Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 38
Filtrar
Más filtros










Base de datos
Intervalo de año de publicación
1.
BMC Plant Biol ; 24(1): 201, 2024 Mar 19.
Artículo en Inglés | MEDLINE | ID: mdl-38500065

RESUMEN

BACKGROUND: The B3 gene family, one of the largest plant-specific transcription factors, plays important roles in plant growth, seed development, and hormones. However, the B3 gene family, especially the REM subfamily, has not been systematically and functionally studied. RESULTS: In this study, we performed genome-wide re-annotation of B3 genes in five Solanaceae plants, Arabidopsis thaliana, and Oryza sativa, and finally predicted 1,039 B3 genes, including 231 (22.2%) newly annotated genes. We found a striking abundance of REM genes in pepper species (Capsicum annuum, Capsicum baccatum, and Capsicum chinense). Comparative motif analysis revealed that REM and other subfamilies (ABI3/VP1, ARF, RAV, and HSI) consist of different amino acids. We verified that the large number of REM genes in pepper were included in the specific subgroup (G8) through the phylogenetic analysis. Chromosome location and evolutionary analyses suggested that the G8 subgroup genes evolved mainly via a pepper-specific recent tandem duplication on chromosomes 1 and 3 after speciation between pepper and other Solanaceae. RNA-seq analyses suggested the potential functions of REM genes under salt, heat, cold, and mannitol stress conditions in pepper (C. annuum). CONCLUSIONS: Our study provides evolutionary and functional insights into the REM gene family in pepper.


Asunto(s)
Arabidopsis , Capsicum , Filogenia , Proteínas de Plantas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Genes de Plantas/genética , Familia de Multigenes , Capsicum/metabolismo , Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas
2.
Nucleic Acids Res ; 51(14): 7424-7437, 2023 08 11.
Artículo en Inglés | MEDLINE | ID: mdl-37394281

RESUMEN

Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.


Asunto(s)
Genes Homeobox , Oryza , Dedos de Zinc , Regulación de la Expresión Génica de las Plantas , Genómica , Filogenia , Proteínas de Plantas/metabolismo , Zinc , Dedos de Zinc/genética , Oryza/genética
3.
Mol Genet Genomics ; 298(3): 653-667, 2023 May.
Artículo en Inglés | MEDLINE | ID: mdl-36943475

RESUMEN

The Korean sweet potatoes were bred by various cultivars introduced from Japanese, American, Porto Rico, China, and Burundi. This issue enriched their genetic diversity but also resulted in a mixture of cultivars. For genotyping, we collected and sequenced 66 sweet potato germplasms from different localities around Korea, including 36 modern cultivars, 5 local cultivars, and 25 foreign cultivars. This identified 447.6 million trimmed reads and 324.8 million mapping reads and provided 39,424 single nucleotide polymorphisms (SNPs) markers. Phylogenetic clustering and population structure analysis distinctly classified these germplasms into 5 genetic groups, group 1, group 2, group 3, group 4, and group 5, containing 20, 15, 10, 7, and 14 accessions, respectively. Sixty-three significant SNPs were selected by genome-wide association for sugar composition-related traits (fructose, glucose, and total sugars), total starch, amylose content, and total carotenoid of the storage root. A total of 37 candidate genes encompassing these significant SNPs were identified, among which, 7 genes were annotated to involve in sugar and starch metabolism, including galactose metabolism (itf04g30630), starch and sucrose metabolism (itf03g13270, itf15g09320), carbohydrate metabolism (itf14g10250), carbohydrate and amino acid metabolism (itf12g19270), and amino sugar and nucleotide sugar metabolism (itf03g21950, itf15g04880). This results indicated that sugar and starch are important characteristics to determine the genetic diversity of sweet potatoes. These findings not only illustrate the importance of component traits to genotyping sweet potatoes but also explain an important reason resulting in genetic diversity of sweet potato.


