scholarly journals Acclimation of the Photosynthetic Machinery to High Temperature in Chlamydomonas reinhardtii Requires Synthesis de Novo of Proteins Encoded by the Nuclear and Chloroplast Genomes

2000 ◽  
Vol 124 (1) ◽  
pp. 441-450 ◽  
Author(s):  
Yuji Tanaka ◽  
Yoshitaka Nishiyama ◽  
Norio Murata
Keyword(s):  
High Temperature ◽  
Chlamydomonas Reinhardtii ◽  
De Novo ◽  
Chloroplast Genomes ◽  
Photosynthetic Machinery

scholarly journals Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Samuel O’Donnell ◽  
Frederic Chaux ◽  
Gilles Fischer
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Genome Size ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Content Type ◽  
Oxford Nanopore ◽  
A Genome ◽  
Reference Quality

ABSTRACT The current Chlamydomonas reinhardtii reference genome remains fragmented due to gaps stemming from large repetitive regions. To overcome the vast majority of these gaps, publicly available Oxford Nanopore Technology data were used to create a new reference-quality de novo genome assembly containing only 21 contigs, 30/34 telomeric ends, and a genome size of 111 Mb.

scholarly journals The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

2019 ◽  
Vol 42 (4) ◽  
pp. 601-611 ◽  
Author(s):  
Yan Li ◽  
Liukun Jia ◽  
Zhihua Wang ◽  
Rui Xing ◽  
Xiaofeng Chi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Single Copy ◽  
Bootstrap Support ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

scholarly journals Target of Rapamycin Inhibition in Chlamydomonas reinhardtii Triggers de Novo Amino Acid Synthesis by Enhancing Nitrogen Assimilation

2018 ◽  
Vol 30 (10) ◽  
pp. 2240.1-2254 ◽  
Author(s):  
Umarah Mubeen ◽  
Jessica Jüppner ◽  
Jessica Alpers ◽  
Dirk K. Hincha ◽  
Patrick Giavalisco
Keyword(s):  
Amino Acid ◽  
Chlamydomonas Reinhardtii ◽  
Nitrogen Assimilation ◽  
De Novo ◽  
Acid Synthesis ◽  
Target Of Rapamycin ◽  
Amino Acid Synthesis

Hydrothermal exploration and astrobiology: oases for life in distant oceans?

2004 ◽  
Vol 3 (2) ◽  
pp. 81-95 ◽  
Author(s):  
Christopher R. German
Keyword(s):  
High Temperature ◽  
Organic Synthesis ◽  
Autonomous Underwater Vehicle ◽  
De Novo ◽  
The Arctic ◽  
Ocean Ridges ◽  
Abiotic Organic Synthesis ◽  
Preliminary Identification ◽  
Slow Spreading ◽  
Hydrothermal Fields

High-temperature submarine hydrothermal fields on Earth's mid-ocean ridges play host to exotic ecosystems with fauna previously unknown to science. Because these systems draw significant energy from chemosynthesis rather than photosynthesis, it has been postulated that the study of such systems could have relevance to the origins of life and, hence, astrobiology. A major flaw to that argument, however, is that modern basalt-hosted submarine vents are too oxidizing and lack the abundant free hydrogen required to drive abiotic organic synthesis and/or the energy yielding reactions that the most primitive anaerobic thermophiles isolated from submarine vent-sites apparently require. Here, however, the progress over the past decade in which systematic search strategies have been used to identify previously overlooked venting on the slow-spreading Mid-Atlantic Ridge and the ultra-slow spreading Arctic and SW Indian Ridges is described. Preliminary identification of fault-controlled venting in a number of these sites has led to the discovery of at least two high-temperature hydrothermal fields hosted in ultramafic rocks which emit complex organic molecules in their greater than 360 °C vent-fluids. Whether these concentrations represent de novo organic synthesis within the hydrothermal cell remains open to debate but it is probable that many more such sites exist throughout the Atlantic, Arctic and SW Indian Oceans. One particularly intriguing example is the Gakkel Ridge, which crosses the floor of the Arctic Ocean. On-going collaborations between oceanographers and astrobiologists are actively seeking to develop a new class of free-swimming autonomous underwater vehicle, equipped with appropriate chemical sensors, to conduct long-range missions that will seek out, locate and investigate new sites of hydrothermal venting at the bottom of this, and other, ice-covered oceans.

scholarly journals Synchronous dissection of chloroplast and mitochondrial genomes remodels the intra- and inter-genus phylogeny for the agriculturally important genus Brassica

2019 ◽  
Author(s):  
Jiangwei Qiao ◽  
Xiaojun Zhang ◽  
Biyun Chen ◽  
Fei Huang ◽  
Kun Xu ◽  
...  
Keyword(s):  
De Novo ◽  
Phylogenetic Analyses ◽  
Parallel Evolution ◽  
Male Sterile ◽  
Plant Populations ◽  
Data Set ◽  
Brassica Crops ◽  
Chloroplast Genomes ◽  
Ornamental Crops ◽  
Allotetraploid Species

Abstract Background : The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of the allotetraploid crops and the overall phylogeny of Brassica genus are still far from completely resolved, which has greatly hindered the development of novel Brassica crops. Here, we target and integrate the chloroplast DNA and mitochondrial DNA to investigate the genetic diversity and relationships in large plant populations centering on Brassica genus. Results : The phylogenetic analyses based on a data set including 72 de novo assembled whole chloroplast genomes, delineated a comprehensive evolutional atlas inside and around Brassica genus. The maternal origin of both B. juncea and B. carinata are monophyletic from cam-type B. rapa and B. nigra , respectively. Nonetheless, the current B. napus contains three major cytoplasmic haplotypes: the cam -type which directly inherited from B. rapa , polima -type which is close to cam -type as a sister, and the predominant nap -type. Intriguingly, nap -type seems phylogenetically integrated with certain sparse C-genome wild species, thus implying that which may have primarily contributed the cytoplasm and the corresponding C subgenome to B. napus . Human breeding creation of the B. napus cytoplasmic male sterile lines (e.g., mori and nsa ) dramatically disturbed the concurrent inheritance between mtDNA and cpDNA. Strong parallel evolution among genera Raphanus , Sinapis, Eruca , Moricandia with Brassica indicates their uncomplete divergence from each other. Conclusions : The overall variation data and elaborated phylogenetic relationships obtained herein can substantially facilitate the development of novel Brassica crops, e.g. the allotetraploid rapeseed with new cytonuclear integrations and the allohexaploid rapeseed.

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