Domain combination of the vertebrate-like TLR gene family: implications for their origin and evolution

CCN gene family members have recently been identified as multifunctional regulators involved in diverse biological functions, especially in vascular and skeletal development. In the present study, a comparative genomic and phylogenetic analysis was performed to show the similarities and differences in structure and function of CCNs from different organisms and to reveal their potential evolutionary relationship. First, CCN homologs of metazoans from different species were identified. Then we made multiple sequence alignments, MEME analysis, and functional sites prediction, which show the highly conserved structural features among CCN metazoans. The phylogenetic tree was further established, and thus CCNs were found undergoing extensive lineage-specific duplication events and lineage-specific expansion during the evolutionary process. Besides, comparative analysis about the genomic organization and chromosomal CCN gene surrounding indicated a clear orthologous relationship among these species counterparts. At last, based on these research results above, a potential evolutionary scenario was generated to overview the origin and evolution of the CCN gene family.

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The Characterization of Sponge NLRs Provides Insight into the Origin and Evolution of This Innate Immune Gene Family in Animals

Molecular Biology and Evolution ◽

10.1093/molbev/mst174 ◽

2013 ◽

Vol 31 (1) ◽

pp. 106-120 ◽

Cited By ~ 43

Author(s):

Benedict Yuen ◽

Joanne M. Bayes ◽

Sandie M. Degnan

Keyword(s):

Gene Family ◽

Innate Immune ◽

Immune Gene ◽

Origin And Evolution ◽

Insight Into ◽

Innate Immune Gene

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Origin and Evolution of the Gene Family of Proteinaceous Pheromones, the Exocrine Gland-Secreting Peptides, in Rodents

Molecular Biology and Evolution ◽

10.1093/molbev/msaa220 ◽

2020 ◽

Author(s):

Yoshihito Niimura ◽

Mai Tsunoda ◽

Sari Kato ◽

Ken Murata ◽

Taichi Yanagawa ◽

...

Keyword(s):

Sexual Behavior ◽

Gene Family ◽

Sequence Similarity ◽

Globin Gene ◽

Vomeronasal Organ ◽

Exocrine Gland ◽

Mouse Strains ◽

Coding Region ◽

Origin And Evolution ◽

Species Specific

Abstract The exocrine-gland secreting peptide (ESP)gene family encodes proteinaceous pheromones that are recognized by the vomeronasal organ in mice. For example, ESP1 is a male pheromone secreted in tear fluid that regulates socio-sexual behavior, and ESP22 is a juvenile pheromone that suppresses adult sexual behavior. The family consists of multiple genes and has been identified only in mouse and rat genomes. The coding region of a mouse ESP gene is separated into two exons, each encoding signal and mature sequences. Here, we report the origin and evolution of the ESP gene family. ESP genes were found only in the Muridea and Cricetidae families of rodents, suggesting a recent origin of ESP genes in the common ancestor of murids and cricetids. ESP genes show a great diversity in number, length, and sequence among different species as well as mouse strains. Some ESPs in rats and golden hamsters are expressed in the lacrimal gland and the salivary gland. We also found that a mature sequence of an ESP gene showed overall sequence similarity to the α-globin gene. The ancestral ESP gene seems to be generated by recombination of a retrotransposed α-globin gene with the signal-encoding exon of the CRISP2 gene located adjacent to the ESP gene cluster. This study provides an intriguing example of molecular tinkering in rapidly evolving species-specific proteinaceous pheromone genes.

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Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

10.21203/rs.3.rs-106970/v1 ◽

2020 ◽

Author(s):

Jiang-Ping Shu ◽

Yue-Hong Yan ◽

Rui-Jiang Wang

Keyword(s):

Gene Family ◽

Convergent Evolution ◽

Carbon Fixation ◽

Protein Structures ◽

Three Dimensional ◽

Cam Plants ◽

Green Plants ◽

Origin And Evolution ◽

Duplication Events ◽

Cam Photosynthesis

Abstract Background: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4 and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulted in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remained lack of understanding. Results: In present study, we identified the members of PEPC gene family across green plants with genomic data, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructed PEPC gene family tree and reconciled with species tree, we found PEPC genes occurred 71 gene duplications and 16 gene losses, which might result from whole-genome duplication events in plants. Based on the integral phylogenetic tree of PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but no one in CAM species. Conclusions: PEPC gene family was ubiquitous and highly conservative in green plants. After originated from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that facilitated the convergent evolution of C4 photosynthesis in Angiosperms, but PEPC gene did not exist molecular convergence corresponded to the multiple independent evolution of CAM photosynthesis. Our findings help to understand the origin and evolution of C4 and CAM pathways and shed new light on the adaptation of plants in drought and high-temperature habitats.

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Phylogenetic diversification of sirtuin genes with a description of a new family member

10.1101/2020.07.17.209510 ◽

2020 ◽

Author(s):

Juan C. Opazo ◽

Kattina Zavala ◽

Michael W. Vandewege ◽

Federico G. Hoffmann

Keyword(s):

Gene Family ◽

Family Member ◽

Gene Families ◽

Last Common Ancestor ◽

Gene Repertoire ◽

Origin And Evolution ◽

New Family ◽

Wide Range ◽

Evolutionary Context ◽

History Of

AbstractStudying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural work, as the correct interpretation of their results needs to be done in a robust evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our goal is to take advantage of the genomic data available in public databases to advance our understanding of how sirtuin genes are related to each other, and to characterize the gene repertoire in species representative of all the main groups of vertebrates. Our results show a well-resolved phylogeny that represents a significant improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin family member (SIRT3-like) that was apparently lost in amniotes, but retained in all other groups of jawed vertebrates. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

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