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Article ; Online: Duplication and diversification of insulin genes in ray-finned fish

David M. Irwin

Zoological Research, Vol 40, Iss 3, Pp 185-

2019 Volume 197

Abstract: Insulin is a key hormone for the regulation of metabolism in vertebrates. Insulin is produced by pancreatic islet cells in response to elevated glucose levels and leads to the uptake of glucose by tissues such as liver and adipose tissue to store energy. ...

Abstract	Insulin is a key hormone for the regulation of metabolism in vertebrates. Insulin is produced by pancreatic islet cells in response to elevated glucose levels and leads to the uptake of glucose by tissues such as liver and adipose tissue to store energy. Insulin also has additional functions in regulating development. Previous work has shown that the proglucagon gene, which encodes hormones counter regulating insulin, is duplicated in teleost fish, and that the peptide hormones encoded by these genes have diversified in function. I sought to determine whether similar processes have occurred to insulin genes in these species. Searches of fish genomes revealed an unexpected diversity of insulin genes. A triplication of the insulin gene occurred at the origin of teleost fish, however one of these three genes, insc, has been lost in most teleost fish lineages. The two other insulin genes, insa and insb, have been retained but show differing levels of selective constraint suggesting that they might have diversified in function. Intriguingly, a duplicate copy of the insa gene, which I named insab, is found in many fish. The coding sequence encoded by insab genes is under weak selective constraint, with its predicted protein sequences losing their potential to be processed into a two-peptide hormone. However, these sequences have retained perfectly conserved cystine residues, suggesting that they maintain insulin’s three-dimensional structure and therefore might modulate the processing and secretion of insulin produced by the other genes.
Keywords	Insulin ; Teleost fish ; Gene duplication ; Adaptive evolution ; Gene loss ; Zoology ; QL1-991
Subject code	612
Language	English
Publishing date	2019-05-01T00:00:00Z
Publisher	Science Press, PR China
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Accelerated evolution of dim-light vision-related arrestin in deep-diving amniotes

Xin Guo / Yimeng Cui / David M. Irwin / Yang Liu

Frontiers in Ecology and Evolution, Vol

2022 Volume 10

Abstract: Arrestins are key molecules involved in the signaling of light-sensation initiated by visual pigments in retinal photoreceptor cells. Vertebrate photoreceptor cells have two types of arrestins, rod arrestin, which is encoded by SAG and is expressed in ... ...

Abstract	Arrestins are key molecules involved in the signaling of light-sensation initiated by visual pigments in retinal photoreceptor cells. Vertebrate photoreceptor cells have two types of arrestins, rod arrestin, which is encoded by SAG and is expressed in both rods and cones, and cone arrestin, encoded by ARR3 in cones. The arrestins can bind to visual pigments, and thus regulate either dim-light vision via interactions with rhodopsin or bright-light vision together with cone visual pigments. After adapting to terrestrial life, several amniote lineages independently went back to the sea and evolved deep-diving habits. Interestingly, the rhodopsins in these species exhibit specialized phenotypes responding to rapidly changing dim-light environments. However, little is known about whether their rod arrestin also experienced adaptive evolution associated with rhodopsin. Here, we collected SAG coding sequences from >250 amniote species, and examined changes in selective pressure experienced by the sequences from deep-diving taxa. Divergent patterns of evolution of SAG were observed in the penguin, pinniped and cetacean clades, suggesting possible co-adaptation with rhodopsin. After verifying pseudogenes, the same analyses were performed for cone arrestin (ARR3) in deep-diving species and only sequences from cetacean species, and not pinnipeds or penguins, have experienced changed selection pressure compared to other species. Taken together, this evidence for changes in selective pressures acting upon arrestin genes strengthens the suggestion that rapid dim-light adaptation for deep-diving amniotes require SAG, but not ARR3.
Keywords	vertebrates ; SAG ; ARR3 ; scotopic vision ; molecular evolution ; visual adaptation ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
Subject code	580
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic organization and evolution of ruminant lysozyme c genes

David M. IRWIN

Zoological Research, Vol 36, Iss 1, Pp 1-

2015 Volume 17

Abstract: Ruminant stomach lysozyme is a long established model of adaptive gene evolution. Evolution of stomach lysozyme function required changes in the site of expression of the lysozyme c gene and changes in the enzymatic properties of the enzyme. In ruminant ... ...

