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1.
Mol Genet Genomics ; 295(1): 55-66, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31446488

RESUMO

Cotton is the most important natural fiber used in textiles. Breeding for "three-lines", i.e., cytoplasmic male sterility (CMS)-based sterile (A), maintainer (B), and restorer (R) line, is a promising approach to harness hybrid vigor in cotton. Pentatricopeptide repeat (PPR) protein-encoding genes play an important role in plant growth and development including restoration of CMS plants to male fertility. However, PPRs, especially those contributing to CMS and fiber development, remain largely unknown in cotton. In this study, a genome-wide identification and characterization of PPR gene family in four Gossypium species with genome sequences (G. arboreum, G. raimondii, G. hirsutum, and G. barbadense) were performed, and expressed PPR genes in developing floral buds, ovules, and fibers were compared to identify possible PPRs related to CMS restoration and fiber development. A total of 539, 558, 1032, and 1055 PPRs were predicted in the above four species, respectively, which were further mapped to chromosomes for a synteny analysis. Through an RNA-seq analysis, 86% (882) PPRs were expressed in flowering buds of upland cotton (G. hirsutum); however, only 11 and 6 were differentially expressed (DE) between restorer R and its near-isogenic (NI) B and between R and its NI A line, respectively. Another RNA-seq analysis identified the expression of only 54% (556) PPRs in 0 and 3 day(s) post-anthesis (DPA) ovules and 24% (247) PPRs in 10 DPA fibers; however, only 59, 6, and 27 PPRs were DE in 0 and 3 DPA ovules, and 10 DPA fibers between two backcross inbred lines (BILs) with differing fiber length, respectively. Only 2 PPRs were DE between Xuzhou 142 and its fiberless and fuzzless mutant. Quantitative RT-PCR analysis confirmed the validity of the RNA-seq results for the gene expression pattern. Therefore, only a very small number of PPRs may be associated with fertility restoration of CMS and genetic differences in fiber initiation and elongation. These results lay a foundation for understanding the roles of PPR genes in cotton, and will be useful in the prioritization of candidate PPR gene functional validation for cotton CMS restoration and fiber development.


Assuntos
Proteínas de Arabidopsis/genética , Flores/genética , Regulação da Expressão Gênica de Plantas/genética , Gossypium/genética , Óvulo Vegetal/genética , Proteínas de Plantas/genética , Mapeamento Cromossômico/métodos , Fibra de Algodão , Perfilação da Expressão Gênica/métodos , Estudo de Associação Genômica Ampla/métodos , Sintenia/genética
2.
BMC Bioinformatics ; 20(Suppl 20): 635, 2019 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-31842736

RESUMO

BACKGROUND: A basic tool for studying the polyploidization history of a genome, especially in plants, is the distribution of duplicate gene similarities in syntenically aligned regions of a genome. This distribution can usually be decomposed into two or more components identifiable by peaks, or local maxima, each representing a different polyploidization event. The distributions may be generated by means of a discrete time branching process, followed by a sequence divergence model. The branching process, as well as the inference of fractionation rates based on it, requires knowledge of the ploidy level of each event, which cannot be directly inferred from the pair similarity distribution. RESULTS: For a sequence of two events of unknown ploidy, either tetraploid, giving rise to whole genome doubling (WGD), or hexaploid, giving rise to whole genome tripling (WGT), we base our analysis on triples of similar genes. We calculate the probability of the four triplet types with origins in one or the other event, or both, and impose a mutational model so that the distribution resembles the original data. Using a ML transition point in the similarities between the two events as a discriminator for the hypothesized origin of each similarity, we calculate the predicted number of triplets of each type for each model combining WGT and/or WGD. This yields a predicted profile of triplet types for each model. We compare the observed and predicted triplet profiles for each model to confirm the polyploidization history of durian, poplar and cabbage. CONCLUSIONS: We have developed a way of inferring the ploidy of up to three successive WGD and/or WGT events by estimating the time of origin of each of the similarities in triples of genes. This may be generalized to a larger number of events and to higher ploidies.


Assuntos
Genoma de Planta , Poliploidia , Sintenia/genética , Bombacaceae/genética , Brassicaceae/genética , Genes de Plantas , Modelos Genéticos , Mutação/genética , Populus/genética
3.
DNA Cell Biol ; 38(11): 1257-1268, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31553224

RESUMO

Recent analyses suggest bacterial and/or mitochondrion-like ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond common ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.


