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Journal articles on the topic 'Gene family expansions'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Janoušek, Václav, Robert C. Karn, and Christina M. Laukaitis. "The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family." BMC Evolutionary Biology 13, no. 1 (2013): 107. http://dx.doi.org/10.1186/1471-2148-13-107.

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2

Liebeskind, Benjamin J., David M. Hillis, and Harold H. Zakon. "Convergence of ion channel genome content in early animal evolution." Proceedings of the National Academy of Sciences 112, no. 8 (2015): E846—E851. http://dx.doi.org/10.1073/pnas.1501195112.

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Multicellularity has evolved multiple times, but animals are the only multicellular lineage with nervous systems. This fact implies that the origin of nervous systems was an unlikely event, yet recent comparisons among extant taxa suggest that animal nervous systems may have evolved multiple times independently. Here, we use ancestral gene content reconstruction to track the timing of gene family expansions for the major families of ion-channel proteins that drive nervous system function. We find that animals with nervous systems have broadly similar complements of ion-channel types but that t

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3

Chattopadhyay, Balaji, Kritika M. Garg, Rajasri Ray, Ian H. Mendenhall, and Frank E. Rheindt. "Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats." Genome Biology and Evolution 12, no. 4 (2020): 259–72. http://dx.doi.org/10.1093/gbe/evaa030.

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Abstract Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as compared with other bats (e.g., loss of ec

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4

Ames, Ryan M., Daniel Money, and Simon C. Lovell. "Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions." PLoS ONE 9, no. 6 (2014): e99480. http://dx.doi.org/10.1371/journal.pone.0099480.

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5

Chattopadhyay, Balaji, Kritika M. Garg, Rajasri Ray, Ian H. Mendenhall, Frank E. Rheindt, and Federico Hoffmann. "Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats." Genome Biology and Evolution 12, no. 4 (2020): 259–72. https://doi.org/10.5281/zenodo.13471722.

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(Uploaded by Plazi for the Bat Literature Project) Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as

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6

Chattopadhyay, Balaji, Kritika M. Garg, Rajasri Ray, Ian H. Mendenhall, Frank E. Rheindt, and Federico Hoffmann. "Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats." Genome Biology and Evolution 12, no. 4 (2020): 259–72. https://doi.org/10.5281/zenodo.13471722.

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(Uploaded by Plazi for the Bat Literature Project) Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as

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7

Chattopadhyay, Balaji, Kritika M. Garg, Rajasri Ray, Ian H. Mendenhall, Frank E. Rheindt, and Federico Hoffmann. "Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats." Genome Biology and Evolution 12, no. 4 (2020): 259–72. https://doi.org/10.5281/zenodo.13471722.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as

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8

Chattopadhyay, Balaji, Kritika M. Garg, Rajasri Ray, Ian H. Mendenhall, Frank E. Rheindt, and Federico Hoffmann. "Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats." Genome Biology and Evolution 12, no. 4 (2020): 259–72. https://doi.org/10.5281/zenodo.13471722.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as

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9

Chattopadhyay, Balaji, Kritika M. Garg, Rajasri Ray, Ian H. Mendenhall, Frank E. Rheindt, and Federico Hoffmann. "Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats." Genome Biology and Evolution 12, no. 4 (2020): 259–72. https://doi.org/10.5281/zenodo.13471722.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as

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10

Que, Feng, Qingnan Liu, Ruofei Zha, Aisheng Xiong, and Qiang Wei. "Genome-Wide Identification, Expansion, and Evolution Analysis of Homeobox Gene Family Reveals TALE Genes Important for Secondary Cell Wall Biosynthesis in Moso Bamboo (Phyllostachys edulis)." International Journal of Molecular Sciences 23, no. 8 (2022): 4112. http://dx.doi.org/10.3390/ijms23084112.

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The TALE gene family is a subfamily of the homeobox gene family and has been implicated in regulating plant secondary growth. However, reports about the evolutionary history and function of the TALE gene family in bamboo are limited. Here, the homeobox gene families of moso bamboo Olyra latifolia and Bonia amplexicaulis were identified and compared. Many duplication events and obvious expansions were found in the TALE family of woody bamboo. PhTALEs were found to have high syntenies with TALE genes in rice. Through gene co-expression analysis and quantitative real-time PCR analysis, the candid

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11

Horn, Kevin M., and Frank E. Anderson. "Spiralian Genomes Reveal Gene Family Expansions Associated with Adaptation to Freshwater." Journal of Molecular Evolution 88, no. 5 (2020): 463–72. http://dx.doi.org/10.1007/s00239-020-09949-x.

