Taxonomic references

Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently underrepresented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling.

20p vibransone 28-03-2024 5 2   Download

Ebok "The prokaryotes: Firmicutes and tenericutes (Fourth edition)" is a comprehensive, multi-authored, peer reviewed reference work on Bacteria and Achaea. This fourth edition of The Prokaryotes is organized to cover all taxonomic diversity, using the family level to delineate chapters. The content of the expanded fourth edition is divided into two parts: Part 1 contains review chapters dealing with the most important general concepts in molecular, applied and general prokaryote biology; Part 2 describes the known properties of specific taxonomic groups.

573p manmanthanhla0201 26-02-2024 2 1   Download

The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used.

14p vihagrid 30-01-2023 8 3   Download

Camellia luuana Orel & Curry is known only from its type locality, Ta Dung Nature Reserve, now Ta Dung National Park, Dak Nong Province, the Central Highlands of Vietnam. No characteristics of fruit and seeds, which are the most important to divide genera in Theaceae (Chang & Ren, 1998; Ming & Bartholomew, 2007; Sealy, 1958), were presented in its protologue.

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In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes.

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The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally.

20p vigalileogalilei 27-02-2022 14 1   Download

Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold.

13p vielonmusk 30-01-2022 9 0   Download

This species has been reported native to China (Yunnan and Guangxi) until now and reported for the first time in Vietnam. In this paper, we confirm the new distribution of L. otophora C.Y.Wu in Vietnam providing suitable references.

6p vimarkzuckerberg 05-11-2021 8 0   Download

High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.

17p vilarryellison 29-10-2021 11 1   Download

Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. Bix

9p vijeeni2711 30-06-2021 10 1   Download

This paper provides an update on the current status of each species based on data from recent field surveys with reference to previous publications and the current IUCN Red List (iucnredlist.org). Results from the recent surveys included eight individuals provisionally identified as Myotis cf. pilosus. The taxonomic status of five species (Aselliscus dongbacanus, Hipposideros gentilis, Hipposideros grandis, Miniopterus magnater, Murina harrisoni) are updated following recent assessments.

7p tamynhan5 10-12-2020 17 2   Download

A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes.

12p vioklahoma2711 19-11-2020 17 2   Download

In this paper, we updated the list of monogenean species from marine fishes of Vietnam. Taxonomic position of monogenean species were arranged according to the current classification system. A total of 220 monogenean species from 152 marine fish species were listed. Distribution, hosts and references of each species were given. In addition, amendations of taxonomic status of taxa were also updated.

27p xilank_of 22-07-2020 10 2   Download

Foliicolous algae are a common occurrence in tropical forests. They are referable to a few simple morphotypes (unicellular, sarcinoid-like or filamentous), which makes their morphology of limited usefulness for taxonomic studies and species diversity assessments.

14p viharuno2711 24-04-2020 7 0   Download

We will refer to embeddings providing a guarantee akin to that of Lemma 1.1 as JL- embeddings. In the last few years, such embeddings have been used in solving a variety of problems. The idea is as follows. By providing a low-dimensional representation of the data, JL-embeddings speed up certain algorithms dramatically, in particular algorithms whose run-time depends exponentially in the dimension of the working space. (For a number of practical problems the best-known algorithms indeed have such behavior.

9p yasuyidol 02-04-2013 47 4   Download

This Manual is divided into four chapters. Chapter 1 contains background information on the reasons for regulating emissions from wood furniture manufacturing including a brief regulatory perspective, an overview of the health effects of the five solvents used in the largest quantities, sources of emissions from a typical wood furniture manufacturing facility, and a summary of the new federal wood furniture regulations. Chapter 2 defines pollution prevention (P2) and discusses the elements of a successful P2 program.

59p can_thai 10-12-2012 64 9   Download