnard, Angélique Berger, Céline Cardi, Fabien De Bellis, Olivier Fouet, Cyril Jourda, Bouchaib Khadari, Claire Lanaud, Thierry Leroy, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28529832/application-of-a-simplified-method-of-chloroplast-enrichment-to-small-amounts-of-tissue-for-chloroplast-genome-sequencing
#8
Shota Sakaguchi, Saneyoshi Ueno, Yoshihiko Tsumura, Hiroaki Setoguchi, Motomi Ito, Chie Hattori, Shogo Nozoe, Daiki Takahashi, Riku Nakamasu, Taishi Sakagami, Guillaume Lannuzel, Bruno Fogliani, Adrien S Wulff, Laurent L'Huillier, Yuji Isagi
PREMISE OF THE STUDY: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. METHODS: Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28526726/are-phloem-sieve-tubes-leaky-conduits-supported-by-numerous-aquaporins
#9
Ryan C Stanfield, Uwe G Hacke, Joan Laur
PREMISE OF THE STUDY: Aquaporin membrane water channels have been previously identified in the phloem of angiosperms, but currently their cellular characterization is lacking, especially in tree species. Pinpointing the cellular location will help generate new hypotheses of how membrane water exchange facilitates sugar transport in plants. METHODS: We studied histological sections of balsam poplar (Populus balsamifera L.) in leaf, petiole, and stem organs. Immuno-labeling techniques were used to characterize the distribution of PIP1 and PIP2 subfamilies of aquaporins along the phloem pathway...
May 19, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28514600/evaluating-five-different-loci-rbcl-rpob-rpoc1-matk-and-its-for-dna-barcoding-of-indian-orchids
#10
Iffat Parveen, Hemant Kumar Singh, Saloni Malik, Saurabh Raghuvanshi, Shashi Bhushan Babbar
Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand due to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS matK, rbcL, rpoB and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species...
May 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28510657/heteroblasty-in-epiphytic-bromeliads-functional-implications-for-species-in-understorey-and-exposed-growing-sites
#11
Joachim Beyschlag, Gerhard Zotz
Background and Aims: The functional relevance of heteroblasty, an abrupt morphological change in the ontogeny of a considerable number of angiosperm species, is still largely unresolved. During the ontogeny of many epiphytic Tillandsioids (Bromeliaceae), such a change occurs when small individuals transform into larger, tank-forming individuals that are capable of external water storage. Apart from its fundamental effect on plant water relations, the associated transition from narrow to broader leaves also affects plant architecture...
May 16, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28510198/investigation-of-floristic-similarities-between-taiwan-and-terrestrial-ecoregions-in-asia-using-gbif-data
#12
Chi-Cheng Liao, Chih-Hui Chen
BACKGROUND: Floristic compositions of non-endemic plants of continental islands were related to the neighboring continents because non-endemic plant species had historically migrated to continental islands from source areas. This study attempts to identify source areas of a continental island by means of floristic analysis and to assess possible migration routes on the basis of geographical distribution ranges of plants. Large quantities of angiosperm data records were downloaded from the Global Biodiversity Information Facility (GBIF)...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28510195/meso-or-xeromorphic-foliar-characters-of-asteraceae-in-a-xeric-scrub-of-mexico
#13
Patricia Rivera, José Luis Villaseñor, Teresa Terrazas
BACKGROUND: The anatomical traits associated with water deficit are also observed in plants growing in poor soils. The species may resist water deficit through three main strategies: escape, avoid or tolerate. The Pedregal de San Ángel Ecological Reserve (REPSA), Mexico, is an environment with low nutrient soil and low water availability. It is set on the basalt formation derived from the Xitle volcano eruption. The main vegetation type is characterized as xerophytic shrub. Thus we expect that species growing in this community will show leaf xeromorphic traits and may have any of the three response strategies...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28510189/multiple-regulatory-roles-of-ap2-erf-transcription-factor-in-angiosperm
#14
REVIEW
Chao Gu, Zhi-Hua Guo, Ping-Ping Hao, Guo-Ming Wang, Zi-Ming Jin, Shao-Ling Zhang
APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) is a superfamily in plant kingdom, which has been reported to be involved in regulation of plant growth and development, fruit ripening, defense response, and metabolism. As the final response gene in ethylene signaling pathway, AP2/ERF TF could feedback modulate phytohormone biosynthesis, including ethylene, cytokinin, gibberellin, and abscisic acid. Moreover, AP2/ERF TF also participates in response to the signals of auxin, cytokinin, abscisic acid, and jasmonate...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28509401/transitions-between-marine-and-freshwater-environments-provide-new-clues-about-the-origins-of-multicellular-plants-and-algae
#15
REVIEW
Simon M Dittami, Svenja Heesch, Jeanine L Olsen, Jonas Collén
Marine-freshwater and freshwater-marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized fresh water on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times...