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12

Duncan, Rebecca P., Honglin Feng, Douglas M. Nguyen, and Alex C. C. Wilson. "Gene Family Expansions in Aphids Maintained by Endosymbiotic and Nonsymbiotic Traits." Genome Biology and Evolution 8, no. 3 (2016): 753–64. http://dx.doi.org/10.1093/gbe/evw020.

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13

Wilson, Ian W., Gareth D. Weedall, Hernan Lorenzi, et al. "Genetic Diversity and Gene Family Expansions in Members of the GenusEntamoeba." Genome Biology and Evolution 11, no. 3 (2019): 688–705. http://dx.doi.org/10.1093/gbe/evz009.

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14

Tian, Jiaqi, and Lizhi Gao. "Evolutionary Dynamics and Expression Divergence of the MADS-Box Gene Family During Recent Speciation of AA-Genome Oryza Species." Plants 14, no. 3 (2025): 379. https://doi.org/10.3390/plants14030379.

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To investigate the evolutionary trajectory during the recent speciation of AA-genome Oryza species, we conducted a comprehensive analysis of the MADS-box gene family across eight Oryza species. We identified 1093 MADS-box genes in total and systematically examined their evolutionary history, gene family expansion, and expression divergence. Our results revealed that extensive lineage-specific expansions occurred in AA-genome Oryza species, which were primarily generated by proximal and tandem duplications, with a particularly notable episode in Type-I genes. Despite the significant expansion,

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15

Mahmud, Ousman, and Jessica C. Kissinger. "Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire." International Journal of Genomics 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/1707231.

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Apicomplexan protist parasites utilize host sugars transported into the parasite by sugar transporter proteins for use as an energy source. We performed a phylum-wide phylogenetic analysis of the apicomplexan sugar transporter repertoire. Phylogenetic analyses revealed six major subfamilies of apicomplexan sugar transporters. Transporters in one subfamily have undergone expansions in Piroplasma species and Gregarina niphandrodes, while other subfamilies are highly divergent and contain genes found in only one or two species. Analyses of the divergent apicomplexan subfamilies revealed their pre

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16

Borrego-Hernández, Daniel, Juan Francisco Vázquez-Costa, Raúl Domínguez-Rubio, et al. "Intermediate Repeat Expansion in the ATXN2 Gene as a Risk Factor in the ALS and FTD Spanish Population." Biomedicines 12, no. 2 (2024): 356. http://dx.doi.org/10.3390/biomedicines12020356.

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Intermediate CAG expansions in the gene ataxin-2 (ATXN2) are a known risk factor for ALS, but little is known about their role in FTD risk. Moreover, their contribution to the risk and phenotype of patients might vary in populations with different genetic backgrounds. The aim of this study was to assess the relationship of intermediate CAG expansions in ATXN2 with the risk and phenotype of ALS and FTD in the Spanish population. Repeat-primed PCR was performed in 620 ALS and 137 FTD patients in three referral centers in Spain to determine the exact number of CAG repeats. In our cohort, ≥27 CAG

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17

Luna, Saara K., and Frédéric J. J. Chain. "Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development." Genes 12, no. 10 (2021): 1628. http://dx.doi.org/10.3390/genes12101628.

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Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each

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18

Faddeeva-Vakhrusheva, Anna, Ken Kraaijeveld, Martijn F. L. Derks, et al. "Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida." BMC Genomics 18, no. 1 (2017): 493. https://doi.org/10.1186/s12864-017-3852-x.

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<strong>Background: </strong> <i>Folsomia candida</i> is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of <i>Wolbachia</i>, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.<strong>Results: </strong>We applied Pacific Bioscience sequencing and assembly to generate a reference genome for <i>F. candida</i> of 221.7 Mbp, comprising only 162 scaffolds. The c

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19

Bai, Zhiyi, Ying Lu, Honghui Hu, et al. "The First High-Quality Genome Assembly of Freshwater Pearl Mussel Sinohyriopsis cumingii: New Insights into Pearl Biomineralization." International Journal of Molecular Sciences 25, no. 6 (2024): 3146. http://dx.doi.org/10.3390/ijms25063146.