Abstract	Ruminant stomach lysozyme is a long established model of adaptive gene evolution. Evolution of stomach lysozyme function required changes in the site of expression of the lysozyme c gene and changes in the enzymatic properties of the enzyme. In ruminant mammals, these changes were associated with a change in the size of the lysozyme c gene family. The recent release of near complete genome sequences from several ruminant species allows a more complete examination of the evolution and diversification of the lysozyme c gene family. Here we characterize the size of the lysozyme c gene family in extant ruminants and demonstrate that their pecoran ruminant ancestor had a family of at least 10 lysozyme c genes, which included at least two pseudogenes. Evolutionary analysis of the ruminant lysozyme c gene sequences demonstrate that each of the four exons of the lysozyme c gene has a unique evolutionary history, indicating that they participated independently in concerted evolution. These analyses also show that episodic changes in the evolutionary constraints on the protein sequences occurred, with lysozyme c genes expressed in the abomasum of the stomach of extant ruminant species showing the greatest levels of selective constraints.
Keywords	Lysozyme c ; Ruminants ; Gene family ; Gene duplication ; Concerted evolution ; Mosaic evolution ; Zoology ; QL1-991
Subject code	572
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Science Press, PR China
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Contrasting Patterns in the Evolution of Vertebrate MLX Interacting Protein (MLXIP) and MLX Interacting Protein-Like (MLXIPL) Genes.

Parmveer Singh / David M Irwin

PLoS ONE, Vol 11, Iss 2, p e

2016 Volume 0149682

Abstract: ChREBP and MondoA are glucose-sensitive transcription factors that regulate aspects of energy metabolism. Here we performed a phylogenomic analysis of Mlxip (encoding MondoA) and Mlxipl (encoding ChREBP) genes across vertebrates. Analysis of extant Mlxip ...

Abstract	ChREBP and MondoA are glucose-sensitive transcription factors that regulate aspects of energy metabolism. Here we performed a phylogenomic analysis of Mlxip (encoding MondoA) and Mlxipl (encoding ChREBP) genes across vertebrates. Analysis of extant Mlxip and Mlxipl genes suggests that the most recent common ancestor of these genes was composed of 17 coding exons. Single copy genes encoding both ChREBP and MondoA, along with their interacting partner Mlx, were found in diverse vertebrate genomes, including fish that have experienced a genome duplication. This observation suggests that a single Mlx gene has been retained to maintain coordinate regulation of ChREBP and MondoA. The ChREBP-β isoform, the more potent and constitutively active isoform, appeared with the evolution of tetrapods and is absent from the Mlxipl genes of fish. Evaluation of the conservation of ChREBP and MondoA sequences demonstrate that MondoA is better conserved and potentially mediates more ancient function in glucose metabolism.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Adaptive Evolution of the Fox Coronavirus Based on Genome-Wide Sequence Analysis

Chunyu Feng / Yuting Liu / Guangqi Lyu / Songyang Shang / Hongyue Xia / Junpeng Zhang / David M. Irwin / Zhe Wang / Shuyi Zhang

BioMed Research International, Vol

2022 Volume 2022

Abstract: Purpose. To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV. Methods. Anal swab samples were collected from 35 foxes to detect the presence of ...

Abstract	Purpose. To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV. Methods. Anal swab samples were collected from 35 foxes to detect the presence of CoV and obtain the virus sequence. Phylogenetic analysis was conducted using MrBayes. The possibility of recombination within these sequences was assessed using GARD. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Data Monkey platforms. Results. Of the 35 samples, two were positive, and complete genome sequences for the viruses were obtained. Phylogenetic analysis, using Bayesian methods, of these sequences, together with other CoV sequences, revealed that the fox CoV sequences clustered with canine coronavirus (CCoV) sequences, with sequences from other carnivores more distantly related. In contrast to the feline, ferret and mink CoV sequences that clustered into species-specific clades, the fox CoV fell within the CCoV clade. Minimal evidence for recombination was found among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes, respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively. Conclusion. The complete genome sequence of fox CoV has been obtained for the first time. The results suggest that the genome sequence of fox CoV may have experienced adaptive evolution in the genes replication, entry, and virulence. The number of sites in each gene that experienced negative selection is far greater than the number that underwent positive selection, suggesting that most of the sequence is highly conserved and important for viral survive. However, positive selection at a few sites likely aided these viruses to adapt to new environments.
Keywords	Medicine ; R
Subject code	572
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolution of the Vertebrate Resistin Gene Family.