Assuntos
Cloroplastos/genética , Evolução Molecular , Mitocôndrias/genética , Mimetismo Molecular/fisiologia , Phycodnaviridae/genética , Sintenia/genética , Imunidade Adaptativa/genética , Genoma Mitocondrial/genética , Genoma Viral/genética , Interações Hospedeiro-Patógeno/genética , Interações Hospedeiro-Patógeno/imunologia , Evasão da Resposta Imune/genética , Organelas/genética , Filogenia , Análise de Sequência de DNA
4.
Int J Mol Sci ; 20(18)2019 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-31514326

RESUMO

In mammals, leptin and tumor-necrosis factor (TNF) are prominent interacting adipokines mediating appetite control and insulin sensitivity. While TNF pleiotropically functions in immune defense and cell survival, leptin is largely confined to signaling energy stores in adipocytes. Knowledge about the function of avian leptin and TNF is limited and they are absent or lowly expressed in adipose, respectively. Employing radiation-hybrid mapping and FISH-TSA, we mapped TNF and its syntenic genes to chicken chromosome 16 within the major histocompatibility complex (MHC) region. This mapping position suggests that avian TNF has a role in regulating immune response. To test its possible interaction with leptin within the immune system and beyond, we compared the transcription patterns of TNF, leptin and their cognate receptors obtained by meta-analysis of GenBank RNA-seq data. While expression of leptin and its receptor (LEPR) were detected in the brain and digestive tract, TNF and its receptor mRNAs were primarily found in viral-infected and LPS-treated leukocytes. We confirmed leptin expression in the duodenum by immunohistochemistry staining. Altogether, we suggest that whereas leptin and TNF interact as adipokines in mammals, in birds, they have distinct roles. Thus, the interaction between leptin and TNF may be unique to mammals.


Assuntos
Galinhas/genética , Mapeamento Cromossômico , Digestão , Regulação da Expressão Gênica , Leptina/genética , Mamíferos/genética , Transdução de Sinais , Fator de Necrose Tumoral alfa/metabolismo , Animais , Linhagem Celular , Galinhas/metabolismo , Duodeno/metabolismo , Feminino , Leptina/metabolismo , Metáfase/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Mapeamento de Híbridos Radioativos , Receptores para Leptina/metabolismo , Receptores do Fator de Necrose Tumoral/genética , Receptores do Fator de Necrose Tumoral/metabolismo , Sintenia/genética , Fator de Necrose Tumoral alfa/genética
5.
Genome Biol ; 20(1): 187, 2019 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-31477173

RESUMO

BACKGROUND: Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. RESULTS: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. CONCLUSIONS: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.


Assuntos
Genoma de Inseto , Genômica , Insetos Vetores/genética , Trypanosoma/parasitologia , Moscas Tsé-Tsé/genética , Animais , Elementos de DNA Transponíveis/genética , Drosophila melanogaster/genética , Feminino , Regulação da Expressão Gênica , Genes de Insetos , Genes Ligados ao Cromossomo X , Geografia , Proteínas de Insetos/genética , Masculino , Mutagênese Insercional/genética , Filogenia , Sequências Repetitivas de Ácido Nucleico/genética , Homologia de Sequência de Aminoácidos , Sintenia/genética , Wolbachia/genética
6.
BMC Bioinformatics ; 20(1): 440, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31455236

RESUMO

BACKGROUND: With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic regions of the genome. If some of these genes survive across speciations, then extant organisms will contain a patchwork of genes whose ancestors first appeared at different times. Standard phylostratigraphy, the technique of partitioning genes by their age, is based solely on protein similarity algorithms. However, this approach relies on negative evidence ─ a failure to detect a homolog of a query gene. An alternative approach is to limit the search for homologs to syntenic regions. Then, genes can be positively identified as de novo orphans by tracing them to non-coding sequences in related species. RESULTS: We have developed a synteny-based pipeline in the R framework. Fagin determines the genomic context of each query gene in a focal species compared to homologous sequence in target species. We tested the fagin pipeline on two focal species, Arabidopsis thaliana (plus four target species in Brassicaseae) and Saccharomyces cerevisiae (plus six target species in Saccharomyces). Using microsynteny maps, fagin classified the homology relationship of each query gene against each target genome into three main classes, and further subclasses: AAic (has a coding syntenic homolog), NTic (has a non-coding syntenic homolog), and Unknown (has no detected syntenic homolog). fagin inferred over half the "Unknown" A. thaliana query genes, and about 20% for S. cerevisiae, as lacking a syntenic homolog because of local indels or scrambled synteny. CONCLUSIONS: fagin augments standard phylostratigraphy, and extends synteny-based phylostratigraphy with an automated, customizable, and detailed contextual analysis. By comparing synteny-based phylostrata to standard phylostrata, fagin systematically identifies those orphans and lineage-specific genes that are well-supported to have originated de novo. Analyzing within-species genomes should distinguish orphan genes that may have originated through rapid divergence from de novo orphans. Fagin also delineates whether a gene has no syntenic homolog because of technical or biological reasons. These analyses indicate that some orphans may be associated with regions of high genomic perturbation.


