Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 29
Filtrar
1.
Int J Mol Sci ; 24(6)2023 Mar 14.
Artículo en Inglés | MEDLINE | ID: mdl-36982649

RESUMEN

The mountain butterfly Parnassius glacialis is a representative species of the genus Parnassius, which probably originated in the high-altitude Qinhai-Tibet Plateau in the Miocene and later dispersed eastward into relatively low-altitude regions of central to eastern China. However, little is known about the molecular mechanisms underlying the long-term evolutionary adaptation to heterogeneous environmental conditions of this butterfly species. In this study, we obtained the high-throughput RNA-Seq data from twenty-four adult individuals in eight localities, covering nearly all known distributional areas in China, and firstly identified the diapause-linked gene expression pattern that is likely to correlate with local adaptation in adult P. glacialis populations. Secondly, we found a series of pathways responsible for hormone biosynthesis, energy metabolism and immune defense that also exhibited unique enrichment patterns in each group that are probably related to habitat-specific adaptability. Furthermore, we also identified a suite of duplicated genes (including two transposable elements) that are mostly co-expressed to promote the plastic responses to different environmental conditions. Together, these findings can help us to better understand this species' successful colonization to distinct geographic areas from the western to eastern areas of China, and also provide us with some insights into the evolution of diapause in mountain Parnassius butterfly species.


Asunto(s)
Mariposas Diurnas , Diapausa , Humanos , Animales , Mariposas Diurnas/genética , Perfilación de la Expresión Génica , China , Expresión Génica , Transcriptoma
2.
Arch Virol ; 166(1): 295-297, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33067649

RESUMEN

Here, we report a novel RNA virus from an encyrtid endoparasitoid wasp (Diversinervus elegans). This virus has a genome of 8845 nucleotides in length with a poly(A) tail. It contains one open reading frame (ORF) encoding a single polyprotein that shares the most significant similarity to the polyproteins of dicistroviruses. Phylogenetic analysis suggested that this virus belongs to the family Dicistroviridae from the order Picornavirales, but its genomic organization is distinct from that of the other known dicistroviruses, which have two ORFs. Consequently, we propose that this virus is a member of a new species in the order Picornavirales, and have named it "Diversinervus elegans virus" (DEV).


Asunto(s)
Dicistroviridae/genética , Genoma Viral/genética , Virus ARN/genética , Avispas/virología , Animales , Sistemas de Lectura Abierta/genética , Filogenia , Poliproteínas/genética , ARN Viral/genética , Alineación de Secuencia , Análisis de Secuencia de ADN/métodos , Proteínas Virales/genética
3.
BMC Genomics ; 20(1): 253, 2019 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-30925896

RESUMEN

BACKGROUND: Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny. RESULTS: Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered. CONCLUSIONS: The divergence time of subgenus Vetrix and Salix was about 17.6-16.0 Mya during the period of Middle Miocene Climate Transition (21-14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.


Asunto(s)
Hibridación Genómica Comparativa/métodos , Perfilación de la Expresión Génica/métodos , Salix/genética , Genes de Plantas , Repeticiones de Microsatélite/genética , Filogenia , Salix/clasificación , Estrés Fisiológico/genética
4.
BMC Genomics ; 19(1): 725, 2018 Oct 03.
Artículo en Inglés | MEDLINE | ID: mdl-30285615

