The expansion and diversity of the CYP75 gene family in Vitaceae

The CYP75 gene family plays an important role in flavonoid biosynthesis in plants. Little is known about the evolution of the gene family within the grape family. Here, we extracted the CYP75 genes from transcriptome data of 15 grape species and 36 representative genomes from other plants to explore the evolutionary history of the CYP75 gene family in Vitaceae. The structure of the CYP75 protein sequences is highly conserved with the variation mainly occurring in the N terminal and the middle region. The evolutionary analyses suggested classifying the CYP75 gene family into three groups in Vitaceae, namely Vitaceae A1, Vitaceae A2 and Vitaceae B. The Vitaceae A1 and A2 belong to the CYP75A subfamily and the Vitaceae B belongs to the CYP75B subfamily. Within the Vitaceae A1, most Vitaceae taxa present only one copy of the CYP75A protein sequence except for Vitis vinifera with a high number of sequences, which might have originated through recent gene duplications after its split from the other species. Vitaceae A2 contain only CYP75A sequences from Vitaceae sister to one from Camellia sinensis, probably representing a relict lineage. The CYP75B proteins were found to be dominated in Vitaceae and other angiosperms. Our results provide important insights into understanding the evolutionary history of the CYP75 gene family in Vitaceae and other angiosperms.

Download Full-text

Evolutionary history of the MTG gene family in vertebrates

Proceedings of the National Academy of Sciences of Belarus Biological Series ◽

10.29235/1029-8940-2019-64-4-391-402 ◽

2019 ◽

Vol 64 (4) ◽

pp. 391-402

Author(s):

A. I. Kavaleuskaya ◽

T. V. Ramanouskaya

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Protein Sequences ◽

Stem Cell Differentiation ◽

Gene Products ◽

Functional Diversification ◽

Rates Of Evolution ◽

Different Types ◽

History Of ◽

Transcriptional Corepressors

The highly conserved MTG gene family includes three homologs in vertebrates (MTG8, MTGR1, MTG16) encoding transcriptional corepressors, which are important in haemopoiesis, neurogenesis and epithelial stem cell differentiation. These genes are of particular interest because they are involved in translocations, associated with different types of cancer. Looking at how this gene family evolved might provide insights into history of its structural and functional diversification. We have performed a phylogenetic analysis of MTG nucleotide and protein sequences to examine the evolutionary events. The domain organization of MTG gene products was clarified, the mechanism of appearance of the first MTG gene was revealed and the ancestor taxon was determined. Also the mechanism of MTG gene family emergence was established. In addition, analysis of the rates of evolution acting on individual domains was made, and conservative positions within each gene of MTG family were determined.

Download Full-text

Evolution of the DAN gene family in vertebrates

10.1101/794404 ◽

2019 ◽

Cited By ~ 2

Author(s):

Juan C. Opazo ◽

Federico G. Hoffmann ◽

Kattina Zavala ◽

Scott V. Edwards

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Cartilaginous Fish ◽

Limb Bud ◽

The Other ◽

Bud Formation ◽

Physiological Information ◽

Evolutionary Context ◽

History Of ◽

Phyletic Distribution

AbstractThe DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.

Download Full-text

Functional evolutionary history of the mouseFgf gene family

Developmental Dynamics ◽

10.1002/dvdy.21388 ◽

2007 ◽

Vol 237 (1) ◽

pp. 18-27 ◽

Cited By ~ 242

Author(s):

Nobuyuki Itoh ◽

David M. Ornitz

Keyword(s):

Gene Family ◽

Evolutionary History ◽

History Of

Download Full-text

Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

10.1101/288530 ◽

2018 ◽

Author(s):

Mónica Lopes-Marques ◽

André M. Machado ◽

Raquel Ruivo ◽

Elza Fonseca ◽

Estela Carvalho ◽

...