Asunto(s)
Estudio de Asociación del Genoma Completo , Ipomoea batatas , Ipomoea batatas/genética , Ipomoea batatas/química , Ipomoea batatas/metabolismo , Filogenia , Fitomejoramiento , Almidón/genética , Polimorfismo de Nucleótido Simple/genética
4.
BMC Plant Biol ; 23(1): 48, 2023 Jan 23.
Artículo en Inglés | MEDLINE | ID: mdl-36683040

RESUMEN

BACKGROUND: The AP2/ERF gene family is a superfamily of transcription factors that are important in the response of plants to abiotic stress and development. However, comprehensive research of the AP2/ERF genes in the Solanaceae family is lacking. RESULTS: Here, we updated the annotation of AP2/ERF genes in the genomes of eight Solanaceae species, as well as Arabidopsis thaliana and Oryza sativa. We identified 2,195 AP2/ERF genes, of which 368 (17%) were newly identified. Based on phylogenetic analyses, we observed expansion of the copy number of these genes, especially those belonging to specific Ethylene-Responsive Factor (ERF) subgroups of the Solanaceae. From the results of chromosomal location and synteny analyses, we identified that the AP2/ERF genes of the pepper (Capsicum annuum), the tomato (Solanum lycopersicum), and the potato (Solanum tuberosum) belonging to ERF subgroups form a tandem array and most of them are species-specific without orthologs in other species, which has led to differentiation of AP2/ERF gene repertory among Solanaceae. We suggest that these genes mainly emerged through recent gene duplication after the divergence of these species. Transcriptome analyses showed that the genes have a putative function in the response of the pepper and tomato to abiotic stress, especially those in ERF subgroups. CONCLUSIONS: Our findings will provide comprehensive information on AP2/ERF genes and insights into the structural, evolutionary, and functional understanding of the role of these genes in the Solanaceae.


Asunto(s)
Variaciones en el Número de Copia de ADN , Solanum tuberosum , Filogenia , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Familia de Multigenes , Solanum tuberosum/genética , Etilenos , Proteínas de Plantas/metabolismo , Regulación de la Expresión Génica de las Plantas
5.
Front Plant Sci ; 13: 967546, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36061789

RESUMEN

The bZIP gene family is one of the largest transcription factor families and has important roles in plant growth, development, and stress responses. However, bZIP genes in the Solanaceae family have not been extensively investigated. Here, we conducted genome-wide re-annotation in nine Solanaceae species and Arabidopsis thaliana. We annotated 935 bZIP genes, including 107 (11%) that were newly identified. Structural analyses of bZIP genes in the Solanaceae family revealed that the bZIP domain displayed two types of architectures depending on the presence of an additional domain, suggesting that these architectures generate diversified structures and functions. Motif analyses indicated that the two types of bZIP genes had distinct sequences adjacent to the bZIP domain. Phylogenetic analyses suggested that the two types of bZIP genes distinctly evolved and ultimately adapted in different lineages. Transcriptome analyses in pepper (Capsicum annuum) and tomato (Solanum lycopersicum) revealed putative functional diversity between the two types of bZIP genes in response to various abiotic stresses. This study extensively updated bZIP gene family annotations and provided novel evolutionary and functional evidence for the role of bZIP genes in Solanaceae plants. Our findings provide evolutionary and functional characteristics of bZIP genes for a better understanding of their roles in Solanaceae plants.

6.
BMC Plant Biol ; 22(1): 206, 2022 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-35443608

RESUMEN

BACKGROUND: The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies. RESULTS: We performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper. CONCLUSIONS: Our data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.


Asunto(s)
Arabidopsis , Capsicum , Oryza , Solanum lycopersicum , Solanum tuberosum , Arabidopsis/genética , Capsicum/genética , Capsicum/metabolismo , Proteínas de Unión al ADN/genética , Regulación de la Expresión Génica de las Plantas , Genes de Plantas/genética , Genómica , Solanum lycopersicum/genética , Oryza/genética , Filogenia , Proteínas de Plantas/metabolismo , Solanum tuberosum/genética , Solanum tuberosum/metabolismo
7.
New Phytol ; 235(2): 743-758, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35403705

RESUMEN

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo genome assembly to examine chromosome behaviors and genome integrity in the hybrid. Transcriptome analysis was conducted to investigate expression of duplicated genes in conjunction with epigenome analysis to address whether genome admixture entails epigenetic reconfiguration. Allotetraploid xBrassicoraphanus retains both parental chromosomes without genome rearrangement. Meiotic synapsis formation and chromosome exchange are avoided between nonhomologous progenitor chromosomes. Reconfiguration of transcription network occurs, and less divergent cis-elements of duplicated genes are associated with convergent expression. Genome-wide DNA methylation asymmetry between progenitors is largely maintained but, notably, B. rapa-originated transposable elements are transcriptionally silenced in xBrassicoraphanus through gain of DNA methylation. Our results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions. Overall, this study suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution.