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China leads the world in freshwater pearl production, an industry in which the triangle sail mussel (Sinohyriopsis cumingii) plays a pivotal role. In this paper, we report a high-quality chromosome-level genome assembly of S. cumingii with a size of 2.90 Gb—the largest yet reported among bivalves—and 89.92% anchorage onto 19 linkage groups. The assembled genome has 37,696 protein-coding genes and 50.86% repeat elements. A comparative genomic analysis revealed expansions of 752 gene families, mostly associated with biomineralization, and 237 genes under strong positive selection. Notably, the f

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20

Legan, Andrew W., Christopher M. Jernigan, Sara E. Miller, Matthieu F. Fuchs, and Michael J. Sheehan. "Expansion and Accelerated Evolution of 9-Exon Odorant Receptors in Polistes Paper Wasps." Molecular Biology and Evolution 38, no. 9 (2021): 3832–46. http://dx.doi.org/10.1093/molbev/msab023.

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Abstract Independent origins of sociality in bees and ants are associated with independent expansions of particular odorant receptor (OR) gene subfamilies. In ants, one clade within the OR gene family, the 9-exon subfamily, has dramatically expanded. These receptors detect cuticular hydrocarbons (CHCs), key social signaling molecules in insects. It is unclear to what extent 9-exon OR subfamily expansion is associated with the independent evolution of sociality across Hymenoptera, warranting studies of taxa with independently derived social behavior. Here, we describe OR gene family evolution i

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21

Xu, Yuanfeng, Jinbin Zheng, Yanan Yang, and Zhaoxia Cui. "Genome-Wide Identification, Characterization, and Expression Analysis of DDE_Tnp_4 Family Genes in Eriocheir sinensis." Antibiotics 10, no. 12 (2021): 1430. http://dx.doi.org/10.3390/antibiotics10121430.

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DDE transposase 4 (DDE_Tnp_4) family is a large endonuclease family involved in a wide variety of biological processes. However, little information is available about this family in crustaceans. In this study, we used HMMER to identify 39 DDE_Tnp_4 family genes in Eriocheir sinensis genome, and the genes were classified into four subfamilies according to phylogenetic analysis. Gene expansions occurred among E. sinensis genome, and synteny analysis revealed that some DDE_Tnp_4 family genes were caused by tandem duplication. In addition, the expression profiles of DDE_Tnp_4 family genes in E. si

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22

Meng, Fanli, and Chengming Tian. "Gene Family Expansion during the Adaptation of Colletotrichum gloeosporioides to Woody Plants." Journal of Fungi 9, no. 12 (2023): 1185. http://dx.doi.org/10.3390/jof9121185.

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Gene gains/losses during evolution are critical for the adaptation of organisms to new environments or hosts. However, it remains unknown whether gene family expansions facilitated the adaptation of phytopathogenic fungi to woody plants. In this study, we compared the newly sequenced genome of the Colletotrichum gloeosporioides strain CFCC80308 with the genomes of two other C. gloeosporioides strains, Cg-14 and Lc-1, isolated from Persea americana and Liriodendron leaves, respectively. The genes in the expanded families, which were associated with plant surface signal recognition, encoded vari

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23

Ritschard, Elena A., Robert R. Fitak, Oleg Simakov, and Sönke Johnsen. "Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction." Proceedings of the Royal Society B: Biological Sciences 286, no. 1897 (2019): 20182929. http://dx.doi.org/10.1098/rspb.2018.2929.

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Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with c

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Fonseca, Luiz Henrique M., Alison G. Nazareno, Verônica A. Thode, Alexandre R. Zuntini, and Lúcia G. Lohmann. "Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine." PeerJ 10 (April 7, 2022): e13207. http://dx.doi.org/10.7717/peerj.13207.

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The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are respons

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25

Soanes, Darren M., Intikhab Alam, Mike Cornell, et al. "Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis." PLoS ONE 3, no. 6 (2008): e2300. http://dx.doi.org/10.1371/journal.pone.0002300.