RESUMEN

BACKGROUND: Pines are widely distributed in the Northern Hemisphere and have a long evolutionary history. The availability of transcriptome data has facilitated comparative transcriptomics for studying the evolutionary patterns associated with the different geographical distributions of species in the Pinus phylogeny. RESULTS: The transcriptome of Pinus kesiya var. langbianensis was sequenced using the Illumina HiSeq 2000 platform, and a total of 68,881 unigenes were assembled by Trinity. Transcriptome sequences of another 12 conifer species were downloaded from public databases. All of the pairwise orthologues were identified by comparative transcriptome analysis in 13 conifer species, from which the rate of diversification was calculated and a phylogenetic tree inferred. All of the fast-evolving positive selection sequences were identified, and some salt-, drought-, and abscisic acid-resistance genes were discovered. CONCLUSIONS: mRNA sequences of P. kesiya var. langbianensis were obtained by transcriptome sequencing, and a large number of simple sequence repeat and short nucleotide polymorphism loci were detected. These data can be used in molecular marker-assisted selected in pine breeding. Divergence times were estimated in the 13 conifer species using comparative transcriptomic analysis. A number of positive selection genes were found to be related to environmental factors. Salt- and abscisic acid-related genes exhibited different selection patterns between coastal and inland Pinus. Our findings help elucidate speciation patterns in the Pinus lineage.


Asunto(s)
Perfilación de la Expresión Génica , Filogenia , Pinus/genética , Análisis de Secuencia , Ambiente , Evolución Molecular , Geografía , Repeticiones de Microsatélite/genética , Polimorfismo de Nucleótido Simple , Homología de Secuencia de Ácido Nucleico
5.
Proc Natl Acad Sci U S A ; 111(46): E4954-62, 2014 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-25368197

RESUMEN

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.


Asunto(s)
Adaptación Fisiológica/genética , Interacción Gen-Ambiente , Genoma de Planta , Oryza/genética , África , Secuencia de Aminoácidos , Asia , Australia , Secuencia de Bases , Diploidia , Evolución Molecular , Dosificación de Gen , Genes de Plantas , Variación Genética , MicroARNs/genética , Datos de Secuencia Molecular , Familia de Multigenes , Oryza/clasificación , Filogenia , Proteínas de Plantas/genética , ARN de Planta/genética , Selección Genética , Alineación de Secuencia , Homología de Secuencia , América del Sur , Especificidad de la Especie
6.
Front Plant Sci ; 15: 1362020, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38855470

RESUMEN

Introduction: Dendrolimus punctatus, a major pest endemic to the native Pinus massoniana forests in China, displays major outbreak characteristics and causes severe destructiveness. In the context of global climate change, this study aims to investigate the effects of climatic variations on the distribution of D. punctatus and its host, P. massoniana. Methods: We predict their potential suitable distribution areas in the future, thereby offering a theoretical basis for monitoring and controlling D. punctatus, as well as conserving P. massoniana forest resources. By utilizing existing distribution data on D. punctatus and P. massoniana, coupled with relevant climatic variables, this study employs an optimized maximum entropy (MaxEnt) model for predictions. With feature combinations set as linear and product (LP) and the regularization multiplier at 0.1, the model strikes an optimal balance between complexity and accuracy. Results: The results indicate that the primary climatic factors influencing the distribution of D. punctatus and P. massoniana include the minimum temperature of the coldest month, annual temperature range, and annual precipitation. Under the influence of climate change, the distribution areas of P. massoniana and its pests exhibit a high degree of similarity, primarily concentrated in the region south of the Qinling-Huaihe line in China. In various climate scenarios, the suitable habitat areas for these two species may expand to varying degrees, exhibiting a tendency to shift toward higher latitude regions. Particularly under the high emission scenario (SSP5-8.5), D. punctatus is projected to expand northwards at the fastest rate. Discussion: By 2050, its migration direction is expected to closely align with that of P. massoniana, indicating that the pine forests will continue to be affected by the pest. These findings provide crucial empirical references for region-specific prevention of D. punctatus infestations and for the rational utilization and management of P. massoniana resources.