Asunto(s)
Brassicaceae , Genoma de Planta , Brassicaceae/genética , Metilación de ADN/genética , Hibridación Genética
8.
Plant Biotechnol J ; 20(6): 1031-1041, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35332665

RESUMEN

Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as consensus genomes consisting of haplotype mixtures, thus increasing the need for genome phasing. Here, we review the operating principles and characteristics of several freely available and widely used phasing tools (TrioCanu, FALCON-Phase, and ALLHiC). An examination of downstream analyses using haplotype-resolved genome assemblies in plants indicated significant differences among haplotypes regarding chromosomal rearrangements, sequence insertions, and expression of specific alleles that contribute to the acquisition of the biological characteristics of plant species. Finally, we suggest directions to solve addressing limitations of current genome-phasing methods. This review provides insights into the current progress, limitations, and future directions of de novo genome phasing, which will enable researchers to easily access and utilize genome-phasing in studies involving highly heterozygous complex plant genomes.


Asunto(s)
Genoma de Planta , Genómica , Alelos , Genoma de Planta/genética , Haplotipos/genética , Plantas/genética , Análisis de Secuencia de ADN/métodos
9.
Nucleic Acids Res ; 49(20): 11765-11777, 2021 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-34725701

RESUMEN

Transposable element (TE)-derived genes are increasingly recognized as major sources conferring essential traits in agriculturally important crops but underlying evolutionary mechanisms remain obscure. We updated previous annotations and constructed 18,744 FAR-RED IMPAIRED RESPONSE1 (FAR1) genes, a transcription factor family derived from Mutator-like elements (MULEs), from 80 plant species, including 15,546 genes omitted in previous annotations. In-depth sequence comparison of the updated gene repertoire revealed that FAR1 genes underwent continuous structural divergence via frameshift and nonsense mutations that caused premature translation termination or specific domain truncations. CRISPR/Cas9-based genome editing and transcriptome analysis determined a novel gene involved in fertility-regulating transcription of rice pollen, denoting the functional capacity of our re-annotated gene models especially in monocots which had the highest copy numbers. Genomic evidence showed that the functional gene adapted by obtaining a shortened form through a frameshift mutation caused by a tandem duplication of a 79-bp sequence resulting in premature translation termination. Our findings provide improved resources for comprehensive studies of FAR1 genes with beneficial agricultural traits and unveil novel evolutionary mechanisms generating structural divergence and subsequent adaptation of TE-derived genes in plants.


Asunto(s)
Especiación Genética , Tasa de Mutación , Proteínas de Plantas/genética , Elementos Transponibles de ADN/genética , Mutación del Sistema de Lectura , Duplicación de Gen , Oryza/genética , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Homología de Secuencia , Transcriptoma
10.
Plants (Basel) ; 10(7)2021 Jul 09.
Artículo en Inglés | MEDLINE | ID: mdl-34371612

RESUMEN

Korean ginseng is one of the most valuable medicinal plants worldwide. However, our understanding of ginseng proteomics is largely limited due to difficulties in the extraction and resolution of ginseng proteins because of the presence of natural contaminants such as polysaccharides, phenols, and glycosides. Here, we compared four different protein extraction methods, namely, TCA/acetone, TCA/acetone-MeOH/chloroform, phenol-TCA/acetone, and phenol-MeOH/chloroform methods. The TCA/acetone-MeOH/chloroform method displayed the highest extraction efficiency, and thus it was used for the comparative proteome profiling of leaf, root, shoot, and fruit by a label-free quantitative proteomics approach. This approach led to the identification of 2604 significantly modulated proteins among four tissues. We could pinpoint differential pathways and proteins associated with ginsenoside biosynthesis, including the methylerythritol 4-phosphate (MEP) pathway, the mevalonate (MVA) pathway, UDP-glycosyltransferases (UGTs), and oxidoreductases (CYP450s). The current study reports an efficient and reproducible method for the isolation of proteins from a wide range of ginseng tissues and provides a detailed organ-based proteome map and a more comprehensive view of enzymatic alterations in ginsenoside biosynthesis.

