Comparative transcriptomic analysis of silkwormBmovo-1 and wild type silkworm ovary

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to Gene Ontology database. The functional enrichment analysis for biological process showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanism of Leishmania, identifying several potential genes for resistance markers and drug targets against leishmaniasis.

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Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

10.21203/rs.3.rs-55997/v2 ◽

2020 ◽

Author(s):

Juvana Moreira Andrade ◽

Leilane Oliveira Gonçalves ◽

Daniel Barbosa Liarte ◽

Davi Alvarenga Lima ◽

Frederico Gonçalves Guimarães ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Transcriptomic Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Cdna Libraries ◽

P Value ◽

Resistant Line ◽

Wild Type ◽

Antimony Resistance ◽

Comparative Transcriptomic Analysis

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the Gene Ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

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Comparative transcriptomic analysis of the l-4i silkworm (Lepidoptera: Bombyx mori) mutants and its wild-type strain P33 by RNA-Seq

Comparative Biochemistry and Physiology Part D Genomics and Proteomics ◽

10.1016/j.cbd.2021.100800 ◽

2021 ◽

Vol 38 ◽

pp. 100800

Author(s):

Chenjie Yang ◽

Lequn Kang ◽

Qiaoling Zhao

Keyword(s):

Bombyx Mori ◽

Type Strain ◽

Wild Type Strain ◽

Transcriptomic Analysis ◽

Rna Seq ◽

Wild Type ◽

Comparative Transcriptomic Analysis

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Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

Parasites & Vectors ◽

10.1186/s13071-020-04486-4 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Juvana Moreira Andrade ◽

Leilane Oliveira Gonçalves ◽

Daniel Barbosa Liarte ◽

Davi Alvarenga Lima ◽

Frederico Gonçalves Guimarães ◽

...

Keyword(s):

Leishmania Infantum ◽

Ribosome Biogenesis ◽

Transcriptomic Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Cdna Libraries ◽

Resistant Line ◽

Wild Type ◽

Antimony Resistance ◽

Comparative Transcriptomic Analysis

Abstract Background One of the major challenges to leishmaniasis treatment is the emergence of parasites resistant to antimony. To study differentially expressed genes associated with drug resistance, we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing. Methods All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search. Results The analytical pipeline considering an adjusted p-value < 0.05 and fold change > 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the gene ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host–parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation. Conclusions The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with the antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

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Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines

10.21203/rs.3.rs-55997/v3 ◽

2020 ◽

Author(s):

Juvana Moreira Andrade ◽

Leilane Oliveira Gonçalves ◽

Daniel Barbosa Liarte ◽

Davi Alvarenga Lima ◽

Frederico Gonçalves Guimarães ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Transcriptomic Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Cdna Libraries ◽

P Value ◽

Resistant Line ◽

Wild Type ◽

Antimony Resistance ◽

Comparative Transcriptomic Analysis

Abstract Background: One of the major challenges for leishmaniasis treatment is the emergence of parasites resistant to antimony. In order to study differentially expressed genes associated with drug resistance we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing.Methods: All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search.Results: The analytical pipeline considering an adjusted p-value lower than 0.05 and fold change greater than 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the Gene Ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host-parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation.Conclusions: The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.

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Comparative Transcriptomic Analysis Uncovers Genes Responsible for the DHA Enhancement in the Mutant Aurantiochytrium sp.

Microorganisms ◽

10.3390/microorganisms8040529 ◽

2020 ◽

Vol 8 (4) ◽

pp. 529

Author(s):

Liangxu Liu ◽

Zhangli Hu ◽

Shuangfei Li ◽

Hao Yang ◽

Siting Li ◽

...

Keyword(s):

Fatty Acid ◽

Mutant Strain ◽

Uv Irradiation ◽

Breeding Strategy ◽

Transcriptomic Analysis ◽

High Yield ◽

Chain Polyunsaturated Fatty Acid ◽

Wild Type ◽

Promising Source ◽

Comparative Transcriptomic Analysis

Docosahexaenoic acid (DHA), a n-3 long-chain polyunsaturated fatty acid, is critical for physiological activities of the human body. Marine eukaryote Aurantiochytrium sp. is considered a promising source for DHA production. Mutational studies have shown that ultraviolet (UV) irradiation (50 W, 30 s) could be utilized as a breeding strategy for obtaining high-yield DHA-producing Aurantiochytrium sp. After UV irradiation (50 W, 30 s), the mutant strain X2 which shows enhanced lipid (1.79-fold, 1417.37 mg/L) and DHA (1.90-fold, 624.93 mg/L) production, was selected from the wild Aurantiochytrium sp. Instead of eicosapentaenoic acid (EPA), 9.07% of docosapentaenoic acid (DPA) was observed in the mutant strain X2. The comparative transcriptomic analysis showed that in both wild type and mutant strain, the fatty acid synthesis (FAS) pathway was incomplete with key desaturases, but genes related to the polyketide synthase (PKS) pathway were observed. Results presented that mRNA expression levels of CoAT, AT, ER, DH, and MT down-regulated in wild type but up-regulated in mutant strain X2, corresponding to the increased intercellular DHA accumulation. These findings indicated that CoAT, AT, ER, DH, and MT can be exploited for high DHA yields in Aurantiochytrium.

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Mechanism study on the enhanced DHA synthesis in the mutant Thraustochytriidae sp. through comparative transcriptomic analysis

10.21203/rs.2.23455/v1 ◽

2020 ◽

Author(s):

liangxu liu ◽

Zhangli Hu ◽

Shuangfei Li ◽

Hao Yang ◽

Siting Li ◽

...

Keyword(s):

Transcriptomic Analysis ◽

Omega 3 ◽

Wild Type ◽

Mechanism Study ◽

Enoyl Reductase ◽

Omega 3 Fatty Acid ◽

Coa Transferase ◽

Dha Enrichment ◽

Promising Source ◽

Comparative Transcriptomic Analysis

Abstract Background: Docosahexaenoic acid (DHA) is an essential omega-3 fatty acid for the human retina, skin, and cerebral cortex. Marine eukaryote Thraustochytriidae sp. was considered as a promising source for the n -3 LC-PUFAs production. However, the mechanism how the LC-PUFAs was synthesized in Thraustochytriidae sp. still remained unclarified. To explore the vital genes responsible for the DHA enrichment, the functional transcriptomic annotation was compared between the wild type and preeminent mutant of Thraustochytriidae sp. X2. Results: After the UV irradiation (50 W, 30 s), the mutant X2 showed enhanced lipid (78.88 % more) and DHA (23.77 % more) production compared with the wild type. Instead of EPA, 9.07 % of DPA was observed in the mutant X2. The comparative transcriptomic analysis showed that in both wild type and mutant strain, FAS was incomplete and lacked key desaturases, but genes related to the PKS pathway were observed. It was oberved that mRNA expression levels of CoA-transferase (CoAT) , acyltransferase (AT), enoyl reductase (ER) , dehydratase (DH) and methyltransferase (MT) down-regulated in wild type but up-regulated in mutant X2, corresponding to the increased intercellular DHA accumulation. Conclusion: These findings indicated the potential genes that can be exploited for high DHA yields in Thraustochytriidae sp..

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Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa042 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Qian-Hao Zhu ◽

Warwick Stiller ◽

Philippe Moncuquet ◽

Stuart Gordon ◽

Yuman Yuan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Agronomic Traits ◽

Gene Families ◽

Mutant Phenotype ◽

Wild Type ◽

Calcium Dependent ◽

Dependent Protein ◽

Flanking Region ◽

Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

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