Qingda Hu / Huanran Tan / David M Irwin

PLoS ONE, Vol 10, Iss 6, p e

2015 Volume 0130188

Abstract: Resistin (encoded by Retn) was previously identified in rodents as a hormone associated with diabetes; however human resistin is instead linked to inflammation. Resistin is a member of a small gene family that includes the resistin-like peptides (encoded ...

Abstract	Resistin (encoded by Retn) was previously identified in rodents as a hormone associated with diabetes; however human resistin is instead linked to inflammation. Resistin is a member of a small gene family that includes the resistin-like peptides (encoded by Retnl genes) in mammals. Genomic searches of available genome sequences of diverse vertebrates and phylogenetic analyses were conducted to determine the size and origin of the resistin-like gene family. Genes encoding peptides similar to resistin were found in Mammalia, Sauria, Amphibia, and Actinistia (coelacanth, a lobe-finned fish), but not in Aves or fish from Actinopterygii, Chondrichthyes, or Agnatha. Retnl originated by duplication and transposition from Retn on the early mammalian lineage after divergence of the platypus, but before the placental and marsupial mammal divergence. The resistin-like gene family illustrates an instance where the locus of origin of duplicated genes can be identified, with Retn continuing to reside at this location. Mammalian species typically have a single copy Retn gene, but are much more variable in their numbers of Retnl genes, ranging from 0 to 9. Since Retn is located at the locus of origin, thus likely retained the ancestral expression pattern, largely maintained its copy number, and did not display accelerated evolution, we suggest that it is more likely to have maintained an ancestral function, while Retnl, which transposed to a new location, displays accelerated evolution, and shows greater variability in gene number, including gene loss, likely evolved new, but potentially lineage-specific, functions.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Hen raising helps chicks establish gut microbiota in their early life and improve microbiota stability after H9N2 challenge

Xiaobing Li / Ran Bi / Kangpeng Xiao / Ayan Roy / Zhipeng Zhang / Xiaoyuan Chen / Jinyu Peng / Ruichen Wang / Rou Yang / Xuejuan Shen / David M. Irwin / Yongyi Shen

Microbiome, Vol 10, Iss 1, Pp 1-

2022 Volume 12

Abstract: Abstract Background Early gut microbial colonization is important for postnatal growth and immune development of the chicken. However, at present, commercial chickens are hatched and raised without adult hens, thus are cut off from the microbiota ... ...

Abstract	Abstract Background Early gut microbial colonization is important for postnatal growth and immune development of the chicken. However, at present, commercial chickens are hatched and raised without adult hens, thus are cut off from the microbiota transfer between hens and chicks. In this study, we compared the gut microbiota composition between hen-reared and separately reared chicks, and its impact on the resistance to H9N2 avian influenza virus, with the motive of investigating the impact of this cutoff in microbiota transfer. Results We used the 16SrRNA sequencing method to assess the composition of the gut microbiota in chicks represented by three hen-reared groups and one separately reared group. We found that the diversity of gut microbes in the chicks from the three hen-reared groups was more abundant than in the separately reared group, both at the phylum and genus levels. Our findings highlight the importance of early parental care in influencing the establishment of gut microbiota in the early life of chicks. SourceTracker analysis showed that the feather and cloaca microbiota of hens are the main sources of gut microbiota of chicks. After H9N2 exposure, the viral infection lasted longer in the separately reared chicks, with the viral titers in their oropharyngeal swabs being higher compared to the hen-reared chicks at day 5 post-infection. Interestingly, our results revealed that the gut microbiota of the hen-reared chicks was more stable after H9N2 infection in comparison to that of the separately reared chicks. Conclusions Microbiota transfer between the hens and their chicks promotes the establishment of a balanced and diverse microbiota in the early life of the chicks and improves microbiota stability after H9N2 challenge. These findings advance our understanding of the protective role of gut microbiota in the early life of chicks and should be instrumental in improving chick rearing in the commercial poultry industry. Video Abstract
Keywords	Gut microbiota ; Maternal microbial transmission ; H9N2 avian influenza virus ; Disease resistance ; Microbial ecology ; QR100-130
Subject code	900
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis

Hongyue Xia / Xibao Li / Wenliang Zhao / Shuran Jia / Xiaoqing Zhang / David M. Irwin / Shuyi Zhang

BioMed Research International, Vol

2020 Volume 2020

Abstract: Purpose. We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this ... ...

