Manual Genomics of Cultivated Palms (Elsevier Insights)

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Introduction
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  2. The genetics of Ptychosperma bleeseri, a rare palm from the Northern Territory, Australia
  3. Similar authors to follow
  4. INTRODUCTION

Delivered from our UK warehouse in 4 to 14 business days. Genomics of Cultivated Palms Elsevier Insights. V Arunachalam. Publisher: Elsevier , This specific ISBN edition is currently not available. View all copies of this ISBN edition:. Synopsis Bioinformatics offers novel tools and resources to analyze plant genomes and genes. Includes the latest information on the molecular breeding and bioinformatics of palms Covers past and current work and future opportunities Written in simple language avoiding technical jargon "synopsis" may belong to another edition of this title.

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The genetics of Ptychosperma bleeseri, a rare palm from the Northern Territory, Australia

New Quantity Available: 1. Seller Rating:. Published by Elsevier New Hardcover Quantity Available: 1. Genomics of Cultivated Palms Hardback V. New Hardcover Quantity Available: Chiron Media Wallingford, United Kingdom. Book Depository hard to find London, United Kingdom. Genomics of Cultivated Palms Arunachalam, V. Published by Elsevier Science Ltd Revaluation Books Exeter, United Kingdom.

New Paperback Quantity Available: Microbial oils are a sustainable feedstock for biofuel and chemical production that does not compete with food production. In contrast to conventional yeasts, this organism not only shows an absence of diauxic effect while fermenting hexoses and pentoses but also effectively utilizes xylose and N -acetylglucosamine, which are building blocks of lignocellulose and chitin, respectively. Transcriptome analysis revealed metabolic networks that govern conversion of xylose or N -acetylglucosamine as well as lipid accumulation.

These data form the basis for a targeted strain optimization strategy. Furthermore, analysis of the mating type of T. The foreseeable end of fossil resources, associated with significant price fluctuations, drives the development of sustainable biomass-based processes in the chemical industry sector. Plant-derived oils are already essential feedstocks in the production of bio-based specialty and commodity chemical building blocks 1 , 2. However, their material utilization competes with food production and has an increasing impact on land use changes 3 , 4.

An emerging alternative is the fermentative conversion of agro-industrial residues for production of microbe-derived lipids. In particular, these organisms can metabolize pentose and hexose sugars from complex biomass hydrolysates and switch on lipogenesis when metabolic stresses, such as nitrogen and phosphorus deprivation, are applied.

The metabolic adaptability of oleaginous yeasts to various carbon sources is of interest for second-generation bioprocess engineering approaches 2. While the exact fatty acid profile of accumulated triglycerides depends on cultivation conditions, the principal chemical composition resembles those of plant-derived lipids, such as palm oil.

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Interestingly, oleaginous yeasts belong to diverse taxonomic groups, indicating that the metabolic capacity for lipid accumulation has evolved independently in basidiomycete 6 and ascomycete fungi 7 — 9. At present, nitrogen limitation has been identified as the strongest inducer of lipogenesis in oleaginous organisms. Biochemical and metabolic engineering studies have identified malic enzyme ME 10 — 12 , diacylglycerol acyltransferase 1 DGA1 13 , and acetyl coenzyme A CoA carboxylase 13 as metabolic regulators of lipogenesis under N stress conditions for selected fungi and microalgae.

However, recent systems biology studies in different oleaginous organisms could not identify a common metabolic mechanism for lipid accumulation under N-limiting conditions 7 , Furthermore, metabolic mechanisms governing lipogenesis under P-limiting conditions have not yet been explored.

Hence, the overall metabolic networks and regulatory mechanisms that drive lipid accumulation in different oleaginous organisms remain elusive 2. Here, we present genome and transcriptome analysis results for the oil-accumulating yeast Trichosporon oleaginosus strain IBC This Trichosporon strain is distinct from conventional yeasts, as it can simultaneously metabolize both pentose and hexose sugars without any catabolic preference.

Sequence identity of the internal transcribed spacer ITS sequences shared with two previously characterized T. Trichosporon species are basidiomycetes that belong to the order Tremellales. While nonpathogenic Trichosporon species have been isolated from environmental soil and milk whey samples, some isolates have recently come to attention as pathogens of immunocompromised hosts.