7.
Ecol Evol ; 14(4): e11218, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38606343

RESUMEN

Insects harbor a remarkable diversity of gut microbiomes critical for host survival, health, and fitness, but the mechanism of this structured symbiotic community remains poorly known, especially for the insect group consisting of many closely related species that inhabit the Qinghai-Tibet Plateau. Here, we firstly analyzed population-level 16S rRNA microbial dataset, comprising 11 Parnassius species covering 5 subgenera, from 14 populations mostly sampled in mountainous regions across northwestern-to-southeastern China, and meanwhile clarified the relative importance of multiple factors on gut microbial community structure and evolution. Our findings indicated that both host genetics and larval host plant modulated gut microbial diversity and community structure. Moreover, the effect analysis of host genetics and larval diet on gut microbiomes showed that host genetics played a critical role in governing the gut microbial beta diversity and the symbiotic community structure, while larval host plant remarkably influenced the functional evolution of gut microbiomes. These findings of the intimate insect-microbe-plant interactions jointly provide some new insights into the correlation among the host genetic background, larval host plant, the structure and evolution of gut microbiome, as well as the mechanisms of high-altitude adaptation in closely related species of this alpine butterfly group.

8.
Sci Rep ; 13(1): 19727, 2023 11 13.
Artículo en Inglés | MEDLINE | ID: mdl-37957311

RESUMEN

Macroevolution can be regarded as the result of evolutionary changes of synergistically acting genes. Unfortunately, the importance of these genes in macroevolution is difficult to assess and hence the identification of macroevolutionary key genes is a major challenge in evolutionary biology. In this study, we designed various word embedding libraries of natural language processing (NLP) considering the multiple mechanisms of evolutionary genomics. A novel method (IKGM) based on three types of attention mechanisms (domain attention, kmer attention and fused attention) were proposed to calculate the weights of different genes in macroevolution. Taking 34 species of diurnal butterflies and nocturnal moths in Lepidoptera as an example, we identified a few of key genes with high weights, which annotated to the functions of circadian rhythms, sensory organs, as well as behavioral habits etc. This study not only provides a novel method to identify the key genes of macroevolution at the genomic level, but also helps us to understand the microevolution mechanisms of diurnal butterflies and nocturnal moths in Lepidoptera.


Asunto(s)
Mariposas Diurnas , Aprendizaje Profundo , Mariposas Nocturnas , Animales , Mariposas Diurnas/genética , Evolución Biológica , Mariposas Nocturnas/genética , Genómica , Filogenia
9.
Plant Commun ; 4(1): 100427, 2023 01 09.
Artículo en Inglés | MEDLINE | ID: mdl-36056558

RESUMEN

Pseudogenes are important resources for investigation of genome evolution and genomic diversity because they are nonfunctional but have regulatory effects that influence plant adaptation and diversification. However, few systematic comparative analyses of pseudogenes in closely related species have been conducted. Here, we present a turnip (Brassica rapa ssp. rapa) genome sequence and characterize pseudogenes among diploid Brassica species/subspecies. The results revealed that the number of pseudogenes was greatest in Brassica oleracea (CC genome), followed by B. rapa (AA genome) and then Brassica nigra (BB genome), implying that pseudogene differences emerged after species differentiation. In Brassica AA genomes, pseudogenes were distributed asymmetrically on chromosomes because of numerous chromosomal insertions/rearrangements, which contributed to the diversity among subspecies. Pseudogene differences among subspecies were reflected in the flavor-related glucosinolate (GSL) pathway. Specifically, turnip had the highest content of pungent substances, probably because of expansion of the methylthioalkylmalate synthase-encoding gene family in turnips; these genes were converted into pseudogenes in B. rapa ssp. pekinensis (Chiifu). RNA interference-based silencing of the gene encoding 2-oxoglutarate-dependent dioxygenase 2, which is also associated with flavor and anticancer substances in the GSL pathway, resulted in increased abundance of anticancer compounds and decreased pungency of turnip and Chiifu. These findings revealed that pseudogene differences between turnip and Chiifu influenced the evolution of flavor-associated GSL metabolism-related genes, ultimately resulting in the different flavors of turnip and Chiifu.


Asunto(s)
Brassica napus , Brassica rapa , Brassica , Brassica rapa/genética , Brassica napus/genética , Seudogenes/genética , Brassica/genética , Genómica/métodos
10.
Nat Commun ; 14(1): 8190, 2023 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-38081828

RESUMEN

Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.


