Mukdenia

Last updated

Mukdenia
Mukdenia rossii 001.JPG
Mukdenia rossii
Scientific classification OOjs UI icon edit-ltr.svg
Kingdom: Plantae
Clade: Tracheophytes
Clade: Angiosperms
Clade: Eudicots
Order: Saxifragales
Family: Saxifragaceae
Genus: Mukdenia
Koidz.
Species

Mukdenia is a genus of plants in the saxifrage family, Saxifragaceae, consisting of 2 species. [1] [2] They are native to woodland areas of east Asia and Japan.

Related Research Articles

<span class="mw-page-title-main">Saxifragales</span> Order of Eudicot flowering plants in the Superrosid clade

The Saxifragales (saxifrages) are an order of flowering plants (Angiosperms). They are an extremely diverse group of plants which include trees, shrubs, perennial herbs, succulent and aquatic plants. The degree of diversity in terms of vegetative and floral features makes it difficult to define common features that unify the order.

<span class="mw-page-title-main">BGI Group</span> Chinese genome sequencing company

BGI Group, formerly Beijing Genomics Institute, is a Chinese genomics company with headquarters in Yantian District, Shenzhen. The company was originally formed in 1999 as a genetics research center to participate in the Human Genome Project. It also sequences the genomes of other animals, plants and microorganisms.

<span class="mw-page-title-main">Saxifragaceae</span> Family of flowering plants in the Eudicot order Saxifragales

Saxifragaceae is a family of herbaceous perennial flowering plants, within the core eudicot order Saxifragales. The taxonomy of the family has been greatly revised and the scope much reduced in the era of molecular phylogenetic analysis. The family is divided into ten clades, with about 640 known species in about 35 accepted genera. About half of these consist of a single species, but about 400 of the species are in the type genus Saxifraga. The family is predominantly distributed in the northern hemisphere, but also in the Andes in South America.

Mark Bender Gerstein is an American scientist working in bioinformatics and Data Science. As of 2009, he is co-director of the Yale Computational Biology and Bioinformatics program.

The Cancer Genome Project is part of the cancer, aging, and somatic mutation research based at the Wellcome Trust Sanger Institute in the United Kingdom. It aims to identify sequence variants/mutations critical in the development of human cancers. Like The Cancer Genome Atlas project within the United States, the Cancer Genome Project represents an effort in the War on Cancer to improve cancer diagnosis, treatment, and prevention through a better understanding of the molecular basis of the disease. The Cancer Genome Project was launched by Michael Stratton in 2000, and Peter Campbell is now the group leader of the project. The project works to combine knowledge of the human genome sequence with high throughput mutation detection techniques.

The Cancer Genome Atlas (TCGA) is a project to catalogue the genetic mutations responsible for cancer using genome sequencing and bioinformatics. The overarching goal was to apply high-throughput genome analysis techniques to improve the ability to diagnose, treat, and prevent cancer through a better understanding of the genetic basis of the disease.

<span class="mw-page-title-main">Pan-genome</span> All genes of all strains in a clade

In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. More generally, it is the union of all the genomes of a clade. The pan-genome can be broken down into a "core pangenome" that contains genes present in all individuals, a "shell pangenome" that contains genes present in two or more strains, and a "cloud pangenome" that contains genes only found in a single strain. Some authors also refer to the cloud genome as "accessory genome" containing 'dispensable' genes present in a subset of the strains and strain-specific genes. Note that the use of the term 'dispensable' has been questioned, at least in plant genomes, as accessory genes play "an important role in genome evolution and in the complex interplay between the genome and the environment". The field of study of pangenomes is called pangenomics.

SOAP is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data.

Campylobacter concisus is a Gram-negative, highly fastidious, mesophilic bacterium that grows under both anaerobic and microaerobic conditions with the presence of hydrogen significantly aiding growth. Motile, with either unipolar or bipolar flagella, the organisms have a characteristic spiral/corkscrew appearance and are oxidase-positive. Although the human oral cavity is the natural colonization site of the bacterium, C. concisus may also colonize the intestinal tract of some individuals. In particular, several studies have reported higher intestinal prevalence of C. concisus in patients with IBD compared to healthy controls, which has led to current speculation of the bacterium's implication in the induction of Crohn's disease.