Trichosporon species mostly grow as yeasts, but many are able to also form pseudohyphae or true hyphae and arthroconidia 16 , A sexual cycle and ploidy level have not been described for Trichosporon species. Strain IBC is able to utilize a variety of carbon sources without showing a diauxic lag in growth unpublished data , making it an interesting candidate for biotechnological applications. Interestingly, it can efficiently utilize pentoses such as xylose XYL and NAG, which are major monomeric sugar building blocks of lignocellulosic and chitin-rich biomass residues, respectively Because XYL and NAG utilization is challenging for conventional industrial yeasts 19 , Trichosporon oleaginosus is poised to be developed as a next-generation microbial production platform for the de novo biosynthesis of sustainable oleochemicals.

In this study, we therefore focused on lipid accumulation and the possible utilization of the two biomass-derived sugars XYL and NAG.

We show that in response to nitrogen starvation this yeast is capable of utilizing xylose as a carbon source for lipid accumulation, and we highlight several pathways of oleaginicity. Transcriptome analysis of a sample using NAG as the sole carbon source showed that NAG is efficiently channeled toward the primary metabolism.

Furthermore, we analyzed the mating-type structure of T. A well-studied member of this group is the pathogenic yeast Cryptococcus neoformans. Comparative analysis suggests that it has undergone independent evolution shaped by a similar trend toward larger mating-type regions, as found in other Tremellomycetes 20 , but in which orthologous genes functioning in sexual development MYO2 , STE11 , IKS1 , STE20 have been differentially incorporated into either one or the other of the ancestral tetrapolar MAT loci in the two lineages.

This reveals a heretofore-unknown level of plasticity in expansion of sex-determining regions in fungi, with implications for sex chromosome evolution in animals and plants. Genome sequencing of Trichosporon oleaginosus strain IBC reveals great evolutionary flexibility in mating-type configurations in Tremellomycetes.

The genome of T. With an assembly size of This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3. Repeat analyses based on similarity to known repeat classes as well as de novo repeat finding showed that in T. The total repeat content of the genome, consisting mostly of small repeats, is 2. To analyze synteny between T. Therefore, an orthology-based approach was chosen, which entailed identification of putative orthologous proteins between T.

Between 4, and 5, putative orthologs were identified in the comparisons of T.

INTRODUCTION

Plotting of genomic positions of orthologous pairs showed a high degree of synteny between the two Cryptococcus species, as expected, but no large-scale synteny for any of the T. This also included the comparison to the sister species T. Phylogenetic and synteny analyses. A Phylogenetic tree of species in the class Tremellomycetes based on analysis of conserved single-copy genes. Bootstrap values percentages are indicated at the corresponding branches.

Coprinopsis cinerea was used as an outgroup. The scale bar indicates the number of amino acid substitutions per site. B Genome-wide synteny between T.


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Positions of orthologous genes were determined along the concatenated scaffolds from each species and are visualized as dot plots for the pairs T. The analysis of C. Scaffolds were not specifically ordered for this analysis; therefore, there is a seemingly somewhat-random organization for the C. C Syntenic gene pairs and triplets in T. On the right, the same comparison for the two Cryptococcus species, C. BioProject numbers and references for genomes used for comparison are as follows: T.

Some research

While our analysis did not show any macrosynteny between T. Nearly 1, syntenic gene pairs and syntenic gene triplets were identified between T. However, these results are still much lower than those from a comparison of C. One major feature of interest in Tremellomycete genomes is the organization and evolution of mating-type regions Sexual development in basidiomycetes is governed by mating-type genes encoding homeodomain transcription factors, pheromones, and pheromone receptors.

In the majority of basidiomycetes, the HD locus comprises at least two genes coding for homeodomain proteins of class 1 HD1 and class 2 HD2 29 , This is the case in the Tremellomycetes Cryptococcus amylolentus , Kwoniella heveanensis , Kwoniella mangrovensis , and Tremella mesenterica , which harbor the basal arrangement of two separate mating-type loci, with two HD genes of classes HD1 and HD2 within the transcription factor-containing locus 31 — An exception to this rule is found in C. With the exception of a gene conversion hot spot 36 , this large mating-type region of C.

To learn more about the mating system of T. Searches with HD proteins from other Tremellomycetes in the predicted T. This was further confirmed by searches in the genomes of the T.