Asunto(s)
Mariposas Diurnas , Animales , Tibet , Mariposas Diurnas/genética , Altitud , Genoma , Análisis de Secuencia de ADN
11.
Comput Math Methods Med ; 2022: 4490154, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35924115

RESUMEN

MicroRNAs (miRNAs) are a kind of noncoding RNA, which plays an essential role in gene regulation by binding to messenger RNAs (mRNAs). Accurate and rapid identification of miRNA target genes is helpful to reveal the mechanism of transcriptome regulation, which is of great significance for the study of cancer and other diseases. Many bioinformatics methods have been proposed to solve this problem, but the previous research did not further study the encoding of the nucleotide sequence. In this paper, we developed a novel method combining word embedding and deep learning for human miRNA targets at the site-level prediction, which is inspired by the similarity between natural language and biological sequences. First, the word2vec model was used to mine the distribution representation of miRNAs and mRNAs. Then, the embedding is extracted automatically via the stacked bidirectional long short-term memory (BiLSTM) network. By testing, our method can effectively improve the accuracy, sensitivity, specificity, and F-measure of other methods. Through our research, it is proved that the distributed representation can improve the accuracy of the deep learning model and better solve the miRNA target site prediction problem.


Asunto(s)
Aprendizaje Profundo , MicroARNs , Biología Computacional/métodos , Humanos , MicroARNs/genética , MicroARNs/metabolismo , ARN Mensajero/genética , Transcriptoma
12.
Sci Rep ; 12(1): 8799, 2022 05 25.
Artículo en Inglés | MEDLINE | ID: mdl-35614118

RESUMEN

Pine nuts are not only the important agent of pine reproduction and afforestation, but also the commonly consumed nut with high nutritive values. However, it is difficult to distinguish among pine nuts due to the morphological similarity among species. Therefore, it is important to improve the quality of pine nuts and solve the adulteration problem quickly and non-destructively. In this study, seven pine nuts (Pinus bungeana, Pinus yunnanensis, Pinus thunbergii, Pinus armandii, Pinus massoniana, Pinus elliottii and Pinus taiwanensis) were used as study species. 210 near-infrared (NIR) spectra were collected from the seven species of pine nuts, five machine learning methods (Decision Tree (DT), Random Forest (RF), Multilayer Perceptron (MLP), Support Vector Machine (SVM) and Naive Bayes (NB)) were used to identify species of pine nuts. 303 images were used to collect morphological data to construct a classification model based on five convolutional neural network (CNN) models (VGG16, VGG19, Xception, InceptionV3 and ResNet50). The experimental results of NIR spectroscopy show the best classification model is MLP and the accuracy is closed to 0.99. Another experimental result of images shows the best classification model is InceptionV3 and the accuracy is closed to 0.964. Four important range of wavebands, 951-957 nm, 1,147-1,154 nm, 1,907-1,927 nm, 2,227-2,254 nm, were found to be highly related to the classification of pine nuts. This study shows that machine learning is effective for the classification of pine nuts, providing solutions and scientific methods for rapid, non-destructive and accurate classification of different species of pine nuts.


Asunto(s)
Nueces , Pinus , Teorema de Bayes , Aprendizaje Automático , Nueces/química , Pinus/química
13.
Insects ; 13(5)2022 Apr 23.
Artículo en Inglés | MEDLINE | ID: mdl-35621742