Assuntos
Arabidopsis/genética , Genes , Filogenia , Saccharomyces cerevisiae/genética , Software , Sintenia/genética , Sequência de Bases , Genoma , Homologia de Sequência
7.
Int J Mol Sci ; 20(13)2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31277435

RESUMO

High-intensity ultraviolet-B (UV-B) irradiation is a complex abiotic stressor resulting in excessive light exposure, heat, and dehydration, thereby affecting crop yields. In the present study, we identified quantitative trait loci (QTLs) for resistance to high-intensity UV-B irradiation in soybean (Glycine max [L.]). We used a genotyping-by-sequencing approach using an F6 recombinant inbred line (RIL) population derived from a cross between Cheongja 3 (UV-B sensitive) and Buseok (UV-B resistant). We evaluated the degree of leaf damage by high-intensity UV-B radiation in the RIL population and identified four QTLs, UVBR12-1, 6-1, 10-1, and 14-1, for UV-B stress resistance, together explaining 20% of the observed phenotypic variation. The genomic regions containing UVBR12-1 and UVBR6-1 and their syntenic blocks included other known biotic and abiotic stress-related QTLs. The QTL with the highest logarithm of odds (LOD) score of 3.76 was UVBR12-1 on Chromosome 12, containing two genes encoding spectrin beta chain, brain (SPTBN, Glyma.12g088600) and bZIP transcription factor21/TGACG motif-binding 9 (bZIP TF21/TGA9, Glyma.12g088700). Their amino acid sequences did not differ between the mapping parents, but both genes were significantly upregulated by UV-B stress in Buseok but not in Cheongja 3. Among five genes in UVBR6-1 on Chromosome 6, Glyma.06g319700 (encoding a leucine-rich repeat family protein) had two nonsynonymous single nucleotide polymorphisms differentiating the parental lines. Our findings offer powerful genetic resources for efficient and precise breeding programs aimed at developing resistant soybean cultivars to multiple stresses. Furthermore, functional validation of the candidate genes will improve our understanding of UV-B stress defense mechanisms.


Assuntos
Locos de Características Quantitativas/genética , Tolerância a Radiação/genética , Soja/genética , Soja/efeitos da radiação , Raios Ultravioleta , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Cruzamentos Genéticos , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Ligação Genética , Genoma de Planta , Endogamia , Escore Lod , Fenótipo , Folhas de Planta/efeitos da radiação , Polimorfismo de Nucleotídeo Único/genética , Estresse Fisiológico/genética , Estresse Fisiológico/efeitos da radiação , Sintenia/genética
8.
Gen Comp Endocrinol ; 282: 113219, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31299224

RESUMO

The melanocortin-4 receptor (MC4R) acts as a member of G-protein coupled receptors and participate in food intake and energy expenditure. Melanocortin 2 receptor accessory protein 2 (MRAP2) plays a critical role in regulating MC4R signaling in mammals and zebrafish. However, evidence on their interaction in other teleost species remains elusive. Here, we cloned and assessed the evolutionary aspect and pharmacological modulation of MRAP2 on MC4R signaling in Nile tilapia (Oreochromis niloticus). Tissue distribution analysis of tmc4r and tmrap2 confirmed their co-expression in the brain region. tMRAP2 protein could form antiparallel homo-dimer and directly interacted with tMC4R in vitro and presence of tMRAP2 led to the reduction of agonist response and surface expression of tMC4R. Overall, our findings provide a comparative overview on the evolutionary conservation, genomic distribution, tissue-specific expression and pharmacological profile of the MC4R and MRAP2 in another non-mammalian teleost.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Ciclídeos/metabolismo , Receptor Tipo 4 de Melanocortina/metabolismo , Sequência de Aminoácidos , Animais , Membrana Celular/metabolismo , Sequência Conservada , Evolução Molecular , Células HEK293 , Humanos , Filogenia , Ligação Proteica , Receptor Tipo 4 de Melanocortina/química , Receptor Tipo 4 de Melanocortina/genética , Transdução de Sinais , Sintenia/genética , Distribuição Tecidual
9.
Cells ; 8(6)2019 05 29.
Artigo em Inglês | MEDLINE | ID: mdl-31146469