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26

Janoušek, Václav, Christina M. Laukaitis, Alexey Yanchukov, and Robert C. Karn. "The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes." Genome Biology and Evolution 8, no. 9 (2016): 2632–50. http://dx.doi.org/10.1093/gbe/evw192.

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27

Kammerer, Robert, Martin Mansfeld, Jana Hänske, et al. "Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup." BMC Genomics 18, no. 1 (2017): 717. https://doi.org/10.5281/zenodo.13452692.

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(Uploaded by Plazi for the Bat Literature Project) Background: Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. The CEA family is composed of CEA-related cell adhesion molecules (CEACAMs) and secreted pregnancy-specific glycoproteins (PSGs). PSGs are almost exclusively expressed

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Kammerer, Robert, Martin Mansfeld, Jana Hänske, et al. "Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup." BMC Genomics 18, no. 1 (2017): 717. https://doi.org/10.5281/zenodo.13452692.

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(Uploaded by Plazi for the Bat Literature Project) Background: Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. The CEA family is composed of CEA-related cell adhesion molecules (CEACAMs) and secreted pregnancy-specific glycoproteins (PSGs). PSGs are almost exclusively expressed

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29

Kammerer, Robert, Martin Mansfeld, Jana Hänske, et al. "Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup." BMC Genomics 18, no. 1 (2017): 717. https://doi.org/10.5281/zenodo.13452692.

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(Uploaded by Plazi for the Bat Literature Project) Background: Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. The CEA family is composed of CEA-related cell adhesion molecules (CEACAMs) and secreted pregnancy-specific glycoproteins (PSGs). PSGs are almost exclusively expressed

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30

Kammerer, Robert, Martin Mansfeld, Jana Hänske, et al. "Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup." BMC Genomics 18, no. 1 (2017): 717. https://doi.org/10.5281/zenodo.13452692.

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(Uploaded by Plazi for the Bat Literature Project) Background: Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. The CEA family is composed of CEA-related cell adhesion molecules (CEACAMs) and secreted pregnancy-specific glycoproteins (PSGs). PSGs are almost exclusively expressed

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31

Kammerer, Robert, Martin Mansfeld, Jana Hänske, et al. "Recent expansion and adaptive evolution of the carcinoembryonic antigen family in bats of the Yangochiroptera subgroup." BMC Genomics 18, no. 1 (2017): 717. https://doi.org/10.5281/zenodo.13452692.

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(Uploaded by Plazi for the Bat Literature Project) Background: Expansions of gene families are predictive for ongoing genetic adaptation to environmental cues. We describe such an expansion of the carcinoembryonic antigen (CEA) gene family in certain bat families. Members of the CEA family in humans and mice are exploited as cellular receptors by a number of pathogens, possibly due to their function in immunity and reproduction. The CEA family is composed of CEA-related cell adhesion molecules (CEACAMs) and secreted pregnancy-specific glycoproteins (PSGs). PSGs are almost exclusively expressed

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32

Souza, Paulo Victor Sgobbi de, Wladimir Bocca Vieira de Rezende Pinto, and Acary Souza Bulle Oliveira. "C9orf72-related disorders: expanding the clinical and genetic spectrum of neurodegenerative diseases." Arquivos de Neuro-Psiquiatria 73, no. 3 (2015): 246–56. http://dx.doi.org/10.1590/0004-282x20140229.

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Neurodegenerative diseases represent a heterogeneous group of neurological conditions primarily involving dementia, motor neuron disease and movement disorders. They are mostly related to different pathophysiological processes, notably in family forms in which the clinical and genetic heterogeneity are lush. In the last decade, much knowledge has been acumulated about the genetics of neurodegenerative diseases, making it essential in cases of motor neuron disease and frontotemporal dementia the repeat expansions of C9orf72 gene. This review analyzes the main clinical, radiological and genetic

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33

Solbakken, Monica Hongrø, Kjetil Lysne Voje, Kjetill Sigurd Jakobsen, and Sissel Jentoft. "Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system." Proceedings of the Royal Society B: Biological Sciences 284, no. 1853 (2017): 20162810. http://dx.doi.org/10.1098/rspb.2016.2810.

