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https://www.readbyqxmd.com/read/28339482/a-genome-wide-identification-and-analysis-of-the-dyw-deaminase-genes-in-the-pentatricopeptide-repeat-gene-family-in-cotton-gossypium-spp
#1
Bingbing Zhang, Guoyuan Liu, Xue Li, Liping Guo, Xuexian Zhang, Tingxiang Qi, Hailin Wang, Huini Tang, Xiuqin Qiao, Jinfa Zhang, Chaozhu Xing, Jianyong Wu
The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants...
2017: PloS One
https://www.readbyqxmd.com/read/28338960/organellar-genomes-from-a-%C3%A2-5-000-years-old-archaeological-maize-sample-are-closely-related-to-nb-genotype
#2
Bernardo Pérez-Zamorano, Miguel Vallebueno-Estrada, Javier Martínez González, Angel García Cook, Rafael Montiel, Jean-Philippe Vielle-Calzada, Luis Delaye
The story of how pre-Columbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040 to 5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected...
March 17, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338876/subcellular-localization-of-arabidopsis-arogenate-dehydratases-suggests-novel-and-non-enzymatic-roles
#3
Crystal D Bross, Travis R Howes, Sara Abolhassani Rad, Ornela Kljakic, Susanne E Kohalmi
Arogenate dehydratases (ADTs) catalyze the final step in phenylalanine biosynthesis in plants. The Arabidopsis thaliana genome encodes a family of six ADTs capable of decarboxylating/dehydrating arogenate into phenylalanine. Using cyan fluorescent protein (CFP)-tagged proteins, the subcellular localization patterns of all six A. thaliana ADTs were investigated in intact Nicotiana benthamiana and A. thaliana leaf cells. We show that A. thaliana ADTs localize to stroma and stromules (stroma-filled tubules) of chloroplasts...
March 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338826/the-evolutionary-fate-of-the-chloroplast-and-nuclear-rps16-genes-as-revealed-through-the-sequencing-and-comparative-analyses-of-four-novel-legume-chloroplast-genomes-from-lupinus
#4
J Keller, M Rousseau-Gueutin, G E Martin, J Morice, J Boutte, E Coissac, M Ourari, M Aïnouche, A Salmon, F Cabello-Hurtado, A Aïnouche
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins...
February 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28337540/the-discovery-of-plastid-to-nucleus-retrograde-signaling-a-personal-perspective
#5
Thomas Börner
DNA and machinery for gene expression have been discovered in chloroplasts during the 1960s. It was soon evident that the chloroplast genome is relatively small, that most genes for chloroplast-localized proteins reside in the nucleus and that chloroplast membranes, ribosomes, and protein complexes are composed of proteins encoded in both the chloroplast and the nuclear genome. This situation has made the existence of mechanisms highly probable that coordinate the gene expression in plastids and nucleus. In the 1970s, the first evidence for plastid signals controlling nuclear gene expression was provided by studies on plastid ribosome deficient mutants with reduced amounts and/or activities of nuclear-encoded chloroplast proteins including the small subunit of Rubisco, ferredoxin NADP+ reductase, and enzymes of the Calvin cycle...
March 23, 2017: Protoplasma
https://www.readbyqxmd.com/read/28337394/chloroplast-microsatellite-markers-for-pseudotaxus-chienii-developed-from-the-whole-chloroplast-genome-of-taxus-chinensis-var-mairei-taxaceae
#6
Qi Deng, Hanrui Zhang, Yipeng He, Ting Wang, Yingjuan Su
PREMISE OF THE STUDY: Pseudotaxus chienii (Taxaceae) is an old rare species endemic to China that has adapted well to ecological heterogeneity with high genetic diversity in its nuclear genome. However, the genetic variation in its chloroplast genome is unknown. METHODS AND RESULTS: Eighteen chloroplast microsatellite markers (cpSSRs) were developed from the whole chloroplast genome of Taxus chinensis var. mairei and successfully amplified in four P. chienii populations and one T...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28336770/ptac10-a-key-subunit-of-plastid-encoded-rna-polymerase-promotes-chloroplast-development
#7
Sun Hyun Chang, Sangyool Lee, Tae Young Um, Ju-Kon Kim, Yang Do Choi, Geupil Jang
Regulation of photosynthetic gene expression by plastid-encoded RNA polymerase (PEP) is essential for chloroplast development. The activity of PEP largely relies on at least 12 PEP-associated proteins (PAPs) encoded in the nuclear genome of plant cells. A recent model proposed that these PAPs regulate the establishment of the PEP complex through broad PAP-PEP or PAP-PAP interactions. In this study, we identified the Arabidopsis thaliana seedling lethal mutant ptac10-1, which has defects in chloroplast development, and found that the mutant phenotype is caused by the suppression of PLASTID S1 RNA-BINDING DOMAIN PROTEIN (pTAC10/PAP3)...
March 23, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28334280/origin-and-genetic-differentiation-of-pink-flowered-sorbus-hybrids-in-the-western-carpathians
#8
Veronika Uhrinová, Judita Zozomová-Lihová, Dana Bernátová, Juraj Paule, Ladislav Paule, Dušan Gömöry
Background and Aims: Diversity of the genus Sorbus has been affected by interspecific hybridizations. Pink-flowered hybrid species have been insufficiently studied so far. They comprise bigenomic hybrid species derived from crosses S. aria s.l. × S. chamaemespilus and trigenomic ones, where S. aucuparia was involved as well. The main objective of the present study was to reconstruct their hybrid origins as well as to assess genetic distinction among several morphologically recognized hybrid species...
March 13, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28333396/conflicting-phylogenomic-signals-reveal-a-pattern-of-reticulate-evolution-in-a-recent-high-andean-diversification-asteraceae-astereae-diplostephium
#9
Oscar M Vargas, Edgardo M Ortiz, Beryl B Simpson
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods...
March 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28330330/a-combined-chloroplast-atpb-rbcl-and-trnl-f-phylogeny-unveils-the-ancestry-of-balsams-impatiens-spp-in-the-western-ghats-of-india
#10
P P Shajitha, N R Dhanesh, P J Ebin, Joseph Laly, Devassy Aneesha, John Reshma, Jomy Augustine, Mathew Linu
Only a few Impatiens spp. from South India (one of the five centers of diversity for Impatiens species) were included in the published datum of molecular phylogeny of the family Balsaminaceae. The present investigation is a novel attempt to reveal the phylogenetic association of Impatiens species of South India, by placing them in the global phylogeny of Impatiens based on a combined analysis of two chloroplast genes. Thirty species of genus Impatiens were collected from different locations of South India. Total genomic DNA was extracted from fresh plant leaf, and polymerase chain reaction was carried out using atpB-rbcL and trnL-F intergenic spacer-specific forward and reverse primers...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330289/progress-in-genome-sequencing-will-accelerate-molecular-breeding-in-cotton-gossypium-spp
#11
REVIEW
Rong Yan, Chengzhen Liang, Zhigang Meng, Waqas Malik, Tao Zhu, Xuefeng Zong, Sandui Guo, Rui Zhang
Cotton (Gossypium spp.) is the single most important spinning fiber that has economic significance worldwide. Cotton is one of the most value-added crops and an excellent model system for the analysis of polyploidization and cell development. Thus, the Cotton Genome Consortium has made rapid and significant progress in whole genome sequencing studies in the last decade. Developments in cotton genome sequencing and assembly provide powerful tools for dissecting the genetic and molecular bases of agronomically important traits and establishing regulatory networks on these processes, which leads to molecular breeding...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330080/transgenic-rice-plants-expressing-synthetic-cry2ax1-gene-exhibits-resistance-to-rice-leaffolder-cnaphalocrosis-medinalis
#12
R Manikandan, N Balakrishnan, D Sudhakar, V Udayasuriyan
Bacillus thuringiensis is a major source of insecticidal genes imparting insect resistance in transgenic plants. Level of expression of transgenes in transgenic plants is important to achieve desirable level of resistance against target insects. In order to achieve desirable level of expression, rice chloroplast transit peptide sequence was fused with synthetic cry2AX1 gene to target its protein in chloroplasts. Sixteen PCR positive lines of rice were generated by Agrobacterium mediated transformation using immature embryos...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28326093/the-complete-chloroplast-genome-of-wild-rice-oryza-minuta-and-its-comparison-to-related-species
#13
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/28303594/the-analysis-of-the-different-functions-of-starch-phosphorylating-enzymes-during-the-development-of-arabidopsis-thaliana-plants-discloses-an-unexpected-role-for-the-cytosolic-isoform-gwd2
#14
Claudia Pirone, Libero Gurrieri, Ivan Gaiba, Alessio Adamiano, Francesco Valle, Paolo Trost, Francesca Sparla
The genome of Arabidopsis thaliana encodes three glucan, water dikinases. Glucan, water dikinase 1 (GWD1; EC 2.7.9.4) and phosphoglucan, water dikinase (PWD; EC 2.7.9.5) are chloroplastic enzymes, while glucan, water dikinase 2 (GWD2) is cytosolic. Both GWDs and PWD catalyze the addition of phosphate groups to amylopectin chains at the surface of starch granules, changing its physicochemical properties. As a result, GWD1 and PWD have a positive effect on transitory starch degradation at night. Because of its cytosolic localization, GWD2 does not have the same effect...