RESUMO

: The accumulation of lignin in fruit has a significant negative impact on the quality of fruit-producing trees, and in particular the lignin formation stimulates the development of stone cells in pear fruit. Reactive oxygen species (ROS) are essential for lignin polymerization. However, knowledge of the RBOH family, a key enzyme in ROS metabolism, remains unknown in most fruit trees. In this study, a total of 40 RBOHs were identified from five fruit-producing trees (Pyrus bretschneideri, Prunus persica, Citrus sinensis, Vitis vinifera, and Prunus mume), and 10 of these sequences came from Pyrus bretschneideri. Multiple sequence alignments revealed that all 10 PbRBOHs contained the NADPH_Ox domain and the six alpha-helical transmembrane domains (TM-I to TM-VI). Chromosome localization and interspecies phylogenetic tree analysis showed that 10 PbRBOHs irregularly distributed on 8 chromosomes and 3 PbRBOHs (PbRBOHA, PbRBOHB, and PbRBOHD) are closely related to known lignification-related RBOHs. Furthermore, hormone response pattern analysis showed that the transcription of PbRBOHs is regulated by SA, ABA and MeJA. Reverse transcription-quantitative real-time polymerase chain reaction (qRT-PCR) and transcriptome sequencing analysis showed that PbRBOHA, PbRBOHB, and PbRBOHD accumulated high transcript abundance in pear fruit, and the transcriptional trends of PbRBOHA and PbRBOHD was consistent with the change of stone cell content during fruit development. In addition, subcellular localization revealed that PbRBOHA and PbRBOHD are distributed on the plasma membrane. Combining the changes of apoplastic superoxide (O2.-) content and spatio-temporal expression analysis, these results indicate that PbRBOHA and PbRBOHD, which are candidate genes, may play an important role in ROS metabolism during the lignification of pear stone cells. This study not only provided insight into the molecular characteristics of the RBOH family in fruit-producing trees, but also lays the foundation for studying the role of ROS in plant lignification.


Assuntos
Simulação por Computador , Frutas/genética , Genes de Plantas , Lignina/metabolismo , Família Multigênica , NADPH Oxidases/genética , Pyrus/enzimologia , Pyrus/genética , Sequência de Aminoácidos , Cromossomos de Plantas/genética , Sequência Conservada/genética , Éxons/genética , Frutas/efeitos dos fármacos , Duplicação Gênica , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Tamanho do Genoma , Íntrons/genética , NADPH Oxidases/química , NADPH Oxidases/metabolismo , Motivos de Nucleotídeos/genética , Especificidade de Órgãos/efeitos dos fármacos , Especificidade de Órgãos/genética , Filogenia , Reguladores de Crescimento de Planta/farmacologia , Regiões Promotoras Genéticas/genética , Pyrus/efeitos dos fármacos , Sintenia/genética , Árvores/enzimologia , Árvores/genética
10.
Int J Mol Sci ; 20(9)2019 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-31083458

RESUMO

To appraise how evolutionary processes, such as gene duplication and loss, influence an organism's xenobiotic sensitivity is a critical question in toxicology. Of particular importance are gene families involved in the mediation of detoxification responses, such as members of the nuclear receptor subfamily 1 group I (NR1I), the pregnane X receptor (PXR), and the constitutive androstane receptor (CAR). While documented in multiple vertebrate genomes, PXR and CAR display an intriguing gene distribution. PXR is absent in birds and reptiles, while CAR shows a tetrapod-specific occurrence. More elusive is the presence of PXR and CAR gene orthologs in early branching and ecologically-important Chondrichthyes (chimaeras, sharks and rays). Therefore, we investigated various genome projects and use them to provide the first identification and functional characterization of a Chondrichthyan PXR from the chimaera elephant shark (Callorhinchus milii, Holocephali). Additionally, we substantiate the targeted PXR gene loss in Elasmobranchii (sharks and rays). Compared to other vertebrate groups, the chimaera PXR ortholog displays a diverse expression pattern (skin and gills) and a unique activation profile by classical xenobiotic ligands. Our findings provide insights into the molecular landscape of detoxification mechanisms and suggest lineage-specific adaptations in response to xenobiotics in gnathostome evolution.


