Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

Comparative transcriptomes reveal the disjunction adaptive strategy of Thuja species in East Asia and North America

The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.

Comparative transcriptome analysis between abundant and deficient spore strains provides novel insight into gene regulatory networks and mechanisms of monospore production in bladed Bangiales

As an important seedling source,monospores closely associate with yields in nori farming.However,the molecular mechanism underlying differences in monospore production for different strains remains unknown.Comparative transcriptome analysis was performed to examine gene expression differences between the spore abundant wild-type strain(WT)and spore deficient mutant(Y1)of Pyropia chauhanii.The WT strain that produces monospores in abundance exhibited more differentially expressed genes(DEGs)in both number and higher fold-changes than the Y1 strain incapable of producing monospores,indicating that the specific regulation of genes is involved in monospore production.Three lists of DEGs were obtained between the two strains using intersection and displayed in Venn diagram:one expressed only in WT strain,another expressed only in Y1 strain,and the third shared in both strains.DEGs annotated as homologous genes of Arabidopsis thaliana in these 3 lists were curated for online functional enrichment analysis on Metascape website.Gene regulatory networks of WT were functionally enriched in the processing,proteolysis,and transport of proteins,especially within the small GTPase protein family,which might be account for the monospore production ability,whereas Y1 were functionally enriched in the metabolism of essential substance and utilization of indispensable energy,which might be account for the rapid growth of blades.We found the differentially enriched gene regulatory networks between strains might be the intrinsic mechanisms of the different monospore production traits.These findings provide novel insights into the genes and regulatory networks associated with monospore production abilities,which are essential for developing accurate breeding technologies for optimal release of monospores and increase of total nori production.

Comparative transcriptomic analysis of Rosa sterilis inflorescence branches with different trichome types reveals an R3-MYB transcription factor that negatively regulates trichome formation

Rosa sterilis S.D.Shi is an important economic tree in China that produces fruits with high nutritional and medicinal value.Many of R.sterills’organs are covered with different types of trichomes or prickles that directly affect fruit appearance and plant management.This study used RNA sequencing technology to analyze the transcriptomes of two parts of the inflorescence branch,namely inflorescence stems with flagellated trichomes and pedicels with both flagellated and glandular trichomes.Comparative transcriptomic analysis showed that many transcription factors(TFs)are potentially involved in the formation and development of trichomes.The accumulation of RsETC1,a TF of the R3-MYB family,was significantly higher in inflorescence stems than in pedicels;quantitative reverse transcription PCR(qRTPCR)verified that its expression was significantly higher in inflorescence stems than in pedicels during the first three development stages,indicating its inhibitory action on the initiation of glandular trichomes in R.sterilis.The mRNA level of RsETC1 accumulated to significantly higher levels in trichomeless tissues than in tissues with trichromes,suggesting that this gene may inhibit the formation of trichomes in R.sterilis.Over-expression of RsETC1 in Arabidopsis resulted in glabrous phenotypes,and the expression of trichome-related endogenous genes,except for TTG1,was markedly reduced.In addition,the contents of the phytohormones jasmonic acid(JA),gibberellin A3(GA_(3)),and cytokinins(CKs)in pedicels were significantly higher than those in inflorescence stems,and the expression patterns of the genes related to hormone biosynthesis and signal transduction presented consistent responses,suggesting that the transduction of these hormones might be crucial for trichome initiation and development.These data provide a new perspective for revealing the molecular mechanism of trichome formation in R.sterilis.

Comparison of transcriptomes undergoing waterlogging at the seedling stage between tolerant and sensitive varieties of Brassica napus L.

RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.

Global regulation of fungal secondary metabolism in Trichoderma reesei by the transcription factor Ypr1,as revealed by transcriptome analysis

Trichoderma reesei Rut-C-30 is a well-known robust producer of cellulolytic enzymes,which are used to degrade lignocellulosic biomass for the sustainable production of biofuels and biochemicals.However,studies of its sec-ondary metabolism and regulation remain scarce.Ypr1 was previously described as a regulator of the biosynthesis of the yellow pigment sorbicillin(a bioactive agent with great pharmaceutical interest)in T.reesei and several other fungi.However,the manner in which this regulator affects global gene transcription has not been explored.In this study,we report the effect of Ypr1 on the regulation of both the secondary and primary metabolism of T.reesei Rut-C30.A global gene transcription profile was obtained using a comparative transcriptomic analysis of the wild-type strain T.reesei Rut-C-30 and its ypr1 deletion mutant.The results of this analysis suggest that,in addition to its role in regulating sorbicillin and the major extracellular(hemi)cellulases,Ypr1 also affects the transcription of genes encoding several other secondary metabolites.Although the primary metabolism of T.reeseiΔypr1 became less active compared with that of T.reesei Rut-C-30,several gene clusters involved in its secondary metabolism were activated,such as the gene clusters for the biosynthesis of specific polyketides and non-ribosomal peptides,together with the“sorbicillinoid-cellulase”super cluster,indicating that specific secondary metabolites and cellulases may be co-regulated in T.reesei Rut-C-30.The results presented in this study may benefit the development of genetic engineering strategies for the production of sorbicillin by T.reesei Rut-C-30,and provide insights for enhancing sorbicillin production in other filamentous fungal producers.

Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication of cassava(Manihot esculenta)

Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics.Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not.Here, we investigated the transcriptional differences of eight c DNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line,W14, using next generation sequencing system. A total of41302 assembled transcripts were obtained and from these,25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and3584 transcripts were found to be differentially expressed in leaf, stem and storage root(150 d after planting),respectively, between Arg7 and W14 and ascribed to 103,93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I(PSA) and photosystem II(PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes(PFK, PGK and PK, GAPDH)coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation(INVs), amylose synthesis(GBSS) and hydrolysis(RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation(ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed therelationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.

Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores

Plants experience different abiotic/biotic stresses,which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonateinduced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.

Modes of genetic adaptations underlying functional innovations in the rumen

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general.

Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait

Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed remain unclear.In this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao chicken.Our results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this breed.These regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and Cryab.Retrieval of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao chicken.We hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail bud.The ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem cells.Our study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken.

Exploiting plant transcriptomic databases:Resources,tools,and approaches

There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plant species.The expression data have great value,as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data.Because gene expression provides essential clues to where and when a gene is active,the data provide powerful tools for predicting gene function,and comparative analyses allow us to study plant evolution from a new perspective.This review describes how we can gain new knowledge from gene expression profiles,expres-sion specificities,co-expression networks,differential gene expression,and experiment correlation.We also introduce and demonstrate databases that provide user-friendly access to these tools.