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Host-intrinsic factors as well as environmental changes are known to be strong evolutionary drivers defining the genetic foundation of immunity. Using a novel set of teleost genomes and a time-calibrated phylogeny, we here investigate the family of Toll-like receptor ( TLR ) genes and address the underlying evolutionary processes shaping the diversity of the first-line defence. Our findings reveal remarkable flexibility within the evolutionary design of teleost innate immunity characterized by prominent TLR gene losses and expansions. In the order of Gadiformes, expansions correlate with the l

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34

Bentkowski, Piotr, and Jacek Radwan. "Mating preferences can drive expansion or contraction of major histocompatibility complex gene family." Proceedings of the Royal Society B: Biological Sciences 287, no. 1921 (2020): 20192706. http://dx.doi.org/10.1098/rspb.2019.2706.

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Major histocompatibility complex (MHC)-based mating rules can evolve as a way to avoid inbreeding or to increase offspring immune competence. While the role of mating preference in shaping the MHC diversity in vertebrates has been acknowledged, its impact on individual MHC diversity has not been considered. Here, we use computer simulations to investigate how simple mating rules favouring MHC-dissimilar partners affect the evolution of the number of MHC variants in individual genomes, accompanying selection for resistance to parasites. We showed that the effect of such preferences could someti

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35

Morello, Giovanna, Giulia Gentile, Rossella Spataro, et al. "Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family." Journal of Personalized Medicine 10, no. 4 (2020): 262. http://dx.doi.org/10.3390/jpm10040262.

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Background: Repeat expansions in the spinocerebellar ataxia type 1 (SCA1) gene ATXN1 increases the risk for amyotrophic lateral sclerosis (ALS), supporting a relationship between these disorders. We recently reported the co-existence, in a large SCA1 family, of a clinically definite ALS individual bearing an intermediate ATXN1 expansion and SCA1 patients with a full expansion, some of which manifested signs of lower motor neuron involvement. Methods: In this study, we employed a systems biology approach that integrated multiple genomic analyses of the ALS patient and some SCA1 family members.

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36

Kahlon, Parvinderdeep S., and Remco Stam. "Polymorphisms in plants to restrict losses to pathogens: From gene family expansions to complex network evolution." Current Opinion in Plant Biology 62 (August 2021): 102040. http://dx.doi.org/10.1016/j.pbi.2021.102040.

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37

Lin, Yan, Jia-Yong Zheng, Yan-Hui Jin, Yan-Chen Xie, and Zi-Bing Jin. "Trinucleotide expansions in the SCA7 gene in a large family with spinocerebellar ataxia and craniocervical dystonia." Neuroscience Letters 434, no. 2 (2008): 230–33. http://dx.doi.org/10.1016/j.neulet.2008.01.077.

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38

Holland, Stephen J., Lesley M. Berghuis, Justin J. King, et al. "Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys." Proceedings of the National Academy of Sciences 115, no. 14 (2018): E3211—E3220. http://dx.doi.org/10.1073/pnas.1720871115.

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Cytidine deaminases of the AID/APOBEC family catalyze C-to-U nucleotide transitions in mRNA or DNA. Members of the APOBEC3 branch are involved in antiviral defense, whereas AID contributes to diversification of antibody repertoires in jawed vertebrates via somatic hypermutation, gene conversion, and class switch recombination. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the generation of somatic diversity of the variable lymphocyte receptors (VLRs). Expression studies linked CDA1 and CDA2 genes to the assembly of VLRA/C genes in T-like

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Denecke, Shane M., Olympia Driva, Hang Ngoc Bao Luong, et al. "The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods." Genome Biology and Evolution 12, no. 8 (2020): 1429–39. http://dx.doi.org/10.1093/gbe/evaa153.

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Abstract The solute carrier (SLC) transporter superfamily comprises an ancient and ubiquitous group of proteins capable of translocating a range of nutrients, endogenous molecules, and xenobiotics. Although the group has been the subject of intense investigation in both bacteria and mammals, its systematic identification in arthropods has not yet been undertaken. Here, we present a genome-wide identification of all 66 human SLC families in 174 arthropod species. A pipeline (SLC_id) was constructed to identify and group SLCs using a combination of hidden Markov model and BLAST searches followed

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Lu, Kunpeng, Chengyu Zhan, Jianghong Shen, et al. "Characterization of Spectrin Family Genes and Their Evolutionary Roles in Domestication and Breeding of the Silkworm Bombyx mori." Insects 16, no. 6 (2025): 556. https://doi.org/10.3390/insects16060556.

