scholarly journals The Transcriptomics of Secondary Growth and Wood Formation in Conifers

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Ana Carvalho ◽  
Jorge Paiva ◽  
José Louzada ◽  
José Lima-Brito
Keyword(s):  
Picea Glauca ◽  
Draft Genome ◽  
Secondary Growth ◽  
Wood Formation ◽  
Gradual Improvement ◽  
Whole Genomes ◽  
Conifer Genome ◽  
Genome Assemblies ◽  
Next Generation Sequencing Ngs ◽  
Selection Of

In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality.

Draft genome sequence of the silver pomfret fish, Pampus argenteus

Genome ◽  
2016 ◽  
Vol 59 (1) ◽  
pp. 51-58 ◽  
Author(s):  
Sabah AlMomin ◽  
Vinod Kumar ◽  
Sami Al-Amad ◽  
Mohsen Al-Hussaini ◽  
Talal Dashti ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Management Strategies ◽  
Draft Genome ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Pampus Argenteus ◽  
Genomic Studies ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Silver Pomfret

Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.

Intra-Annual Spiral Compression Wood: A Record of Low-Frequency Gravitropic Circumnutational Movement in Trees

IAWA Journal ◽  
1988 ◽  
Vol 9 (3) ◽  
pp. 269-274 ◽  
Author(s):  
Frank W. Telewski
Keyword(s):  
Pinus Taeda ◽  
Woody Plants ◽  
Compression Wood ◽  
Secondary Growth ◽  
Low Frequency ◽  
Wood Formation ◽  
Growth Rings ◽  
Movement Data ◽  
Annual Growth Rings ◽  
Plant Seedlings

The majority of detailed studies on circumnutational growth movements have focused on herbaceous plants or on the primary growth of woody plant seedlings, ignoring completely secondary growth in woody plants. The relatively rapid movement in herbaceous tissues consists of two components: an autonomous growth rhythm and a gravitropic response. Since there is a gravitropic component to circumnutational movement and a gravitropic stimulus can induce compression wood formation, the formation of a compression wood spiral may be expected if there is a circumnutational movement of a woody stern. It is suggested here, that observed spirals of compression wood within annual growth rings in Pinus taeda L. and Abies concolor (Gord. ' Glend.) Lindl. ex Hildebr. represents an annual record of a slower circumnutational growth movement. Data derived from observations of greenhouse- grown 3-year-old Pinus taeda seedlings indicate that there are two distinct circumnutational patterns of different rotation al frequency present in woody plants associated with primary and secondary tissues.

scholarly journals A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Model Organism ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Extracellular Proteome ◽  
Protein Encoding ◽  
Gene Models ◽  
Genome Assemblies ◽  
Encoding Genes

Abstract Background Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. Conclusions This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.

scholarly journals Selection of a DNA barcode for Nectriaceae from fungal whole-genomes

2012 ◽  
Vol 55 (1) ◽  
pp. 80-88 ◽  
Author(s):  
ZhaoQing Zeng ◽  
Peng Zhao ◽  
Jing Luo ◽  
WenYing Zhuang ◽  
ZhiHe Yu
Keyword(s):  
Dna Barcode ◽  
Whole Genomes ◽  
Selection Of

scholarly journals Draft Genome Assemblies of Xylose-Utilizing Candida tropicalis and Candida boidinii with Potential Application in Biochemical and Biofuel Production

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Abhishek Somani ◽  
Daniel Smith ◽  
Matthew Hegarty ◽  
Narcis Fernandez-Fuentes ◽  
Sreenivas R. Ravella ◽  
...  
Keyword(s):  
Candida Tropicalis ◽  
Potential Application ◽  
Draft Genome ◽  
Biofuel Production ◽  
Candida Boidinii ◽  
Industrial Biotechnology ◽  
Genome Sequences ◽  
Genome Assemblies

ABSTRACT Non- albicans Candida species are growing in prominence in industrial biotechnology due to their ability to utilize hemicellulose. Here, we present the draft genome sequences of an inhibitor-tolerant Candida tropicalis strain (Y6604) and Candida boidinii NCAIM Y01308 T .

scholarly journals Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods

2020 ◽  
Vol 9 (7) ◽  
pp. 2036
Author(s):  
Jaroslaw Bilinski ◽  
Mikolaj Dziurzynski ◽  
Pawel Grzesiowski ◽  
Edyta Podsiadly ◽  
Anna Stelmaszczyk-Emmel ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Fecal Microbiota ◽  
Dead Cell ◽  
Series Of Experiments ◽  
Multi Method Approach ◽  
The Stability ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Selection Of

Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find “super-donor” indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of “good” donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and Anaeroplasma found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately.

scholarly journals Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

2014 ◽  
Vol 10 (12) ◽  
pp. e1003998 ◽  
Author(s):  
James F. Denton ◽  
Jose Lugo-Martinez ◽  
Abraham E. Tucker ◽  
Daniel R. Schrider ◽  
Wesley C. Warren ◽  
...  
Keyword(s):  
Draft Genome ◽  
Number Of Genes ◽  
Genome Assemblies

scholarly journals Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01

2014 ◽  
Vol 2 (5) ◽  
Author(s):  
T. D. Minogue ◽  
H. E. Daligault ◽  
K. W. Davenport ◽  
K. A. Bishop-Lilly ◽  
D. C. Bruce ◽  
...  
Keyword(s):  
Draft Genome ◽  
Enterobacter Aerogenes ◽  
Enterobacter Cloacae ◽  
Pantoea Agglomerans ◽  
Genome Assemblies

scholarly journals Eight Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. caucasica Isolated from the Common Vole (Microtus arvalis) Plague Focus in Dagestan, Russia

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Angelina A. Kislichkina ◽  
Aleksandr G. Bogun ◽  
Lidiya A. Kadnikova ◽  
Nadezhda V. Maiskaya ◽  
Viktor I. Solomentsev ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Draft Genome ◽  
Common Vole ◽  
Whole Genome ◽  
Microtus Arvalis ◽  
Genome Sequences ◽  
Content Type ◽  
The Common ◽  
Common Voles ◽  
Genome Assemblies

ABSTRACT We here report the draft genome sequences of 8 Yersinia pestis subsp. microtus bv. caucasica strains isolated from the East Caucasian (previous name, Dagestan) mountain focus (no. 39), representing the most ancient branch of the 0.PE2 phylogroup circulating in populations of common voles (Microtus arvalis).

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