Assuntos
Elasmobrânquios/classificação , Elasmobrânquios/genética , Evolução Molecular , Redes Reguladoras de Genes , Filogenia , Receptor de Pregnano X/genética , Animais , Células COS , Genes Reporter , Inativação Metabólica/genética , Luciferases/metabolismo , Receptor de Pregnano X/metabolismo , Receptores Citoplasmáticos e Nucleares/genética , Receptores Citoplasmáticos e Nucleares/metabolismo , Sintenia/genética , Ativação Transcricional/genética
11.
Gen Comp Endocrinol ; 281: 49-57, 2019 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-31121162

RESUMO

Potassium channel subfamily K member 3 (KCNK3) has been reported to play important roles in membrane potential conduction, pulmonary hypertension and thermogenesis regulation in mammals. However, its roles remain largely unknown and scarce reports were seen in fish. In the present study, we for the first time identified two kcnk3 genes (kcnk3a and kcnk3b) from the carnivorous Northern snakehead (Channa argus) by molecular cloning and a genomic survey. Subsequently, their transcription changes in response to different feeding status were investigated. Full-length coding sequences of the kcnk3a and kcnk3b genes are 1203 and 1176 bp, encoding 400 and 391 amino acids, respectively. Multiple alignments, 3D-structure prediction and phylogenetic analysis further suggested that these kcnk3 genes may be highly conserved in vertebrates. Tissue distribution analysis by real-time PCR demonstrated that both the snakehead kcnk3s were widely transcribed in majority of the examined tissues but with different distribution patterns. In a short-term (24-h) fasting experiment, we observed that brain kcnk3a and kcnk3b genes showed totally opposite transcription patterns. In a long-term (2-week) fasting and refeeding experiment, we also observed differential change patterns for the brain kcnk3 genes. In summary, our findings suggest that the two kcnk3 genes are close while present different transcription responses to fasting and refeeding. They therefore can be potentially selected as novel target genes for improvement of production and quality of this economically important fish.


Assuntos
Jejum/fisiologia , Comportamento Alimentar , Peixes/genética , Canais de Potássio de Domínios Poros em Tandem/genética , Transcrição Genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Clonagem Molecular , DNA Complementar/genética , Genoma , Filogenia , Canais de Potássio de Domínios Poros em Tandem/química , Canais de Potássio de Domínios Poros em Tandem/metabolismo , Sintenia/genética , Distribuição Tecidual , Peixe-Zebra/genética
12.
Gen Comp Endocrinol ; 279: 196-202, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31002825

RESUMO

The gonadotropin-inhibitory hormone (GnIH) plays a negative role in the hypothalamic-pituitary-gonadal (HPG) axis by inhibiting gonadotropin secretion in vertebrates. Male pregnancy and ovoviviparous behavior are unique phenomena among vertebrates. To better understand the neuroendocrine regulatory mechanisms in ovoviviparous fish with male pregnancy, we identified the orthologous GnIH gene in the lined seahorse (Hippocampus erectus). The full-length cDNA of the GnIH precursor was 658 base pairs with an open reading frame of 528 base pairs that encoded a 175-amino acid prepro-GnIH peptide. The seahorse GnIH precursor contained two putative LPXRFamide peptides. Both seahorse LPXRFa-1 and LPXRFa-2 were found to be unique among vertebrates. The synteny blocks of GnIH gene loci were conserved in mammals and teleosts. Tissue distribution analysis revealed that seahorse GnIH mRNA was mainly expressed in the hypothalamus, with relatively high levels observed in the brood pouch. The expression patterns of seahorse GnIH during different reproductive stages and pregnancy stages were also detected, and GnIH mRNA expression was significantly reduced during the early puberty stage. In addition, GnIH mRNA expression was significantly increased during the pregnancy stage compared to non-pregnancy stages. In summary, our results reveal the existence of GnIH in ovoviviparous fish and suggest its involvement in regulation of reproductive behavior and male pregnancy in the male seahorse.


Assuntos
Gonadotropinas/genética , Hormônios Hipotalâmicos/genética , Smegmamorpha/genética , Smegmamorpha/fisiologia , Sequência de Aminoácidos , Animais , Sequência de Bases , DNA Complementar/genética , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Gonadotropinas/química , Gonadotropinas/metabolismo , Hormônios Hipotalâmicos/química , Hormônios Hipotalâmicos/metabolismo , Masculino , Filogenia , Gravidez , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reprodução , Maturidade Sexual/genética , Smegmamorpha/crescimento & desenvolvimento , Sintenia/genética , Distribuição Tecidual
13.
BMC Plant Biol ; 19(1): 161, 2019 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-31023218

RESUMO

BACKGROUND: Although the genome of Chinese white pear ('Dangshansuli') has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date. RESULTS: In this study, we identified a total of 183 NAC transcription factors (TFs) in the pear genome, among which 146 pear NAC (PbNAC) members were mapped onto 16 chromosomes, and 37 PbNAC genes were located on scaffold contigs. No PbNAC genes were mapped to chromosome 2. Based on gene structure, protein motif analysis, and topology of the phylogenetic tree, the pear PbNAC family was classified into 33 groups. By comparing and analyzing the unique NAC subgroups in Rosaceae, we identified 19 NAC subgroups specific to pear. We also found that whole-genome duplication (WGD)/segmental duplication played critical roles in the expansion of the NAC family in pear, such as the 83 PbNAC duplicated gene pairs dated back to the two WGD events. Further, we found that purifying selection was the primary force driving the evolution of PbNAC family genes. Next, we used transcriptomic data to study responses to drought and cold stresses in pear, and we found that genes in groups C2f, C72b, and C100a were related to drought and cold stress response. CONCLUSIONS: Through the phylogenetic, evolutionary, and expression analyses of the NAC gene family in Chinese white pear, we indentified 11 PbNAC TFs associated with abiotic stress in pear.