May 16, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28505712/sugar-export-limits-size-of-conifer-needles
#16
Hanna Rademaker, Maciej A Zwieniecki, Tomas Bohr, Kaare H Jensen
Plant leaf size varies by more than three orders of magnitude, from a few millimeters to over one meter. Conifer leaves, however, are relatively short and the majority of needles are no longer than 6 cm. The reason for the strong confinement of the trait-space is unknown. We show that sugars produced near the tip of long needles cannot be exported efficiently, because the pressure required to drive vascular flow would exceed the greatest available pressure (the osmotic pressure). This basic constraint leads to the formation of an inactive region of stagnant fluid near the needle tip, which does not contribute to sugar flow...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28505373/gene-duplication-leads-to-altered-membrane-topology-of-a-cytochrome-p450-enzyme-in-seed-plants
#17
Hugues Renault, Minttu De Marothy, Gabriella Jonasson, Patricia Lara, David R Nelson, IngMarie Nilsson, François André, Gunnar von Heijne, Danièle Werck-Reichhart
Evolution of the phenolic metabolism was critical for the transition of plants from water to land. A cytochrome P450, CYP73, with cinnamate 4-hydroxylase (C4H) activity, catalyzes the first plant-specific and rate-limiting step in this pathway. The CYP73 gene is absent from green algae, and first detected in bryophytes. A CYP73 duplication occurred in the ancestor of seed plants and was retained in Taxaceae and most angiosperms. In spite of a clear divergence in primary sequence, both paralogs can fulfill comparable cinnamate hydroxylase roles both in vitro and in vivo...
May 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28505304/phytoplasma-conserved-phyllogen-proteins-induce-phyllody-across-the-plantae-by-degrading-floral-mads-domain-proteins
#18
Yugo Kitazawa, Nozomu Iwabuchi, Misako Himeno, Momoka Sasano, Hiroaki Koinuma, Takamichi Nijo, Tatsuya Tomomitsu, Tetsuya Yoshida, Yukari Okano, Nobuyuki Yoshikawa, Kensaku Maejima, Kenro Oshima, Shigetou Namba
ABCE-class MADS domain transcription factors (MTFs) are key regulators of floral organ development in angiosperms. Aberrant expression of these genes can result in abnormal floral traits such as phyllody. Phyllogen is a virulence factor conserved in phytoplasmas, plant pathogenic bacteria of the class Mollicutes. It triggers phyllody in Arabidopsis thaliana by inducing degradation of A- and E-class MTFs. However, it is still unknown whether phyllogen can induce phyllody in plants other than A. thaliana, although phytoplasma-associated phyllody symptoms are observed in a broad range of angiosperms...
May 15, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28500291/the-complete-chloroplast-genome-sequence-of-tung-tree-vernicia-fordii-organization-and-phylogenetic-relationships-with-other-angiosperms
#19
Ze Li, Hongxu Long, Lin Zhang, Zhiming Liu, Heping Cao, Mingwang Shi, Xiaofeng Tan
Tung tree (Vernicia fordii) is an economically important tree widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized its genome using PacBio RS II sequencing platforms. The chloroplast genome was sequenced with 161,528 bp in length, composed with one pair of inverted repeats (IRs) of 26,819 bp, which were separated by one small single copy (SSC; 18,758 bp) and one large single copy (LSC; 89,132 bp)...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28494025/sequencing-of-small-rnas-of-the-fern-pleopeltis-minima-polypodiaceae-offers-insight-into-the-evolution-of-the-microrna-repertoire-in-land-plants
#20
Florencia Berruezo, Flávio S J de Souza, Pablo I Picca, Sergio I Nemirovsky, Leandro Martínez Tosar, Mercedes Rivero, Alejandro N Mentaberry, Alicia M Zelada
MicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, playing key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plants. Among these, the fern group (monilophytes) occupies a key phylogenetic position, as it represents the closest extant cousin taxon of seed plants, i...
2017: PloS One
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