<i>Prunus <span style="font-style:normal;">subg.</span> Prunus</i> Subgenus of plants

Prunus subg. Prunus is a subgenus of Prunus. This subgenus includes plums, apricots and bush cherries. Some species conventionally included in Prunus subg. Amygdalus are clustered with plum/apricot species according to molecular phylogenetic studies. Shi et al. (2013) has incorporated subg. Amygdalus into subg. Prunus, thereby including almonds and peaches in this subgenus. The species in this subgenus have solitary flowers or 2–3 in a fascicle.

Pan-cancer analysis aims to examine the similarities and differences among the genomic and cellular alterations found across diverse tumor types. International efforts have performed pan-cancer analysis on exomes and the whole genomes of cancers, the latter including their non-coding regions. In 2018, The Cancer Genome Atlas (TCGA) Research Network used exome, transcriptome, and DNA methylome data to develop an integrated picture of commonalities, differences, and emergent themes across tumor types.

<span class="mw-page-title-main">Wang Jun (scientist)</span> Chinese scientist

Wang Jun is a Chinese scientist, founder and CEO of iCarbonX, and former CEO of the Beijing Genomics Institute.

<span class="mw-page-title-main">Multiomics</span>

Multiomics, multi-omics, integrative omics, "panomics" or "pan-omics" is a biological analysis approach in which the data sets are multiple "omes", such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome ; in other words, the use of multiple omics technologies to study life in a concerted way. By combining these "omes", scientists can analyze complex biological big data to find novel associations between biological entities, pinpoint relevant biomarkers and build elaborate markers of disease and physiology. In doing so, multiomics integrates diverse omics data to find a coherently matching geno-pheno-envirotype relationship or association. The OmicTools service lists more than 99 softwares related to multiomic data analysis, as well as more than 99 databases on the topic.

In the field of genetic sequencing, genotyping by sequencing, also called GBS, is a method to discover single nucleotide polymorphisms (SNP) in order to perform genotyping studies, such as genome-wide association studies (GWAS). GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples. After digestion, PCR is performed to increase fragments pool and then GBS libraries are sequenced using next generation sequencing technologies, usually resulting in about 100bp single-end reads. It is relatively inexpensive and has been used in plant breeding. Although GBS presents an approach similar to restriction-site-associated DNA sequencing (RAD-seq) method, they differ in some substantial ways.

Flammeovirga is a Gram-negative, aerobic, non-spore-forming and chemoorganotrophic genus of bacteria in the family Flammeovirgaceae which occur in marine environments.

This article summarizes the genetic makeup and population history of East Asian peoples and their connection to genetically related populations, as well as Oceanians and partly, Central Asians and South Asians, which are collectively referred to as "East Eurasians" in population genomics.

<span class="mw-page-title-main">Genome skimming</span> Method of genome sequencing

Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome, to generate fragments of DNA, known as genome skims. These genome skims contain information about the high-copy fraction of the genome. The high-copy fraction of the genome consists of the ribosomal DNA, plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear repeats such as microsatellites and transposable elements. It employs high-throughput, next generation sequencing technology to generate these skims. Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods. Due to the small amount of DNA required for genome skimming, its methodology can be applied in other fields other than genomics. Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.

References

  1. Liu, Luxian; Wang, Yuewen; He, Peizi; Li, Pan; Lee, Joongku; Soltis, Douglas E.; Fu, Chengxin (2018-04-04). "Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data". BMC Genomics. 19 (1): 235. doi: 10.1186/s12864-018-4633-x . ISSN   1471-2164. PMC   5885378 . PMID   29618324.
  2. Liu, Lu‐Xian; Deng, Pan; Chen, Meng‐Zhen; Yu, Li‐Min; Lee, Joongku; Jiang, Wei‐Mei; Fu, Cheng‐Xin; Shang, Fu‐De; Li, Pan (2022-03-22). "Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data". Journal of Systematics and Evolution. 61 (1): 99–114. doi:10.1111/jse.12833. ISSN   1674-4918.