Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms

Abstract. Testicular transcriptomes were analyzed to characterize the differentially expressed genes between mulard and Pekin ducks, which will help establish gene expression datasets to assist in further determination of the mechanisms of genetic sterility in mulard ducks. Paraffin sections were made to compare the developmental differences in testis tissue between mulard and Pekin ducks. Comparative transcriptome sequencing of testis tissues was performed, and the expression of candidate genes was verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). In mulard ducks, spermatogonia and spermatocytes were arranged in a disordered manner, and no mature sperm were observed in the testis tissue. However, different stages of development of sperm were observed in seminiferous tubules in the testis tissue of Pekin ducks. A total of 43.84 Gb of clean reads were assembled into 193 535 UniGenes. Of these, 2131 transcripts exhibited differential expression (false discover rate <0.001 and fold change ≥2), including 997 upregulated and 1134 downregulated transcripts in mulard ducks as compared to those in Pekin duck testis tissues. Several upregulated genes were related to reproductive functions, including ryanodine receptor 2 (RYR2), calmodulin (CALM), argininosuccinate synthase and delta-1-pyrroline-5-carboxylate synthetase ALDH18A1 (P5CS). Downregulated transcripts included the testis-specific serine/threonine-protein kinase 3, aquaporin-7 (AQP7) and glycerol kinase GlpK (GK). The 10 related transcripts involved in the developmental biological process were identified by GO (Gene Ontology) annotation. The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways indicated that peroxisome proliferator-activated receptors (PPARs) and calcium signaling pathways were significantly (P<0.001) associated with normal testis physiology. The differential expression of select genes implicated in reproductive processes was verified by qRT-PCR, which was consistent with the expression trend of transcriptome sequencing (RNA-seq). Differentially expressed candidate genes RYR2, CALM, P5CS, AQP7 and GK were identified by transcriptional analysis in mulard and Pekin duck testes. These were important for the normal development of the male duck reproductive system. These data provide a framework for the further exploration of the molecular and genetic mechanisms of sterility in mulard ducks. Highlights. The mulard duck is an intergeneric sterile hybrid offspring resulting from mating between Muscovy and Pekin ducks. The transcriptomes of testis tissue from mulard and Pekin ducks were systematically characterized, and differentially expressed genes were screened, in order to gain insights into potential gonad gene expression mechanisms contributing to genetic sterility in mulard ducks.

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Comprehensive Transcriptome Analyses Reveal Candidate Genes for Variation in Seed Size/Weight During Peanut (Arachis hypogaea L.) Domestication

Frontiers in Plant Science ◽

10.3389/fpls.2021.666483 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhongfeng Li ◽

Xingguo Zhang ◽

Kunkun Zhao ◽

Kai Zhao ◽

Chengxin Qu ◽

...

Keyword(s):

Candidate Genes ◽

Seed Development ◽

Seed Size ◽

Snp Markers ◽

Pentatricopeptide Repeat ◽

Significant Differential Expression ◽

Ppr Protein ◽

Cultivated Peanut ◽

Transcriptome Analyses ◽

Wild Peanut

Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8–34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.

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Comparative transcriptome analysis reveals candidate genes for the biosynthesis of natural insecticide in Tanacetum cinerariifolium

BMC Genomics ◽

10.1186/s12864-016-3409-4 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 6

Author(s):

Sana Khan ◽

Swati Upadhyay ◽

Feroz Khan ◽

Sudeep Tandon ◽

Rakesh Kumar Shukla ◽

...

Keyword(s):

Candidate Genes ◽

Transcriptome Analysis ◽

Comparative Transcriptome ◽

Comparative Transcriptome Analysis ◽

Natural Insecticide ◽

Tanacetum Cinerariifolium

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Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.)

BMC Plant Biology ◽

10.1186/s12870-019-2196-x ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Zihan Liu ◽

Sha Li ◽

Wei Li ◽

Qi Liu ◽

Lingli Zhang ◽

...

Keyword(s):

Male Sterility ◽

Candidate Genes ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Interaction Mechanism ◽

Outer Wall ◽

Comparative Transcriptome ◽

Male Sterile ◽

Comparative Transcriptome Analysis ◽

The Impact

Abstract Background Cytoplasmic male sterility (CMS) plays a crucial role in the utilization of heterosis and various types of CMS often have different abortion mechanisms. Therefore, it is important to understand the molecular mechanisms related to anther abortion in wheat, which remain unclear at present. Results In this study, five isonuclear alloplasmic male sterile lines (IAMSLs) and their maintainer were investigated. Cytological analysis indicated that the abortion type was identical in IAMSLs, typical and stainable abortion, and the key abortive period was in the binucleate stage. Most of the 1,281 core shared differentially expressed genes identified by transcriptome sequencing compared with the maintainer in the vital abortive stage were involved in the metabolism of sugars, oxidative phosphorylation, phenylpropane biosynthesis, and phosphatidylinositol signaling, and they were downregulated in the IAMSLs. Key candidate genes encoding chalcone--flavonone isomerase, pectinesterase, and UDP-glucose pyrophosphorylase were screened and identified. Moreover, further verification elucidated that due to the impact of downregulated genes in these pathways, the male sterile anthers were deficient in sugar and energy, with excessive accumulations of ROS, blocked sporopollenin synthesis, and abnormal tapetum degradation. Conclusions Through comparative transcriptome analysis, an intriguing core transcriptome-mediated male-sterility network was proposed and constructed for wheat and inferred that the downregulation of genes in important pathways may ultimately stunt the formation of the pollen outer wall in IAMSLs. These findings provide insights for predicting the functions of the candidate genes, and the comprehensive analysis of our results was helpful for studying the abortive interaction mechanism in CMS wheat.

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