11.
Plants (Basel) ; 10(6)2021 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-34064088

RESUMEN

Aquaporins (AQPs) are known to have a vital role in water transport in all living organisms including agriculturally important crops, but a comprehensive genomic study of AQPs in pepper has not been implemented. Here, we updated previous gene annotations and generated a total of 259 AQP genes from five plants, including pepper. Phylogenetic and motif analyses revealed that a large proportion of pepper AQP genes belong to the specific subgroup of tonoplast intrinsic protein (TIP) subfamily, TIP4. Chromosomal localization and estimated duplication times illustrated that genes in TIP4 formed a tandem array on the short arm of chromosome 1, resulting from pepper-specific expansion after its divergence with Solanaceae species. Transcriptome analyses under various abiotic stress conditions revealed that transport-, photosystem-, and thylakoid-related genes were generally enriched in expression clusters containing AQP genes in pepper. These results provide valuable genomic resources and insight into the evolutionary mechanism that generate genomic diversity of the AQP gene family in pepper.

12.
BMC Plant Biol ; 21(1): 247, 2021 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-34059006

RESUMEN

BACKGROUND: Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper. RESULTS: Here, we report de novo genome assemblies of Capsicum annuum 'Early Calwonder (non-pungent, ECW)' and 'Small Fruit (pungent, SF)' along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers. CONCLUSIONS: Our analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in Capsicum species.


Asunto(s)
Capsicum/genética , Evolución Molecular , Genoma de Planta , Leucina/genética , Secuencias Repetitivas de Aminoácido/genética , Variaciones en el Número de Copia de ADN , Resistencia a la Enfermedad/genética , Anotación de Secuencia Molecular , Filogenia , Fitomejoramiento , Enfermedades de las Plantas/genética , Especificidad de la Especie
13.
New Phytol ; 227(5): 1568-1581, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32392385

RESUMEN

Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.


Asunto(s)
Genoma de Planta , Plantas , Genoma de Planta/genética , Anotación de Secuencia Molecular , Plantas/genética
14.
Genes Genomics ; 42(5): 581-596, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32240514

RESUMEN

BACKGROUND: Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear. OBJECTIVE: To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato. METHODS: RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression. RESULTS: 42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation. CONCLUSIONS: The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.


Asunto(s)
Ipomoea batatas/genética , Raíces de Plantas/genética , Transcriptoma , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Giberelinas/metabolismo , Ácidos Indolacéticos/metabolismo , Ipomoea batatas/crecimiento & desarrollo , Estrés Oxidativo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raíces de Plantas/crecimiento & desarrollo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
15.
Sci Data ; 6(1): 220, 2019 10 22.
Artículo en Inglés | MEDLINE | ID: mdl-31641135

RESUMEN

Oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits, and is grown widely in Northeast Asian countries. With increasing interest in its biological properties and economic importance, oriental melon has become an attractive model crop for studying various horticultural traits. A previous genome sequence of the melon was constructed from a homozygous double-haploid line. Thus, individual reference genomes are required to perform functional studies and further breeding applications. Here, we report draft genome sequences of two oriental melons, Chang Bougi and SW3. The assembled 344 Mb genome of Chang Bougi was obtained with scaffold N50 1.0 Mb, and 36,235 genes were annotated. The 354 Mb genome of SW3 was assembled with scaffold N50 1.6 Mb, and has 38,173 genes. These newly constructed genomes will enable studies of fruit development, disease resistance, and breeding applications in the oriental melon.


Asunto(s)
Cucumis melo/genética , Genoma de Planta , Mapeo Cromosómico
16.
Curr Biol ; 29(18): 3041-3052.e4, 2019 09 23.
Artículo en Inglés | MEDLINE | ID: mdl-31522940

RESUMEN

Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.


Asunto(s)
Interacciones Huésped-Parásitos/genética , Striga/genética , Animales , Evolución Biológica , Evolución Molecular , Transferencia de Gen Horizontal/genética , Germinación , Orobanchaceae/genética , Parásitos/genética , Parásitos/metabolismo , Raíces de Plantas , Semillas , Simbiosis
17.
DNA Res ; 25(6): 561-575, 2018 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-30060137

