Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A phylogenetic study of the squid family Onychoteuthidae (Cephalopoda: Oegopsida).

ABSTRACT: The oegopsid squid family Onychoteuthidae presently comprises six genera (Moroteuthis, Onychoteuthis, Ancistroteuthis, Kondakovia, Onykia and Chaunoteuthis) but the status of some of these is still uncertain. An interdisciplinary study was undertaken to clarify the phylogenetic relationships, which included a morphological approach (morphometric analysis), and a molecular study of a mitochondrial gene portion (l-rRNA gene, 16S). The morphometric analysis identified two groups, one including some Onychoteuthis and some Moroteuthis knipovitchi, and another including the remaining genera or species. At the intrageneric level, M. knipovitchi appears to be separated from the other species of the genus; M. robusta is closely related to M. ingens and M. pacifica. Morphometric analysis confirmed that Kondakovia longimana is different from M. ingens. Likewise, Onychoteuthis was clearly separated from the other genera, but there is neither geographical grouping nor morphometric differentiation of the Onychoteuthis species with the parameters measured. Some specimens were apparently intermediate between the Onychoteuthis and Ancistroteuthis groups. On a molecular basis, the Onychoteuthidae appeared to be monophyletic. Monophyly of the genus Moroteuthis (four species studied) was not strongly supported: M. knipovitchi was distinct from the others. The molecular analysis showed three Hawaiian species, Onychoteuthis compacta, O. sp. B and O. sp. C, to be closely related. The gene sequence for the newly created species of Onykia is clearly different from all the others, indicating that it is a true species.

SUBMITTER: Bonnaud L

PROVIDER: S-EPMC1689357 | biostudies-other | 1998 Sep

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Squid

Project description:A Molecular Tandem-Repeat Strategy For Elucidating Mechanical Properties of High Strength Proteins

| PRJNA320263 | ENA

Phylogenetic study of Melanoseris

Project description:A new species of Melanoseris (Lactucinae, Cichorieae, Asteraceae) from SW Xizang, China, based on morphological and molecular data

| PRJEB23167 | ENA

A Bayesian phylogenetic study of the Dravidian language family.

Project description:The Dravidian language family consists of about 80 varieties (Hammarström H. 2016 Glottolog 2.7) spoken by 220 million people across southern and central India and surrounding countries (Steever SB. 1998 In The Dravidian languages (ed. SB Steever), pp. 1-39: 1). Neither the geographical origin of the Dravidian language homeland nor its exact dispersal through time are known. The history of these languages is crucial for understanding prehistory in Eurasia, because despite their current restricted range, these languages played a significant role in influencing other language groups including Indo-Aryan (Indo-European) and Munda (Austroasiatic) speakers. Here, we report the results of a Bayesian phylogenetic analysis of cognate-coded lexical data, elicited first hand from native speakers, to investigate the subgrouping of the Dravidian language family, and provide dates for the major points of diversification. Our results indicate that the Dravidian language family is approximately 4500 years old, a finding that corresponds well with earlier linguistic and archaeological studies. The main branches of the Dravidian language family (North, Central, South I, South II) are recovered, although the placement of languages within these main branches diverges from previous classifications. We find considerable uncertainty with regard to the relationships between the main branches.

| S-EPMC5882685 | biostudies-literature

Autoimmune family study

Project description:Patients with autoimmune disorders exhibit highly reproducible gene expression profiles in their peripheral blood mononuclear cells. These signatures may result from chronic inflammation, other disease manifestations, or may reflect family resemblance. To test the latter hypothesis, we determined gene expression profiles in unaffected first-degree relatives of individuals with autoimmune disease. Gene expression profiles in unaffected first-degree relatives resembled the profiles found in individuals with autoimmune diseases. A high percentage of differentially expressed genes in unaffected first-degree relatives were previously identified as autoimmune signature genes. Examination of the linear regression relationship of gene transcript levels between parent-offspring pairs revealed that autoimmune signature genes display high levels of family resemblance. Taken together, these results support the hypothesis that these variations in gene transcript levels are associated with family resemblance rather than clinical manifestations of disease. Keywords: Gene expression profiling

2005-10-18 | GSE3459 | GEO

Molecular phylogenetic study of flavonoids in medicinal plants: a case study family Apiaceae.