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The spectrin family genes play critical roles in cytoskeletal organization and cellular integrity, yet their evolutionary and functional significance in non-classical model organisms remains poorly explored. Here, we systematically identified and characterized spectrin family genes in the silkworm Bombyx mori. Genome-wide analysis identified 17 predicted spectrin genes, which were integrated into eight optimized members through transcriptome-guided structural refinement. Multi-species genomic analysis revealed 8, 23, and 24 spectrin family genes in Drosophila melanogaster, Mus musculus, and Ho

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Ma, Xiaoya, Shasha Liang, Aixin Liang, Hossam Eldin Rushdi, and Tingxian Deng. "Evolutionary Analysis of OAT Gene Family in River and Swamp Buffalo: Potential Role of SLCO3A1 Gene in Milk Performance." Genes 12, no. 9 (2021): 1394. http://dx.doi.org/10.3390/genes12091394.

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The organic anion transporter (OAT) family is the subfamily of the solute carrier (SLC) superfamily, which plays a vital role in regulating essential nutrients in milk. However, little is known about the members’ identification, evolutionary basis, and function characteristics of OAT genes associated with milk performance in buffalo. Comparative genomic analyses were performed to identify the potential role of buffalo OAT genes in milk performance in this study. The results showed that a total of 10 and 7 OAT genes were identified in river buffalo and swamp buffalo, respectively. These sequenc

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Li, Qi, Yifang Peng, Tao Zhao, et al. "Phylogeny and Functional Differentiation of the Terpene Synthase Gene Family in Angiosperms with Emphasis on Rosa chinensis." International Journal of Molecular Sciences 26, no. 5 (2025): 2113. https://doi.org/10.3390/ijms26052113.

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Terpenes are pivotal for plant growth, development, and adaptation to environmental stresses. With the advent of extensive genomic data and sophisticated bioinformatics tools, new insights into the evolutionary dynamics and functional diversification of terpene synthases (TPSs) have emerged. Despite genome-wide identifications of the TPS family in certain species, comprehensive cross-species analyses remain scarce. In this study, we conducted a genome-wide identification and subgroup classification of TPS families across 115 angiosperms with available genomic sequences. Our phylogenomic synten

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Tang, Lixin, Shiwu Dong, and Xiumei Xing. "Comparative Genomics Reveal Phylogenetic Relationship and Chromosomal Evolutionary Events of Eight Cervidae Species." Animals 14, no. 7 (2024): 1063. http://dx.doi.org/10.3390/ani14071063.

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Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the singl

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Fijarczyk, Anna, Louis Bernier, Monique L. Sakalidis, Carmen M. Medina-Mora, and Ilga Porth. "Independent Evolution Has Led to Distinct Genomic Signatures in Dutch Elm Disease-Causing Fungi and Other Vascular Wilts-Causing Fungal Pathogens." Journal of Fungi 9, no. 1 (2022): 2. http://dx.doi.org/10.3390/jof9010002.

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Vascular wilts are important diseases caused by plant pathogenic fungi that result in the rapid death of their plant hosts. This is due to a systemic defense mechanism whereby the plant induces the compartmentalization of the infected vascular system in order to reduce the propagation of the fungus. The ascomycete class Sordariomycetes contains several species that cause vascular wilts in diverse plant hosts, and they can be classified into four taxonomic orders. The genetic mechanisms of pathogenesis have already been investigated in Fusarium and Verticillium species, but they have not yet be

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Coppola, Ugo, and Joshua S. Waxman. "Origin and evolutionary landscape of Nr2f transcription factors across Metazoa." PLOS ONE 16, no. 11 (2021): e0254282. http://dx.doi.org/10.1371/journal.pone.0254282.