RESUMEN

We studied 239 imagoes of 12 Parnassius species collected from the mountains of the Qinghai-Tibet Plateau (QTP) and its neighbouring areas in China. We selected three mitochondrial gene (COI, ND1, and ND5) sequences, along with the homologous gene sequences of other Parnassius species from GenBank, to reconstruct the phylogenetic tree and biogeographic history of this genus. Our results show that Parnassius comprises eight monophyletic subgenera, with subgenus Parnassius at the basal position; the genus crown group originated during the Middle Miocene (ca. 16.99 Ma), and species diversification continued during sustained cooling phases after the Middle Miocene Climate Optimum (MMCO) when the QTP and its neighbouring regions experienced rapid uplift and extensive orogeny. A phylogenetic network analysis based on transcriptomes from GenBank suggests that ancient gene introgression might have contributed to the spread of the Parnassius genus to different altitudes. Ancestral area reconstruction indicates that Parnassius most likely originated in West China (QTP and Xinjiang) and then spread to America in two dispersal events as subgenera Driopa and Parnassius, along with their host plants Papaveraceae and Crassulaceae, respectively. Our study suggests that extensive mountain-building processes led to habitat fragmentation in the QTP, leading to the early diversification of Parnassius, and climate cooling after MMCO was the driving mechanism for the dispersal of Parnassius butterflies from West China to East Asia, Europe, and North America.

14.
Genes (Basel) ; 14(1)2022 12 26.
Artículo en Inglés | MEDLINE | ID: mdl-36672814

RESUMEN

Pieridae is one of the largest and almost cosmopolitan groups of butterflies, which plays an important role in natural ecosystems; however, to date, its phylogeny and evolutionary history have not been fully resolved. In this study, we obtained the complete or nearly complete mitochondrial genomes of 100 pierid taxa (six newly sequenced, sixty extracted from the whole-genome data, and thirty-four directly available from GenBank). At the same time, for the first time, we conducted comparative mitogenomic and phylogenetic analyses based on these mitogenomic data, to further clarify their spatio-temporal evolutionary patterns. Comparative mitogenomic analysis showed that, except for cox2, the GC content of each of the 13 protein-coding genes (PCGs) in the rapidly diverging subfamily Pierinae was higher than in its sister group Coliadinae. Moreover, the dN/dS values of nine genes (atp6, atp8, cox1, cox3, cob, nad1, nad3, nad5, and nad6) in Pierinae were also relatively higher than those in its sister group, Coliadinae. Phylogenetic analysis showed that all the resultant phylogenetic trees were generally in agreement with those of previous studies. The Pierinae family contained six clades in total with the relationship of (Leptosiaini + (((Nepheroniini + Arthocharidini) + Teracolini) + (Pierini + Elodini))). The Pieridae originated in the Palearctic region approximately 72.3 million years ago in the late Cretaceous, and the subfamily Pierinae diverged from this family around 57.9 million years ago in the Oriental region, shortly after the K-Pg mass extinction event; in addition, the spatio-temporal evolutionary patterns of Pierinae were closely correlated with geological events and environmental changes, as well as the host plant coevolutionary scenario in Earth's history. However, some incongruencies were observed between our results and those of previous studies in terms of shallow phylogenies for a few taxa, and should be further investigated.


Asunto(s)
Mariposas Diurnas , Animales , Mariposas Diurnas/genética , Filogenia , Ecosistema , Evolución Biológica , Secuencia de Bases
15.
Mitochondrial DNA B Resour ; 6(7): 2007-2008, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34235271

RESUMEN

The complete mitochondrial genome (mitogenome) of Biston thoracicaria (Lepidoptera: Geometridae) is 15,538 bp in length, containing 13 PCGs, 22 tRNAs, two rRNAs, and an A + T-rich region. All PCGs initiate with typical start codon of ATN and share the complete stop codon of TAA, whereas cox1 starts with CGA. The ML analysis was performed using a dataset matrix containing 13 PCGs concatenated from the mitogenomes of Geometridae species. Our study presented the phylogenetic relationship of (Larentiinae + ((Sterrhinae + (Ennominae + Geometrinae))). Within the genera Biston, B. thoracicaria grouped with other species as the sister group.

16.
Sci Data ; 8(1): 174, 2021 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-34267227

RESUMEN

LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.