Project description:The current study examined the phylogenetic pattern of medicinal species of the family Apiaceae based on flavonoid groups production, as well as the overall mechanism of the key genes involved in flavonol and flavone production. Thirteen species of the family Apiaceae were used, including Eryngium campestre from the subfamily Saniculoideae, as well as Cuminum cyminum, Carum carvi, Coriandrum sativum, Apium graveolens, Petroselinum crispum, Pimpinella anisum, Anethum graveolens, Foeniculum vulgare, Daucus carota, Ammi majus, Torilis arvensis, and Deverra tortuosa from the subfamily Apioideae. The seeds were cultivated, and the leaves were collected to estimate flavonoids and their groups, physiological factors, transcription levels of flavonol and flavone production-related genes. The phylogenetic relationship between the studied species was established using the L-ribosomal 16 (rpl16) chloroplast gene. The results revealed that the studied species were divided into two patterns: six plant species, E. campestre, C. carvi, C. sativum, P. anisum, An. graveolens, and D. carota, contained low content of flavonoids, while the other seven species had high content. This pattern of flavonoids production coincided with the phylogenetic relationships between the studied species. In contrast, the phylogeny of the flavonol and flavone synthase genes was incompatible with the quantitative production of their products. The study concluded that the increment in the production of flavonol depends on the high expression of chalcone synthase, chalcone isomerase, flavanone 3 hydroxylase, flavonol synthase, the increase of Abscisic acid, sucrose, and phenyl ammonia lyase, while flavone mainly depends on evolution and on the high expression of the flavone synthase gene.

| S-EPMC10126080 | biostudies-literature

A phylogenetic framework to study the evolution of transcriptional regulatory networks

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-07-01 | GSE94628 | GEO

Phylogenetic & expression analysis of the bHLH transcription factor family: genomic approach to cellular differentiation

Project description:A phylogenetic analysis of seven different species (human, mouse, rat, worm, fly, yeast, and plant) utilizing all (541) basic helix-loop-helix (bHLH) genes identified, including expressed sequence tags (EST), was performed. A super-tree involving six clades and a structural categorization involving the entire coding sequence was established. A nomenclature was developed based on clade distribution to discuss the functional and ancestral relationships of all the genes. The position/location of specific genes on the phylogenetic tree in relation to known bHLH factors allows for predictions of the potential functions of uncharacterized bHLH factors, including EST's. A genomic analysis using microarrays for four different mouse cell types (i.e. Sertoli, Schwann, thymic, and muscle) was performed and considered all known bHLH family members on the microarray for comparison. Cell-specific groups of bHLH genes helped clarify those bHLH genes potentially involved in cell specific differentiation. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique aspects of the evolution and functional relationships of the different genes in the bHLH gene family. PMID: 18557763 We used microarrays to determine bHLH expression in 20d rat Sertoli cells.

2010-02-11 | GSE20259 | GEO

Autoimmune family study

2010-06-09 | E-GEOD-3459 | biostudies-arrayexpress

Bobtail squid (Sepiolinae)

Project description:Species from Japan, USA and Australia Transcriptome

| PRJNA485404 | ENA

Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin.

Project description:Upon absorption of light, the retinal chromophore in rhodopsin isomerizes from the 11-cis to the trans configuration, initiating a photoreaction cycle. The primary photoreaction state, bathorhodopsin (BATHO), relaxes thermally through lumirhodopsin (LUMI) into a photoactive state, metarhodopsin (META), which stimulates the conjugated G-protein. Previous crystallographic studies of squid and bovine rhodopsins have shown that the structural change in the primary photoreaction of squid rhodopsin is considerably different from that observed in bovine rhodopsin. It would be expected that there is a fundamental difference in the subsequent thermal relaxation process between vertebrate and invertebrate rhodopsins. In this work, we performed crystallographic analyses of the LUMI state of squid rhodopsin using the P62 crystal. When the crystal was illuminated at 100 K with blue light, a half fraction of the protein was converted into BATHO. This reaction state relaxed into LUMI when the illuminated crystal was warmed in the dark to 170 K. It was found that, whereas trans retinal is largely twisted in BATHO, it takes on a more planar configuration in LUMI. This relaxation of retinal is accompanied by reorientation of the Schiff base NH bond, the hydrogen-bonding partner of which is switched to Asn185 in LUMI. Unlike bovine rhodopsin, the BATHO-to-LUMI transition in squid rhodopsin was accompanied by no significant change in the position/orientation of the beta-ionone ring of retinal.

| S-EPMC4449009 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data