Assuntos
Regulação da Expressão Gênica de Plantas , Genoma de Planta , Estudo de Associação Genômica Ampla , Pyrus/genética , Estresse Fisiológico/genética , Fatores de Transcrição/metabolismo , Temperatura Baixa , Secas , Éxons/genética , Duplicação Gênica , Genes de Plantas , Íntrons/genética , Família Multigênica , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Domínios Proteicos , Sintenia/genética , Fatores de Transcrição/química
14.
Genes (Basel) ; 10(4)2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30939837

RESUMO

Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32⁻52), but also for the basic chromosome number (x = 5⁻9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.


Assuntos
Evolução Molecular , Genoma de Planta/genética , Cariótipo , Lupinus/genética , Aberrações Cromossômicas , Mapeamento Cromossômico , Duplicação Gênica/genética , Ligação Genética/genética , Hibridização in Situ Fluorescente , Cariotipagem , Poliploidia , Sintenia/genética
15.
Mol Phylogenet Evol ; 136: 128-137, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30946898

RESUMO

BACKGROUND: Extensive research efforts have been made to reconstruct the Tree of Life, aiming to explain the evolutionary history of life on earth. We expect the advent of next generation sequencing methods to bring us close to solving this challenge. Notwithstanding, with the accumulation of this mass of molecular data, it becomes evident that this solution is more complex and far from reach, especially among prokaryotes. One of the reasons for this is the ability of bacteria to perform horizontal gene transfer (HGT), creating substantial conflicts between different genes histories. Fortunately, evolution has equipped us with several markers with different levels of resolution, among which is synteny - the conservation of gene order along the chromosome. RESULTS: We have performed a comprehensive phylogenomic study via synteny based footprints. We build on the synteny index (SI) concept, defined in a pilot work of ours, and extend it to a systematic phylogenetic method with well defined valid regions of operations. Applying it to the EggNOG repository, divides all species into 39 clusters, agreeing with the conventional taxonomy. We show analytically that the signal of the standard phylogenetic marker, the 16S, is too faint for reliable classification. CONCLUSIONS: This work exhibits three separate yet related contributions. In terms of phylogenetics, it demonstrates quantitatively the advantage of the SI-based approach over the standard sequence based marker. Evolutionarily, the tree we produce is unique both in its specificity and broadness. Methodologically, the U-shape approach we developed, from synthetic realm, to real life and back to simulation, is novel and allow us to simulate the exact realistic conditions.


Assuntos
Filogenia , Células Procarióticas/classificação , Sintenia/genética , Sequência de Bases , Simulação por Computador , Bases de Dados Genéticas , Reprodutibilidade dos Testes
16.
Gen Comp Endocrinol ; 277: 90-103, 2019 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-30905760

RESUMO

The melanocortin-3 receptor (MC3R) is known to be involved in regulation of energy homeostasis, regulating feed efficiency and nutrient partitioning in mammals. Its physiological roles in non-mammalian vertebrates, especially economically important aquaculture species, are not well understood. Channel catfish (Ictalurus punctatus) is the main freshwater aquaculture species in North America. In this study, we characterized the channel catfish MC3R. The mc3r of channel catfish encoded a putative protein (ipMC3R) of 367 amino acids. We transfected HEK293T cells with ipMC3R plasmid for functional studies. Five agonists, including adrenocorticotropin, α-melanocyte stimulating hormone (α-MSH), ß-MSH, [Nle4, D-Phe7]-α-MSH, and D-Trp8-γ-MSH, were used in the pharmacological studies. Our results showed that ipMC3R bound ß-MSH with higher affinity and D-Trp8-γ-MSH with lower affinity compared with human MC3R. All agonists could stimulate ipMC3R and increase intracellular cAMP production with sub-nanomolar potencies. The extracellular signal-regulated kinases 1 and 2 (ERK1/2) activation could also be triggered by ipMC3R. The ipMC3R exhibited constitutive activities in both cAMP and ERK1/2 pathways, and Agouti-related protein served as an inverse agonist at ipMC3R, potently inhibiting the high basal cAMP level. Moreover, we showed that melanocortin receptor accessory protein 2 (MRAP2) preferentially modulated ipMC3R in cAMP production rather than ERK1/2 activation. Our study will assist further investigation of the physiological roles of the ipMC3R, especially in energy homeostasis, in channel catfish.