Abstract	Purpose. We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. Methods. Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms. Results. Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified. Conclusion. Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the ...
Keywords	Medicine ; R
Subject code	572
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish

Yang, Liandong / David M. Irwin / Shunping He

Gene. 2015 May 01, v. 561

2015

Abstract: The molecular genetic basis of teleost phenotypic diversity remains poorly understood, despite the increasing availability of genome and transcriptome data. Changes in gene expression, resulting from regulatory mutations, contribute to many or even most ... ...

Abstract	The molecular genetic basis of teleost phenotypic diversity remains poorly understood, despite the increasing availability of genome and transcriptome data. Changes in gene expression, resulting from regulatory mutations, contribute to many or even most phenotypic innovations. In this study, we performed comparative genomic analyses to identify 44 Conserved Teleost-Specific MicroRNAs (CTSMs). An analysis of the sequences of CTSMs demonstrated that their sequence variability is significantly higher than that of Evolutionarily Conserved microRNAs (ECs â microRNAs conserved throughout vertebrates), and that this difference primarily results from variation in the loop regions. We computationally predicted target genes for CTSMs and found that the targets of CTSMs show significantly lower SNP density compared with targets of ECs as well as non-targets of CTSMs. The temporal expression profile of targets of CTSMs obtained from RNA-seq data revealed that the targets of CTSMs are specifically enriched in early-stage embryos and exhibit a broader expression spectrum. Finally, functional enrichment analysis (GO and KEGG) indicated that the targets of CTSMs play diverse functional roles, with a significantly enriched category being the âimmune responseâ. Our study provides the first systematic identification and characterization of conserved teleost-specific microRNAs and their targets and presents valuable foundation for a better understanding the genomic basis for the diversification of teleosts.
Keywords	Danio rerio ; gene expression regulation ; genes ; genetic variation ; immune response ; microRNA ; phenotype ; phenotypic variation ; sequence analysis ; single nucleotide polymorphism ; transcriptome ; vertebrates
Language	English
Dates of publication	2015-0501
Size	p. 181-189.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2015.02.055
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Differences in the gut microbiomes of dogs and wolves

Yuting Liu / Bo Liu / Chengwu Liu / Yumiao Hu / Chang Liu / Xiaoping Li / Xibao Li / Xiaoshuang Zhang / David M. Irwin / Zhiqiang Wu / Zeliang Chen / Qi Jin / Shuyi Zhang

BMC Veterinary Research, Vol 17, Iss 1, Pp 1-

roles of antibiotics and starch

2021 Volume 8

Abstract: Abstract Background Dogs are domesticated wolves. Change of living environment, such as diet and veterinary care may affect the gut bacterial flora of dogs. The aim of this study was to assess the gut bacterial diversity and function in dogs compared ... ...

Abstract	Abstract Background Dogs are domesticated wolves. Change of living environment, such as diet and veterinary care may affect the gut bacterial flora of dogs. The aim of this study was to assess the gut bacterial diversity and function in dogs compared with captive wolves. We surveyed the gut bacterial diversity of 27 domestic dogs, which were fed commercial dog food, and 31 wolves, which were fed uncooked meat, by 16S rRNA sequencing. In addition, we collected fecal samples from 5 dogs and 5 wolves for shotgun metagenomic sequencing to explore changes in the functions of their gut microbiome. Results Differences in the abundance of core bacterial genera were observed between dogs and wolves. Together with shotgun metagenomics, the gut microbiome of dogs was found to be enriched in bacteria resistant to clinical drugs (P < 0.001), while wolves were enriched in bacteria resistant to antibiotics used in livestock (P < 0.001). In addition, a higher abundance of putative α-amylase genes (P < 0.05; P < 0.01) was observed in the dog samples. Conclusions Living environment of dogs and domestic wolves has led to increased numbers of bacteria with antibiotic resistance genes, with exposure to antibiotics through direct and indirect methods. In addition, the living environment of dogs has allowed the adaptation of their microbiota to a starch-rich diet. These observations align with a domestic lifestyle for domestic dogs and captive wolves, which might have consequences for public health.
Keywords	Dog ; Wolf ; Gut bacteria ; Antibiotic ; Public health ; Veterinary medicine ; SF600-1100
Subject code	630
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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