Transcriptomic study of the red palm weevil <i>Rhynchophorus ferrugineus</i> embryogenesis

Yin, An; Pan, Li-Long; Zhang, Xiaowei; Wang, Lei; Yin, Yuxin; Jia, Shangang; Liu, Wanfei; Xin, Chengqi; Liu, Kan; Yu, Xiongbin; Sun, Gaoyuan; Alhudaib, Khalid; Hu, Songnian; Al-Mssallem, Ibrahim S.; Yu, Jun

doi:10.1111/1744-7917.12092

Cited by 17 publications

(11 citation statements)

References 96 publications

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“…Also, we identified the enrichment of Rho guanyl-nucleotide exchange factor activity (GO: 0005089), which is a modulator in the signaling pathway of Ras/MAPK and Wnt. Previous studies have shown that this activity is associated with neuronal growth cone and planar cell polarity formation [42, 43]. In B. mori , consistent with [30], we identified the enrichment of monooxygenase activity (GO: 0004497), which might be associated with detoxification.…”

Section: Resultssupporting

confidence: 84%

Segmental duplications: evolution and impact among the current Lepidoptera genomes

Zhao

Vasseur

et al. 2017

BMC Evol Biol

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BackgroundStructural variation among genomes is now viewed to be as important as single nucleoid polymorphisms in influencing the phenotype and evolution of a species. Segmental duplication (SD) is defined as segments of DNA with homologous sequence.ResultsHere, we performed a systematic analysis of segmental duplications (SDs) among five lepidopteran reference genomes (Plutella xylostella, Danaus plexippus, Bombyx mori, Manduca sexta and Heliconius melpomene) to understand their potential impact on the evolution of these species. We find that the SDs content differed substantially among species, ranging from 1.2% of the genome in B. mori to 15.2% in H. melpomene. Most SDs formed very high identity (similarity higher than 90%) blocks but had very few large blocks. Comparative analysis showed that most of the SDs arose after the divergence of each linage and we found that P. xylostella and H. melpomene showed more duplications than other species, suggesting they might be able to tolerate extensive levels of variation in their genomes. Conserved ancestral and species specific SD events were assessed, revealing multiple examples of the gain, loss or maintenance of SDs over time. SDs content analysis showed that most of the genes embedded in SDs regions belonged to species-specific SDs (“Unique” SDs). Functional analysis of these genes suggested their potential roles in the lineage-specific evolution. SDs and flanking regions often contained transposable elements (TEs) and this association suggested some involvement in SDs formation. Further studies on comparison of gene expression level between SDs and non-SDs showed that the expression level of genes embedded in SDs was significantly lower, suggesting that structure changes in the genomes are involved in gene expression differences in species.ConclusionsThe results showed that most of the SDs were “unique SDs”, which originated after species formation. Functional analysis suggested that SDs might play different roles in different species. Our results provide a valuable resource beyond the genetic mutation to explore the genome structure for future Lepidoptera research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-1007-y) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 84%

Segmental duplications: evolution and impact among the current Lepidoptera genomes

Zhao

Vasseur

et al. 2017

BMC Evol Biol

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“…MFC, STDEV, and interquartile of expression level are the most commonly-used metrics to evaluate the variation among the data, with CV as the most popular parameter to evaluate expression stability of genes (Benedito et al, 2008 ; Severin et al, 2010 ; Wang et al, 2010 ; Daines et al, 2011 ; Graveley et al, 2011 ; Yin et al, 2015 ). Typically, the top 1,000 expressed transcripts with the lowest CV values in contrasting environments are taken as the stably expressed genes (Zhu et al, 2008 ; Van Hiel et al, 2009 ; Severin et al, 2010 ; Yin et al, 2015 ), with cut-off threshold values that are typically CV < 16 or < 20% (Benedito et al, 2008 ; Severin et al, 2010 ; Wang et al, 2010 ). An alternative method for selection of stably expressed genes is to choose genes whose RNA-seq has a sufficiently low CV of its logarithmically transformed RPKM and logarithmically transformed transcript copy numbers (threshold typically CV < 4%) (Fernández-Aparicio et al, 2013 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Constitutively Expressed Gene Analysis and New Reference Gene Selection Based on Transcriptome Data: A Case Study from Poplar/Canker Disease Interaction

et al. 2017

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A number of transcriptome datasets for differential expression (DE) genes have been widely used for understanding organismal biology, but these datasets also contain untapped information that can be used to develop more precise analytical tools. With the use of transcriptome data generated from poplar/canker disease interaction system, we describe a methodology to identify candidate reference genes from high-throughput sequencing data. This methodology will improve the accuracy of RT-qPCR and will lead to better standards for the normalization of expression data. Expression stability analysis from xylem and phloem of Populus bejingensis inoculated with the fungal canker pathogen Botryosphaeria dothidea revealed that 729 poplar transcripts (1.11%) were stably expressed, at a threshold level of coefficient of variance (CV) of FPKM < 20% and maximum fold change (MFC) of FPKM < 2.0. Expression stability and bioinformatics analysis suggested that commonly used house-keeping (HK) genes were not the most appropriate internal controls: 70 of the 72 commonly used HK genes were not stably expressed, 45 of the 72 produced multiple isoform transcripts, and some of their reported primers produced unspecific amplicons in PCR amplification. RT-qPCR analysis to compare and evaluate the expression stability of 10 commonly used poplar HK genes and 20 of the 729 newly-identified stably expressed transcripts showed that some of the newly-identified genes (such as SSU_S8e, LSU_L5e, and 20S_PSU) had higher stability ranking than most of commonly used HK genes. Based on these results, we recommend a pipeline for deriving reference genes from transcriptome data. An appropriate candidate gene should have a unique transcript, constitutive expression, CV value of expression < 20% (or possibly 30%) and MFC value of expression <2, and an expression level of 50–1,000 units. Lastly, when four of the newly identified HK genes were used in the normalization of expression data for 20 differential expressed genes, expression analysis gave similar values to Cufflinks output. The methods described here provide an alternative pathway for the normalization of transcriptome data, a process that is essential for integrating analyses of transcriptome data across environments, laboratories, sequencing platforms, and species.

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“…Limiting mitochondrial data to a handful of genes illustrates this point well as resolution fades rapidly [ 8 ]. Larger data volumes are now available from nuclear genome sequencing, either in terms of entire genomes [ 88 – 90 ], or transcribed genomes [ 91 , 92 ]. Each of these approaches has their own disadvantages with respect to high cost and labor intensity.…”

Section: Discussionmentioning

confidence: 99%

Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

2016

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Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

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Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

Cited by 17 publications

References 96 publications

Segmental duplications: evolution and impact among the current Lepidoptera genomes

Segmental duplications: evolution and impact among the current Lepidoptera genomes

Genome-Wide Constitutively Expressed Gene Analysis and New Reference Gene Selection Based on Transcriptome Data: A Case Study from Poplar/Canker Disease Interaction

Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

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