De novo transcriptome analysis of Ammopiptanthus nanus and its comparative analysis with A. mongolicus

Gao, Fei; Li, Huayun; Xiao, Zihua; Wei, Chunxiang; Feng, Jinchao; Zhou, Yijun

doi:10.1007/s00468-017-1631-6

Cited by 18 publications

(9 citation statements)

References 48 publications

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“…In recent years, high-throughput sequencing technology has provided a great deal of nucleic acid data for A. nanus [32], especially recently, the whole genome sequencing was completed using single-molecule sequencing [33], which makes it possible to identify chitinase family at the genome level. In the present study, the genome-wide identification of chitinase in A. nanus was conducted and expression profiling of the chitinase family under cold and osmotic stress was performed using quantitative real-time PCR (qRT-PCR).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic Stress in Ammopiptanthus nanus

Cao

Wang

et al. 2019

Genes

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Chitinase is a kind of hydrolase with chitin as a substrate and is proposed to play an essential role in plant defense system by functioning against fungal pathogens through degrading chitin. Recent studies indicated chitinase is also involved in abiotic stress response in plants, helping plants to survive in stressful environments. A. nanus, a rare evergreen broad-leaved shrub distrusted in deserts in Central Asia, exhibits a high level of tolerance to drought and low temperature stresses. To identify the chitinase gene involved in drought and low temperature responses in A. nanus, we performed genome-wide identification, classification, sequence alignment, and spatio-temporal gene expression analysis of the chitinases in A. nanus under osmotic and low temperature stress. A total of 32 chitinase genes belonging to glycosyl hydrolase 18 (GH18) and GH19 families were identified from A. nanus. Class III chitinases appear to be amplified quantitatively in A. nanus, and their genes carry less introns, indicating their involvement in stress response in A. nanus. The expression level of the majority of chitinases varied in leaves, stems, and roots, and regulated under environmental stress. Some chitinases, such as EVM0022783, EVM0020238, and EVM0003645, are strongly induced by low temperature and osmotic stress, and the MYC/ICE1 (inducer of CBF expression 1) binding sites in promoter regions may mediate the induction of these chitinases under stress. These chitinases might play key roles in the tolerance to these abiotic stress in A. nanus and have potential for biotechnological applications. This study provided important data for understanding the biological functions of chitinases in A. nanus.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic Stress in Ammopiptanthus nanus

Cao

Wang

et al. 2019

Genes

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“…Finally, to combine the three processes, EVM (v1.1.1, RRID:SCR 014659) (Tang et al, 2015) was adopted, following which the results were updated using PASA v2.0.2. Compared these predicted genes with those in the non-redundant protein sequences (NR), eukaryotic orthologous protein classes (KOG) (Campbell et al, 2006), Kyoto Encyclopedia of Genes and Genomes (KEGG) (KEGG, RRID:SCR 001120) (Burge and Karlin, 1997), Swissprot (Swissprot, RRID:SCR 002380) (Gao et al, 2018), TrEMBL (Haas et al, 2008), and Pfam (Pfam, RRID:SCR 004726) (Tatusov et al, 2001) databases for gene annotation using the Basic Local Alignment Search Tool (BLAST) with an e-value cut off of 1E-5 and hmmer V3.0 (Kanehisa and Goto, 2000). With the BLAST2GO pipeline (Boeckmann et al, 2003), Gene ontology (GO) annotation was done.…”

Section: Genome Annotation and Comparative Genomicsmentioning

confidence: 99%

Chromosome-Level Genome Assembly of Cyrtotrachelus buqueti and Mining of Its Specific Genes

Long

Luo

et al. 2021

Front. Ecol. Evol.

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Background: The most severe insect damage to bamboo shoots is the bamboo-snout beetle (Cyrtotrachelus buqueti). Bamboo is a perennial plant that has significant economic value. C. buqueti also plays a vital role in the degradation of bamboo lignocellulose and causing damage. The genome sequencing and functional gene annotation of C. buqueti are of great significance to reveal the molecular mechanism of its efficient degradation of bamboo fiber and the development of the bamboo industry.Results: The size of C. buqueti genome was close to 600.92 Mb by building a one paired-end (PE) library and k-mer analysis. Then, we developed nine 20-kb SMRTbell libraries for genome sequencing and got a total of 51.12 Gb of the original PacBio sequel reads. Furthermore, after filtering with a coverage depth of 85.06×, clean reads with 48.71 Gb were obtained. The final size of C. buqueti genome is 633.85 Mb after being assembled and measured, and the contig N50 of C. buqueti genome is 27.93 Mb. The value of contig N50 shows that the assembly quality of C. buqueti genome exceeds that of most published insect genomes. The size of the gene sequence located on chromosomes reaches 630.86 Mb, accounting for 99.53% of the genome sequence. A 1,063 conserved genes were collected at this assembled genome, comprising 99.72% of the overall genes with 1,066 using the Benchmark Uniform Single-Copy Orthology (BUSCO). Moreover, 63.78% of the C. buqueti genome is repetitive, and 57.15% is redundant with long-term elements. A 12,569 protein-coding genes distributed on 12 chromosomes were acquired after function annotation, of which 96.18% were functional genes. The comparative genomic analysis results revealed that C. buqueti was similar to D. ponderosae. Moreover, the comparative analysis of specific genes in C. buqueti genome showed that it had 244 unique lignocellulose degradation genes and 240 genes related to energy production and conversion. At the same time, 73 P450 genes and 30 GST genes were identified, respectively, in the C. buqueti genome.Conclusion: The high-quality C. buqueti genome has been obtained in the present study. The assembly level of this insect’s genome is higher than that of other most reported insects’ genomes. The phylogenetic analysis of P450 and GST gene family showed that C. buqueti had a vital detoxification function to plant chemical components.

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“…The reciprocal-best-BLAST-hits (RBH) has been considered the most robust and effective in identifying the orthologs genes between closely related species (Osada et al, 2008;Elmer et al, 2010;Gao et al, 2018). In our study, we applied this approach to identify orthologs between E. ivorense and E. suaveolens.…”

Section: Identification Of Orthologsmentioning

confidence: 99%

Comparative analysis of two sister Erythrophleum species (Leguminosae) reveal contrasting transcriptome-wide responses to early drought stress

Neji

Gorel

Ojeda

et al. 2019

Gene

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A B S T R A C TWith the ongoing climate change, African rainforests are expected to experience severe drought events in the future. In Africa, the tropical genus Erythrophleum (Fabaceae) includes two forest sister timber tree species displaying contrasting geographical distributions. Erythrophleum ivorense is adapted to wet evergreen Guineo-Congolian forests, whereas E. suaveolens occurs in a wider range of climates, being found in moist dense forests but also in gallery forests under a relatively drier climate. This geographical distribution pattern suggests that the two species might cope differently to drought at the genomic level. Yet, the genetic basis of tolerance response to drought stress in both species is still uncharacterized. To bridge this gap, we performed an RNA-seq approach on seedlings from each species to monitor their transcriptional responses at different levels of drought stress (0, 2 and 6 weeks after stopping watering seedlings).Monitoring of wilting symptoms revealed that E. suaveolens displayed an earlier phenotypic response to drought stress than E. ivorense. At the transcriptomic level, results revealed 2020 (1204 down-regulated/816 upregulated) and 1495 differentially expressed genes (DEGs) in response to drought stress from a total of 67,432 and 66,605 contigs assembled in E. ivorense and E. suaveolens, respectively. After identifying 30,374 orthologs between species, we found that only 7 of them were DEGs shared between species, while 587 and 458 were differentially expressed only in E. ivorense or E. suaveolens, respectively. GO and KEGG enrichment analysis revealed that the two species differ in terms of significantly regulated pathways as well as the number and expression profile of DEGs (Up/Down) associated with each pathway in the two stress stages. Our results suggested that the two studied species react differently to drought. E. suaveolens seems displaying a prompt response to drought at its early stage strengthened by the down-regulation of many DEGs encoding for signaling and metabolism-related pathways. A considerable up-regulation of these pathways was also found in E. ivorense at the late stage of drought, suggesting this species may be a late responder. Overall, our data may serve as basis for further understanding the genetic control of drought tolerance in tropical trees and favor the selection of crucial genes for genetically enhancing drought resistance.

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De novo transcriptome analysis of Ammopiptanthus nanus and its comparative analysis with A. mongolicus

Cited by 18 publications

References 48 publications

Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic Stress in Ammopiptanthus nanus

Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic Stress in Ammopiptanthus nanus

Chromosome-Level Genome Assembly of Cyrtotrachelus buqueti and Mining of Its Specific Genes

Comparative analysis of two sister Erythrophleum species (Leguminosae) reveal contrasting transcriptome-wide responses to early drought stress

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