Assuntos
Metabolismo Energético , Homeostase , Ictaluridae/metabolismo , Receptor Tipo 3 de Melanocortina/metabolismo , Sequência de Aminoácidos , Animais , Sequência de Bases , Cromossomos/genética , AMP Cíclico/metabolismo , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Células HEK293 , Homeostase/efeitos dos fármacos , Humanos , Ligantes , Filogenia , Receptor Tipo 3 de Melanocortina/química , Receptor Tipo 3 de Melanocortina/genética , Análise de Sequência de DNA , Transdução de Sinais , Sintenia/genética
17.
Mol Phylogenet Evol ; 135: 193-202, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30914393

RESUMO

Holoparasitism has led to extreme plastome reduction. Plastomes in the legume holoparasite Pilostyles (Apodanthaceae) are the most reduced in both size and gene content known so far in Embryophytes. Here, we found that the Pilostyles boyacensis plastome, the only American species sequenced so far, is reduced to seven functional genes, accD, rpl2, rrn16 (=16S), rrn23 (=23S), rps3, rps12 and a putative oxidoreductase (PbOx). An additional gene, not annotated in the genome, is actively transcribed between accD and rps12, and by synteny we predict corresponds to rps4. We present data on plastome assembly, transcriptomic data that confirm the transcriptional activity of all genes and describe for the first time six transcript variants of a putative ORF likely having oxidoreductase activity. Our data show that such extreme reduction in P. boyacensis is similar but not identical to that reported in one Australian and one African species of the genus. Such intercontinental similarity suggests that the legume-Pilostyles holoparasitism was already in place during the main African-Australian-South American break-up. We compare plastome content and synteny between the three sequenced species, perform phylogenetic analyses across angiosperms of the six annotated plastome genes, and discuss the odd phylogenetic affinities of 16S and 23S, likely caused by HGT prior the diversification of both legumes and Pilostyles.


Assuntos
Genes de Plantas , Genomas de Plastídeos/genética , Magnoliopsida/genética , África , Sequência de Aminoácidos , Austrália , Sequência de Bases , Mapeamento de Sequências Contíguas , Anotação de Sequência Molecular , Filogenia , Sintenia/genética , Transcrição Genética
18.
Gen Comp Endocrinol ; 279: 139-147, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-30836103

RESUMO

The somatostatin (SST) family members are a group of neuropeptides that are best known for their role in the regulation of growth, development and metabolism. The occurrence of six paralogous SST genes named SST1, SST2, SST3, SST4, SST5 and SST6 has been reported in vertebrates. It has been proposed that SST1, SST2 and SST5 arose in 2R from a common ancestral gene. SST3 and SST6 would have been subsequently generated by tandem duplications of the SST1 and SST2 genes respectively, at the base of the actinopterygian lineage. SST4 is thought to have appeared more recently from SST1, in teleost-specific 3R. In order to gain more insights into the SST gene family in vertebrates, we sought to identify which paralogs of this family are present in cartilaginous fish. For this purpose, we first searched the recently available genome and transcriptome databases from the catshark Scyliorhinus canicula. In a previous study, three S. canicula SST genes, called at that time SSTa, SSTb and SSTc, were identified and proposed to correspond to SST1, SST5 and SST2 respectively. In the present work, two additional SST genes, called SSTd and SSTe, were found in S. canicula plus two other chondrichtyan species, elephant shark (Callorhinchus milii) and whale shark (Rhincodon typus). Phylogeny and synteny analyses were then carried out in order to reveal the evolutionary relationships of SSTd and SSTe with other vertbrates SSTs. We showed that SSTd and SSTe correspond to SST2 and SST3 respectively, while SSTc corresponds to SST6 and not to SST2 as initially proposed. Our investigations in other vertebrate species also led us to find that the so-called SST2 gene in chicken, lungfish, sturgeons and teleosts actually corresponds to SST6. Conversely, the so-called SST6 gene in actinopterygians corresponds to SST2. Taken together, our results suggest that: i) SST3 and SST6 were already present in the gnathostome ancestor, much earlier than previously thought; ii) SST6 was also present in the tetrapod ancestor and still occurs in living birds; with this respect, it is likely that SST6 was independently lost several times during evolution: in amphibians, squamates and mammals; iii) SST2, SST3 and SST5 were probably lost in euteleosts, sarcopterygians and tetrapods, respectively.