Asunto(s)
Genoma de Planta , Plantas/genética , Retroelementos , Secuencias Repetidas Terminales , Evolución Molecular , Anotación de Secuencia Molecular
17.
Toxicon ; 183: 29-35, 2020 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-32445842

RESUMEN

The ant-like bethylid ectoparasitoid Scleroderma guani (Hymenoptera: Bethylidae) envenomates host to suppress immune response. Yet, the roles of its venom in inhibiting melanization of the host hemolymph have not been fully characterized. Here, we demonstrated that S. guani envenomation induced strong inhibition of melanization of the hemolymph from Tenebrio molitor (Coleoptera: Tenebrionidae), permitting the successful development of parasitoid offspring. To reveal venom component associated with such function, a serine proteinase homolog (SguaSPH) rich in the venom of S. guani was characterized. It was found that one of the catalytic triad residues for serine proteinase is absent in the amino acid sequence of SguaSPH. This venom component was abundantly expressed in venom apparatus and adult stages. By enzymatic assays, SguaSPH displayed low trypsin and no chymotrypsin activity, and was able to inhibit phenoloxidase activity in the hemolymph of Ostrinia furnacalis (Lepidoptera: Crambidae). The findings suggest that SguaSPH is essential for interfering with hemolymph melanization of S. guani envenomated host via phenoloxidase cascade disruption.


Asunto(s)
Monofenol Monooxigenasa/metabolismo , Serina Proteasas/metabolismo , Animales , Hemolinfa/metabolismo , Proteínas de Insectos/metabolismo , Larva , Tenebrio/metabolismo
18.
Plant Direct ; 4(6): e00232, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32537559

RESUMEN

Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.

19.
Plant Genome ; 13(1): e20001, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-33016624

RESUMEN

African wild rice Oryza longistaminata, one of the eight AA- genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high-quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately ∼363.5 Mb, representing ∼92.7% of the estimated African wild rice genome (∼392 Mb). The N50 lengths of the assembled contigs and scaffolds were ∼46.49 Kb and ∼6.83 Mb, indicating ∼3.72-fold and ∼18.8-fold improvement in length compared to the earlier released assembly (∼12.5 Kb and 364 Kb, respectively). Aided with Hi-C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo-chromosomes. Genome annotation and comparative genomic analysis reveal that lineage-specific expansion of gene families that respond to biotic- and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs.


Asunto(s)
Oryza , Genoma , Genómica , Oryza/genética , Análisis de Secuencia de ADN
20.
Saudi J Biol Sci ; 26(3): 605-613, 2019 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-30899179

RESUMEN

The roots of Codonopis bulleynana Forest ex diels (cbFed), locally known as Tsoong, have been used as a tonic food. Tsoong has wide range of pharmacological effects, including anticancer effects. In the present study, the anticancer activity of Tsoong and its potential molecular mechanisms were investigated. Using high throughput sequencing the apoptotic pathway was ranked as one of the most important pathways and the differential expressions of apoptosis-related genes such as Casp3, Casp6 and Apaf1 were identified. The following experiments were qRT-PCR which were used to verify the genes. In vitro, cell counting kit-8 (CCK-8) assays and flow cytometry in HCT116 and SW480 colon cancer cell were used to assess the anti-proliferation and apoptosis-promoting activities of Tsoong. In vivo, the antitumor effect of Tsoong was assessed in colon cancer-bearing nude mice as a xenograft model. H&E staining was performed with oxaliplatin set as a positive control. The results showed that Tsoong up-regulated apoptosis-related genes, inhibited tumor cell proliferation, promoted tumor cellapoptosis in a dose-dependent manner and restrained the growth of colon neoplasm. The effects of a high dose of Tsoong on colon cancer cells were similar to those of oxaliplatin. Our results may ultimately help in the development of diagnostic and therapeutic strategies to control this devastating disease. Therefore, Tsoong may be a promising Chinese herbal compound for development for use in cancer therapy.

SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA