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https://www.readbyqxmd.com/read/29144427/the-chloroplast-genome-of-symplocarpus-renifolius-a-comparison-of-chloroplast-genome-structure-in-araceae
#1
Kyoung Su Choi, Kyu Tae Park, SeonJoo Park
Symplocarpus renifolius is a member of Araceae family that is extraordinarily diverse in appearance. Previous studies on chloroplast genomes in Araceae were focused on duckweeds (Lemnoideae) and root crops (Colocasia, commonly known as taro). Here, we determined the chloroplast genome of Symplocarpus renifolius and compared the factors, such as genes and inverted repeat (IR) junctions and performed phylogenetic analysis using other Araceae species. The chloroplast genome of S. renifolius is 158,521 bp and includes 113 genes...
November 16, 2017: Genes
https://www.readbyqxmd.com/read/29142022/balance-between-cytosolic-and-chloroplast-translation-affects-leaf-variegation
#2
Ruijuan Wang, Jun Zhao, Min Jia, Ni Xu, Shuang Liang, Jingxia Shao, Yafei Qi, Xiayan Liu, Lijun An, Fei Yu
The development of functional chloroplasts relies on the fine coordination of expressions of both nuclear and chloroplast genomes. We have been using the Arabidopsis yellow variegated (var2) leaf variegation mutant as a tool to dissect the regulation of chloroplast development. In this work, we screened for var2 genetic enhancer modifiers termed enhancer of variegation (evr) mutants and report the characterization of the first EVR locus, EVR1. We showed that EVR1 encodes the cytosolic 80S ribosome 40S small subunit protein RPS21B and the loss of EVR1 causes the enhancement of var2 leaf variegation...
November 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29139059/evolution-of-rubisco-activase-gene-in-plants
#3
Ragupathi Nagarajan, Kulvinder S Gill
Rubisco activase of plants evolved in a stepwise manner without losing its function to adapt to the major evolutionary events including endosymbiosis and land colonization. Rubisco activase is an essential enzyme for photosynthesis, which removes inhibitory sugar phosphates from the active sites of Rubisco, a process necessary for Rubisco activation and carbon fixation. The gene probably evolved in cyanobacteria as different species differ for its presence. However, the gene is present in all other plant species...
November 14, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29134154/a-comparison-of-chloroplast-genome-sequences-in-aconitum-ranunculaceae-a-traditional-herbal-medicinal-genus
#4
Hanghui Kong, Wanzhen Liu, Gang Yao, Wei Gong
The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia...
2017: PeerJ
https://www.readbyqxmd.com/read/29133466/shine-dalgarno-sequences-play-an-essential-role-in-the-translation-of-plastid-mrnas-in-tobacco
#5
Lars B Scharff, Miriam Ehrnthaler, Marcin Janowski, Liam H Childs, Claudia Hasse, Jürgen Gremmels, Stephanie Ruf, Reimo Zoschke, Ralph Bock
In prokaryotic systems, the translation initiation of many, though not all, mRNAs depends on interaction between a sequence element upstream of the start codon (the Shine-Dalgarno sequence, SD) and a complementary sequence in the 3' end of the 16S ribosomal RNA (anti-Shine-Dalgarno sequence, aSD). Although many chloroplast mRNAs harbor putative SDs in their 5' untranslated regions and the aSD displays strong conservation, the functional relevance of SD-aSD interactions in plastid translation is unclear. Here, by generating transplastomic tobacco (Nicotiana tabacum) mutants with point mutations in the aSD coupled with genome-wide analysis of translation by ribosome profiling, we provide a global picture of SD-dependent translation in plastids...
November 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/29132310/rapid-evolutionary-divergence-of-diploid-and-allotetraploid-gossypium-mitochondrial-genomes
#6
Zhiwen Chen, Hushuai Nie, Yumei Wang, Haili Pei, Shuangshuang Li, Lida Zhang, Jinping Hua
BACKGROUND: Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29131848/high-throughput-m6a-seq-reveals-rna-m6a-methylation-patterns-in-the-chloroplast-and-mitochondria-transcriptomes-of-arabidopsis-thaliana
#7
Zegang Wang, Kai Tang, Dayong Zhang, Yizhen Wan, Yan Wen, Quanyou Lu, Lei Wang
This study is the first to comprehensively characterize m6A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus...
2017: PloS One
https://www.readbyqxmd.com/read/29129375/light-controls-protein-localization-through-phytochrome-mediated-alternative-promoter-selection
#8
Tomokazu Ushijima, Kousuke Hanada, Eiji Gotoh, Wataru Yamori, Yutaka Kodama, Hiroyuki Tanaka, Miyako Kusano, Atsushi Fukushima, Mutsutomo Tokizawa, Yoshiharu Y Yamamoto, Yasuomi Tada, Yutaka Suzuki, Tomonao Matsushita
Alternative promoter usage is a proteome-expanding mechanism that allows multiple pre-mRNAs to be transcribed from a single gene. The impact of this mechanism on the proteome and whether it is positively exploited in normal organismal responses remain unclear. We found that the plant photoreceptor phytochrome induces genome-wide changes in alternative promoter selection in Arabidopsis thaliana. Through this mechanism, protein isoforms with different N termini are produced that display light-dependent differences in localization...
November 7, 2017: Cell
https://www.readbyqxmd.com/read/29124465/the-origin-of-wild-populations-of-toxicodendron-succedaneum-on-mainland-japan-revealed-by-genetic-variation-in-chloroplast-and-nuclear-dna
#9
Yuichiro Hiraoka, Ichiro Tamaki, Atsushi Watanabe
Toxicodendron succedaneum: (L.) Kuntze is a tree cultivated for the production of sumac wax, which is extracted from the mesocarp. There are several hypotheses regarding the origin of T. succedaneum on mainland Japan. In this study, the geographical distribution of genetic variation in 13 wild populations on Honshu, Shikoku, Kyushu, and Ryukyu Islands, Japan was investigated and compared with that of individuals from continental Asia. Seven chloroplast DNA haplotypes of T. succedaneum were observed in Japan and could be divided into three lineages based on relatedness between haplotypes...
November 9, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/29118779/development-of-chloroplast-genomic-resources-for-oryza-species-discrimination
#10
Yun Song, Yan Chen, Jizhou Lv, Jin Xu, Shuifang Zhu, MingFu Li, Naizhong Chen
Rice is the most important crop in the world as the staple food for over half of the population. The wild species of Oryza represent an enormous gene pool for genetic improvement of rice cultivars. Accurate and rapid identification of these species is critical for effective utilization of the wild rice germplasm. In this study, we developed valuable chloroplast molecular markers by comparing the chloroplast genomes for species identification. Four chloroplast genomes of Oryza were newly sequenced on the Illumina HiSeq platform and other 14 Oryza species chloroplast genomes from Genbank were simultaneously taken into consideration for comparative analyses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29117184/from-songlines-to-genomes-prehistoric-assisted-migration-of-a-rain-forest-tree-by-australian-aboriginal-people
#11
Maurizio Rossetto, Emilie J Ens, Thijs Honings, Peter D Wilson, Jia-Yee S Yap, Oliver Costello, Erich R Round, Claire Bowern
BACKGROUND: Prehistoric human activities have contributed to the dispersal of many culturally important plants. The study of these traditional interactions can alter the way we perceive the natural distribution and dynamics of species and communities. Comprehensive research on native crops combining evolutionary and anthropological data is revealing how ancient human populations influenced their distribution. Although traditional diets also included a suite of non-cultivated plants that in some cases necessitated the development of culturally important technical advances such as the treatment of toxic seed, empirical evidence for their deliberate dispersal by prehistoric peoples remains limited...
2017: PloS One
https://www.readbyqxmd.com/read/29115917/the-complete-chloroplast-genome-of-primulina-and-two-novel-strategies-for-development-of-high-polymorphic-loci-for-population-genetic-and-phylogenetic-studies
#12
Chao Feng, Meizhen Xu, Chen Feng, Eric J B von Wettberg, Ming Kang
BACKGROUND: Primulina Hance is an emerging model for studying evolutionary divergence, adaptation and speciation of the karst flora. However, phylogenetic relationships within the genus have not been resolved due to low variation detected in the cpDNA regions. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. Recent advances in next-generation sequencing (NGS) techniques greatly facilitate sequencing whole chloroplast genomes for multiple individuals...
November 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29114403/transcriptomic-analysis-of-aerobic-respiratory-and-anaerobic-photosynthetic-states-in-rhodobacter-capsulatus-and-their-modulation-by-global-redox-regulators-rega-fnrl-and-crtj
#13
Joseph E Kumka, Heidi Schindel, Mingxu Fang, Sebastien Zappa, Carl E Bauer
Anoxygenicphotosynthetic prokaryotes have simplified photosystems that represent ancient lineages that predate the more complex oxygen evolving photosystems present in cyanobacteria and chloroplasts. These organisms thrive under illuminated anaerobic photosynthetic conditions, but also have the ability to grow under dark aerobic respiratory conditions. This study provides a detailed snapshot of transcription ground states of both dark aerobic and anaerobic photosynthetic growth modes in the purple photosynthetic bacterium Rhodobactercapsulatus...
September 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29111566/complete-sequence-and-comparative-analysis-of-the-chloroplast-genome-of-plinia-trunciflora
#14
Maria Eguiluz, Priscila Mary Yuyama, Frank Guzman, Nureyev Ferreira Rodrigues, Rogerio Margis
Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes...
November 6, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29111476/phylogenomics-and-evolution-of-floral-traits-in-the-neotropical-tribe-malmeeae-annonaceae
#15
J C Lopes, L W Chatrou, R Mello-Silva, P J Rudall, M G Sajo
Androdioecy is the rarest sexual system among plants. The majority of androdioecious species are herbaceous plants that have evolved from dioecious ancestors. Nevertheless, some woody and androdioecious plants have hermaphrodite ancestors, as in the Annonaceae, where androdioecious genera have arisen several times in different lineages. The majority of androdioecious species of Annonaceae belong to the Neotropical tribe Malmeeae. In addition to these species, Pseudoxandra spiritus-sancti was recently confirmed to be androdioecious...
October 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29109920/using-genomic-data-to-develop-chloroplast-dna-ssrs-for-the-neotropical-liana-stizophyllum-riparium-bignonieae-bignoniaceae
#16
Maila Beyer, Alison G Nazareno, Lúcia G Lohmann
Premise of the study: We developed chloroplast microsatellite markers (cpSSRs) to be used to study the patterns of genetic structure and genetic diversity of populations of Stizophyllum riparium (Bignonieae, Bignoniaceae). Methods and Results: We used genomic data obtained through an Illumina HiSeq sequencing platform to develop a set of cpSSRs for S. riparium. A total of 36 primer pairs were developed, of which 28 displayed polymorphisms across 59 individuals from three populations...
October 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29104233/the-complete-amomum-kravanh-chloroplast-genome-sequence-and-phylogenetic-analysis-of-the-commelinids
#17
Mingli Wu, Qing Li, Zhigang Hu, Xiwen Li, Shilin Chen
Amomum kravanh is an important edible and medicinal herb, the dried fruits of which are widely used in traditional herbal medicine as cardamom. We sequenced and analyzed the complete chloroplast (cp) genome of A. kravanh with herbgenomics technologies. The size of the A. kravanh cp genome was 162,766 bp, which consisted of long (LSC; 87,728 bp) and short (SSC; 15,390 bp) single-copy regions, separated by a pair of inverted repeats (IRs; 29,824 bp). The genome encoded 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs...
November 1, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29095905/the-complete-chloroplast-genome-sequence-of-the-cam-epiphyte-spanish-moss-tillandsia-usneoides-bromeliaceae-and-its-comparative-analysis
#18
Péter Poczai, Jaakko Hyvönen
Spanish moss (Tillandsia usneoides) is an epiphytic bromeliad widely distributed throughout tropical and warm temperate America. This plant is highly adapted to extreme environmental conditions. Striking features of this species include specialized trichomes (scales) covering the surface of its shoots aiding the absorption of water and nutrients directly from the atmosphere and a specific photosynthesis using crassulacean acid metabolism (CAM). Here we report the plastid genome of Spanish moss and present the comparison of genome organization and sequence evolution within Poales...
2017: PloS One
https://www.readbyqxmd.com/read/29081691/genome-wide-discovery-of-circular-rnas-in-the-leaf-and-seedling-tissues-of-arabidopsis-thaliana
#19
REVIEW
Yongchao Dou, Shengjun Li, Weilong Yang, Kan Liu, Qian Du, Guodong Ren, Bin Yu, Chi Zhang
BACKGROUND: Recently, identification and functional studies of circular RNAs, a type of non-coding RNAs arising from a ligation of 3' and 5' ends of a linear RNA molecule, were conducted in mammalian cells with the development of RNA-seq technology. METHOD: Since compared with animals, studies on circular RNAs in plants are less thorough, a genome-wide identification of circular RNA candidates in Arabidopsis was conducted with our own developed bioinformatics tool to several existing RNA-seq datasets specifically for non-coding RNAs...
August 2017: Current Genomics
https://www.readbyqxmd.com/read/29079841/mir156-switches-on-vegetative-phase-change-under-the-regulation-of-redox-signals-in-apple-seedlings
#20
Xiao Lin Jia, Ya Kun Chen, Xiao Zhao Xu, Fei Shen, Qing Bo Zheng, Zhen Du, Yi Wang, Ting Wu, Xue Feng Xu, Zhen Hai Han, Xin Zhong Zhang
In higher plants, miR156 regulates the vegetative phase change via the target SBP/SPL genes. The regulation of miR156 during ontogenetic processes is not fully understood. In the apple genome, of 31 putative MdMIR156 genes that encode pre-miR156, seven were dominantly expressed. However, the transcript levels of only MdMIR156a5 and MdMIR156a12 decreased significantly during the vegetative phase change, which was consistent with the mature miR156 level, indicating that miR156 is under transcriptional regulation...
October 27, 2017: Scientific Reports
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