Keyword(s):

Gene Family ◽

Metabolic Pathways ◽

Evolutionary History ◽

Gene Families ◽

Gene Repertoire ◽

Physiological Processes ◽

Complex Lipid ◽

History Of ◽

Enzyme Families ◽

Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

Download Full-text

Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

10.1101/766360 ◽

2019 ◽

Author(s):

Laura Hernández ◽

Alberto Vicens ◽

Luis Enrique Eguiarte ◽

Valeria Souza ◽

Valerie De Anda ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Common Ancestor ◽

Functional Divergence ◽

Gene Families ◽

Recent Common Ancestor ◽

Common Ancestry ◽

Demethylation Pathway ◽

History Of ◽

New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

Download Full-text

Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes

BMC Evolutionary Biology ◽

10.1186/1471-2148-10-308 ◽

2010 ◽

Vol 10 (1) ◽

pp. 308 ◽

Cited By ~ 63

Author(s):

Matteo Citarelli ◽

Sachin Teotia ◽

Rebecca S Lamb

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Polymerase Gene ◽

History Of

Download Full-text

An early fossil remora (Echeneoidea) reveals the evolutionary assembly of the adhesion disc

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.1200 ◽

2013 ◽

Vol 280 (1766) ◽

pp. 20131200 ◽

Cited By ~ 15

Author(s):

Matt Friedman ◽

Zerina Johanson ◽

Richard C. Harrington ◽

Thomas J. Near ◽

Mark R. Graham

Keyword(s):

Evolutionary History ◽

Body Plan ◽

The Other ◽

Ontogenetic Changes ◽

Dorsal Fin ◽

Early Oligocene ◽

Stem Group ◽

History Of ◽

And Migration ◽

Fin Spines

The adhesion disc of living remoras (Echeneoidea: Echeneidae) represents one of the most remarkable structural innovations within fishes. Although homology between the spinous dorsal fin of generalized acanthomorph fishes and the remora adhesion disc is widely accepted, the sequence of evolutionary—rather than developmental—transformations leading from one to the other has remained unclear. Here, we show that the early remora † Opisthomyzon (Echeneoidea: †Opisthomyzonidae), from the early Oligocene (Rupelian) of Switzerland, is a stem-group echeneid and provides unique insights into the evolutionary assembly of the unusual body plan characteristic of all living remoras. The adhesion disc of † Opisthomyzon retains ancestral features found in the spiny dorsal fins of remora outgroups, and corroborates developmental interpretations of the homology of individual skeletal components of the disc. † Opisthomyzon indicates that the adhesion disc originated in a postcranial position, and that other specializations (including the origin of pectination, subdivision of median fin spines into paired lamellae, increase in segment count and migration to a supracranial position) took place later in the evolutionary history of remoras. This phylogenetic sequence of transformation finds some parallels in the order of ontogenetic changes to the disc documented for living remoras.

Download Full-text

Evolutionary History of the 11p15 Human Mucin Gene Family

Journal of Molecular Evolution ◽

10.1007/pl00006276 ◽

1998 ◽

Vol 46 (1) ◽

pp. 102-106 ◽

Cited By ~ 51

Author(s):

Jean-Luc Desseyn ◽

Marie-Pierre Buisine ◽

Nicole Porchet ◽

Jean-Pierre Aubert ◽

Pierre Degand ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Mucin Gene ◽

History Of

Download Full-text

The shared evolutionary history of kinship classifications and language

Behavioral and Brain Sciences ◽

10.1017/s0140525x10001421 ◽

2010 ◽

Vol 33 (5) ◽

pp. 402-403 ◽

Cited By ~ 3

Author(s):

Robert M. Seyfarth ◽

Dorothy L. Cheney

Keyword(s):

Human Evolution ◽

Evolutionary History ◽

The Other ◽

History Of ◽

System Maps

AbstractAmong monkeys and apes, both the recognition and classification of individuals and the recognition and classification of vocalizations constitute discrete combinatorial systems. One system maps onto the other, suggesting that during human evolution kinship classifications and language shared a common cognitive precursor.

Download Full-text