March 17, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28303220/anemone-medicinal-plants-ethnopharmacology-phytochemistry-and-biology
#15
REVIEW
Da-Cheng Hao, Xiaojie Gu, Peigen Xiao
The Ranunculaceae genus Anemone (order Ranunculales), comprising more than 150 species, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine. Various medicinal compounds have been found in Anemone plants, especially triterpenoid saponins, some of which have shown anti-cancer activities. Some Anemone compounds and extracts display immunomodulatory, anti-inflammatory, antioxidant, and antimicrobial activities. More than 50 species have ethnopharmacological uses, which provide clues for modern drug discovery...
March 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28303008/an-analysis-of-echinacea-chloroplast-genomes-implications-for-future-botanical-identification
#16
Ning Zhang, David L Erickson, Padmini Ramachandran, Andrea R Ottesen, Ruth E Timme, Vicki A Funk, Yan Luo, Sara M Handy
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28295776/compartmentalisation-of-fefe-hydrogenase-maturation-in-chlamydomonas-reinhardtii
#17
Anne Sawyer, Yu Bai, Yinghua Lu, Anja Hemschemeier, Thomas Happe
Molecular hydrogen (H2 ) can be produced in green microalgae by [FeFe]-hydrogenases as a direct product of photosynthesis. The Chlamydomonas reinhardtii hydrogenase HYDA1 contains a catalytic site comprising a classic [4Fe4S] cluster linked to a unique 2Fe sub-cluster. From in vitro studies it appears that the [4Fe4S] cluster is incorporated first by the housekeeping FeS cluster assembly machinery, followed by the 2Fe sub-cluster, whose biosynthesis requires the specific maturases HYDEF and HYDG. To investigate the maturation process in vivo, we expressed HYDA1 from the C...
March 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28295310/a-rare-case-of-plastid-protein-coding-gene-duplication-in-the-chloroplast-genome-of-euglena-archaeoplastidiata-euglenophyta
#18
Matthew S Bennett, Shin-Han Shiu, Richard E Triemer
Gene duplication is an important evolutionary process that allows duplicate functions to diverge, or, in some cases, allows for new functional gains. However, in contrast to the nuclear genome, gene duplications within the chloroplast are extremely rare. Here, we present the chloroplast genome of the photosynthetic protist Euglena archaeoplastidiata. Upon annotation it was found that the chloroplast genome contained a novel tandem direct duplication which encoded a portion of RuBisCO large subunit (rbcL) followed by a complete copy of ribosomal protein L32 (rpl32) as well as the associated intergenic sequences...
March 12, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28294981/the-complete-chloroplast-genome-sequences-of-six-rehmannia-species
#19
Shuyun Zeng, Tao Zhou, Kai Han, Yanci Yang, Jianhua Zhao, Zhan-Lin Liu
Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order...
March 15, 2017: Genes
https://www.readbyqxmd.com/read/28286710/the-complete-chloroplast-genome-sequence-of-morus-cathayana-and-morus-multicaulis-and-comparative-analysis-within-genus-morus-l
#20
Wei Qing Kong, Jin Hong Yang
Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis were sequenced. The plastomes of the two species are 159,265 bp and 159,103 bp, respectively, with corresponding 83 and 82 simple sequence repeats (SSRs). Similar to the SSRs of M. mongolica and M. indica cp genomes, more than 70% are mononucleotides, ten are in coding regions, and one exhibits nucleotide content polymorphism...
2017: PeerJ
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