Assuntos
Somatostatina/genética , Vertebrados/genética , Sequência de Aminoácidos , Animais , DNA Complementar/genética , Loci Gênicos , Genoma , Especificidade de Órgãos/genética , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Somatostatina/química , Sintenia/genética , Transcriptoma/genética
19.
Aquat Toxicol ; 209: 56-69, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30735907

RESUMO

In this study, the entire glutathione S-transferases (GSTs), the major phase II detoxification enzyme, were identified in two marine copepod species Tigriopus japonicus and Paracyclopina nana. The genome-wide identification of GSTs in T. japonicus and P. nana resulted in 32 and 20 GSTs in total, respectively. Among the identified GSTs, two specific classes of GSTs, specifically sigma and delta/epsilon GSTs were the dominant form of cytosolic GSTs in T. japonicus, while delta/epsilon and mu classes were dominant cytosolic GSTs in P. nana. In addition, Membrane-Associated Proteins in Eicosanoid and Glutathione metabolism (MAPEG) family were found in relatively higher proportion compared to other classes. Moreover, sigma, delta/epsilon, and microsomal GSTs have shown to expand through tandem duplication. To validate the detoxification function of the identified GSTs, both copepods were exposed to copper (Cu2+) and the reactive oxygen species (ROS) level and GST activity were measured. With integration of phylogenetic analysis and xenobiotic-mediated GST mRNA expression patterns along with previous enzymatic activities, the functional divergence among species-specific GST genes was clearly observed. This study covers full identification of GST classes in two marine copepod species and their important role in marine environmental ecotoxicology.


Assuntos
Organismos Aquáticos/genética , Copépodes/enzimologia , Copépodes/genética , Cobre/toxicidade , Regulação Enzimológica da Expressão Gênica/efeitos dos fármacos , Genoma , Glutationa Transferase/genética , Família Multigênica , Animais , Organismos Aquáticos/efeitos dos fármacos , Organismos Aquáticos/enzimologia , Copépodes/efeitos dos fármacos , Duplicação Gênica , Inativação Metabólica/efeitos dos fármacos , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Sintenia/genética , Fatores de Tempo , Testes de Toxicidade Aguda , Transcrição Genética/efeitos dos fármacos , Poluentes Químicos da Água/toxicidade
20.
BMC Evol Biol ; 19(1): 38, 2019 01 30.
Artigo em Inglês | MEDLINE | ID: mdl-30700248

RESUMO

BACKGROUND: Many physiological processes are influenced by nicotinic acetylcholine receptors (nAChR), ranging from neuromuscular and parasympathetic signaling to modulation of the reward system and long-term memory. Due to the complexity of the nAChR family and variable evolutionary rates among its members, their evolution in vertebrates has been difficult to resolve. In order to understand how and when the nAChR genes arose, we have used a broad approach of analyses combining sequence-based phylogeny, chromosomal synteny and intron positions. RESULTS: Our analyses suggest that there were ten subunit genes present in the vertebrate predecessor. The two basal vertebrate tetraploidizations (1R and 2R) then expanded this set to 19 genes. Three of these have been lost in mammals, resulting in 16 members today. None of the ten ancestral genes have kept all four copies after 2R. Following 2R, two of the ancestral genes became triplicates, five of them became pairs, and three seem to have remained single genes. One triplet consists of CHRNA7, CHRNA8 and the previously undescribed CHRNA11, of which the two latter have been lost in mammals but are still present in lizards and ray-finned fishes. The other triplet consists of CHRNB2, CHRNB4 and CHRNB5, the latter of which has also been lost in mammals. In ray-finned fish the neuromuscular subunit gene CHRNB1 underwent a local gene duplication generating CHRNB1.2. The third tetraploidization in the predecessor of teleosts (3R) expanded the repertoire to a total of 31 genes, of which 27 remain in zebrafish. These evolutionary relationships are supported by the exon-intron organization of the genes. CONCLUSION: The tetraploidizations explain all gene duplication events in vertebrates except two. This indicates that the genome doublings have had a substantial impact on the complexity of this gene family leading to a very large number of members that have existed for hundreds of millions of years.


Assuntos
Evolução Molecular , Receptores Nicotínicos/genética , Vertebrados/genética , Animais , Sequência de Bases , Cromossomos/genética , Éxons/genética , Duplicação Gênica , Humanos , Íntrons/genética , Funções Verossimilhança , Filogenia , Poliploidia , Subunidades Proteicas/genética , Sintenia/genética , Fatores de Tempo
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