RESUMEN

MicroRNAs (miRNAs) play roles in various biological processes in plants including growth, development, and disease resistance. Previous studies revealed that some plant miRNAs produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs), and they regulate a cascade of gene expression. We performed a genome-wide comparative analysis of miRNAs in Solanaceous species (pepper, tomato, and potato), from an evolutionary perspective. Microsynteny of miRNAs was analysed based on the genomic loci and their flanking genes and most of the well-conserved miRNA genes maintained microsynteny in Solanaceae. We identified target genes of the miRNAs via degradome analysis and found that several miRNAs target many genes encoding nucleotide-binding leucine-rich repeat (NLR) or receptor-like proteins (RLPs), which are known to be major players in defense responses. In addition, disease-resistance-associated miRNAs trigger phasiRNA production in pepper, indicating amplification of the regulation of disease-resistance gene families. Among these, miR-n033a-3p, whose target NLRs have been duplicated in pepper, targets more NLRs belonging to specific subgroup in pepper than those in potato. miRNAs targeting resistance genes might have evolved to regulate numerous targets in Solanaceae, following expansion of target resistance genes. This study provides an insight into evolutionary relationship between miRNAs and their target defense genes in plants.


Asunto(s)
Capsicum/genética , Evolución Molecular , MicroARNs/genética , Cromosomas de las Plantas , Resistencia a la Enfermedad/genética , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Solanaceae/genética , Solanum tuberosum/genética
18.
Sci Data ; 5: 180103, 2018 06 05.
Artículo en Inglés | MEDLINE | ID: mdl-29870035

RESUMEN

Hot pepper (Capsicum annuum) is one of the most consumed vegetable crops in the world and useful to human as it has many nutritional and medicinal values. Genomic resources of pepper are publically available since the pepper genomes have been completed and massive data such as transcriptomes have been deposited. Nevertheless, global transcriptome profiling is needed to identify molecular mechanisms related to agronomic traits in pepper, but limited analyses are published. Here, we report the comprehensive analysis of pepper transcriptomes during fruit ripening and pathogen infection. For the ripening, transcriptome data were obtained from placenta and pericarp at seven developmental stages. To reveal global transcriptomic landscapes during infection, leaves at six time points post-infection by one of three pathogens (Phytophthora infestans, Pepper mottle virus, and Tobacco mosaic virus P0 strain) were profiled. The massive parallel transcriptome profiling in this study will serve as a valuable resource for detection of molecular networks of fruit development and disease resistance in Capsicum annuum.


Asunto(s)
Capsicum/genética , Perfilación de la Expresión Génica , Enfermedades de las Plantas/genética , Transcriptoma , Capsicum/parasitología , Capsicum/virología , Phytophthora infestans , Enfermedades de las Plantas/parasitología , Enfermedades de las Plantas/virología , Potyvirus , Virus del Mosaico del Tabaco
19.
Plant Biotechnol J ; 16(11): 1904-1917, 2018 11.
Artículo en Inglés | MEDLINE | ID: mdl-29604169

RESUMEN

Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.


Asunto(s)
Genoma de Planta/genética , Panax/genética , Adaptación Biológica/genética , Evolución Biológica , Diploidia , Genes del Cloroplasto/genética , Genes de Plantas/genética , Ginsenósidos/biosíntesis , Panax/metabolismo , Tetraploidía
20.
BMB Rep ; 51(2): 55-56, 2018 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-29353598

RESUMEN

Long terminal repeat retrotransposons (LTR-Rs) are major elements creating new genome structure for expansion of plant genomes. However, in addition to the genome expansion, the role of LTR-Rs has been unexplored. In this study, we constructed new reference genome sequences of two pepper species (Capsicum baccatum and C. chinense), and updated the reference genome of C. annuum. We focused on the study for speciation of Capsicum spp. and its driving forces. We found that chromosomal translocation, unequal amplification of LTR-Rs, and recent gene duplications in the pepper genomes as major evolutionary forces for diversification of Capsicum spp. Specifically, our analyses revealed that the nucleotide-binding and leucine-rich-repeat proteins (NLRs) were massively created by LTR-R-driven retroduplication. These retoduplicated NLRs were abundant in higher plants, and most of them were lineage-specific. The retroduplication was a main process for creation of functional disease-resistance genes in Solanaceae plants. In addition, 4-10% of whole genes including highly amplified families such as MADS-box and cytochrome P450 emerged by the retroduplication in the plants. Our study provides new insight into creation of disease-resistance genes and high-copy number gene families by retroduplication in plants. [BMB Reports 2018; 51(2): 55-56].


Asunto(s)
Resistencia a la Enfermedad/genética , Dosificación de Gen , Genes de Plantas , Familia de Multigenes , Enfermedades de las Plantas/genética , Plantas/genética , Retroelementos/genética , Secuencias Repetidas Terminales/genética , Evolución Molecular , Variación Genética
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA
...