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Background Nuclear Receptor Subfamily 2 Group F (Nr2f) orphan nuclear hormone transcription factors (TFs) are fundamental regulators of many developmental processes in invertebrates and vertebrates. Despite the importance of these TFs throughout metazoan development, previous work has not clearly outlined their evolutionary history. Results We integrated molecular phylogeny with comparisons of intron/exon structure, domain architecture, and syntenic conservation to define critical evolutionary events that distinguish the Nr2f gene family in Metazoa. Our data indicate that a single ancestral eu

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Takeuchi, Takeshi, Yoshihiko Suzuki, Eiichi Shoguchi, et al. "Nearly T2T, phased genome assemblies of corals reveal haplotype diversity and the evolutionary process of gene expansion." DNA Research, July 1, 2025. https://doi.org/10.1093/dnares/dsaf017.

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Abstract Gene family expansion illustrates a critical aspect of evolutionary adaptation. However, the mechanisms by which gene family expansions emerge and are maintained in the genome remain unclear. Here, we report de novo, nearly telomere-to-telomere (T2T), haplotype-phased genome assemblies of two coral species, Acropora tenuis and A. digitifera. By comparing haplotypes within a single individual and across species, we identified genomic regions spanning several megabases with highly disordered gene arrangements, termed non-syntenic regions (nSRs). In these nSRs, there are clusters of gene

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Stanley, Taylor R., Karen S. Kim Guisbert, Sabrina M. Perez, et al. "Stress response gene family expansions correlate with invasive potential in teleost fish." Journal of Experimental Biology 225, Suppl_1 (2022). http://dx.doi.org/10.1242/jeb.243263.

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ABSTRACT The bluegill sunfish Lepomis macrochirus and the closely related redear sunfish Lepomis microlophus have important ecological and recreational value and are widely used for research and aquaculture. While both species have been introduced outside of their native ranges, only the bluegill is considered invasive. Here, we report de novo transcriptome assemblies for these fish as a resource for sunfish biology. Comparative analyses of the transcriptomes revealed an unexpected, bluegill-specific expansion in the HSP70 and HSP90 molecular chaperone gene families. These expansions were not

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Breeschoten, Thijmen, Corné F. H. van der Linden, Vera I. D. Ros, M. Eric Schranz, and Sabrina Simon. "Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera?" Genome Biology and Evolution 14, no. 1 (2021). http://dx.doi.org/10.1093/gbe/evab283.

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Abstract Evolutionary expansions and contractions of gene families are often correlated with key innovations and/or ecological characteristics. In butterflies and moths (Lepidoptera), expansions of gene families involved in detoxification of plant specialized metabolites are hypothesized to facilitate a polyphagous feeding style. However, analyses supporting this hypothesis are mostly based on a limited number of lepidopteran species. We applied a phylogenomics approach, using 37 lepidopteran genomes, to analyze if gene family evolution (gene gain and loss) is associated with the evolution of

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Latorre-Estivalis, Jose Manuel, Francisca C. Almeida, Gina Pontes, Hernán Dopazo, Romina B. Barrozo, and Marcelo Gustavo Lorenzo. "Evolution of the Insect PPK Gene Family." Genome Biology and Evolution 13, no. 9 (2021). http://dx.doi.org/10.1093/gbe/evab185.

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Abstract Insect pickpocket (PPK) receptors mediate diverse functions, among them the detection of mechano- and chemo-sensory stimuli. Notwithstanding their relevance, studies on their evolution only focused on Drosophila. We have analyzed the genomes of 26 species of eight orders including holometabolous and hemimetabolous insects (Blattodea, Orthoptera, Hemiptera, Phthiraptera, Hymenoptera, Lepidoptera, Coleoptera, and Diptera), to characterize the evolution of this gene family. PPKs were detected in all genomes analyzed, with 578 genes distributed in seven subfamilies. According to our phylo

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Murray, Connor S., and Alan O. Bergland. "Patterns of Gene Family Evolution and Selection Across Daphnia." Ecology and Evolution 15, no. 5 (2025). https://doi.org/10.1002/ece3.71453.

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ABSTRACTGene family expansion underlies a host of biological innovations across the tree of life. Understanding why specific gene families expand or contract requires comparative genomic investigations clarifying further how species adapt in the wild. This study investigates the gene family change dynamics within several species of Daphnia, a group of freshwater microcrustaceans that are insightful model systems for evolutionary genetics' research. We employ comparative genomics approaches to understand the forces driving gene evolution and draw upon candidate gene families that change gene nu

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