scholarly journals De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1017
Author(s):  
Mohammed Bakkali ◽  
Rubén Martín-Blázquez ◽  
Mercedes Ruiz-Estévez ◽  
Manuel A. Garrido-Ramos
Keyword(s):  
Functional Annotation ◽  
Vascular Plants ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Systematic Position ◽  
Important Data ◽  
Ecological Requirements ◽  
Physiological Adaptations ◽  
Fern Species ◽  
Go Terms

We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.

scholarly journals De novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo

2022 ◽  
Author(s):  
Masanao Sato ◽  
Masahide Seki ◽  
Yutaka Suzuki ◽  
Shoko Ueki
Keyword(s):  
Functional Annotation ◽  
De Novo ◽  
Molecular Level ◽  
Transcriptome Assembly ◽  
Practical Interest ◽  
Heterosigma Akashiwo ◽  
Sequence Information ◽  
Biological Characterization ◽  
Nucleotide Database

Heterosigma akashiwo is a eukaryotic, cosmopolitan, and unicellular alga (class: Raphidophyceae), and produces fish-killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information enables researchers to characterize organisms using modern molecular technology. The Chloroplast and the mitochondrial genome sequences and transcriptome sequence assembly (TSA) datasets with limited sizes for H. akashiwo are available in NCBI nucleotide database on December 2021: there is no doubt that more genetic information of the species will greatly enhance the progress of biological characterization of the species. Here, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assembly (NCBI TSA ICRV01) of a large number of high-quality short-read sequences, and the functional annotation of predicted genes. Based on our transcriptome, we confirmed that the organism possesses genes that were predicted to function in phagocytosis, supporting the earlier observations of H. akashiwo bacterivory. Along with its capability for photosynthesis, the mixotrophy of H. akashiwo may partially explain its high adaptability to various environmental conditions. Our study here will provide an important toehold to decipher H. akashiwo ecophysiology at a molecular level.

scholarly journals De novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo

2022 ◽  
Author(s):  
Masanao Sato ◽  
Masahide Seki ◽  
Yutaka Suzuki ◽  
Shoko Ueki
Keyword(s):  
Functional Annotation ◽  
De Novo ◽  
Molecular Level ◽  
Transcriptome Assembly ◽  
Practical Interest ◽  
Heterosigma Akashiwo ◽  
Sequence Information ◽  
Biological Characterization ◽  
Nucleotide Database

Heterosigma akashiwo is a eukaryotic, cosmopolitan, and unicellular alga (class: Raphidophyceae), and produces fish-killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information enables researchers to characterize organisms using modern molecular technology. The Chloroplast and the mitochondrial genome sequences and transcriptome sequence assembly (TSA) datasets with limited sizes for H. akashiwo are available in NCBI nucleotide database on December 2021: there is no doubt that more genetic information of the species will greatly enhance the progress of biological characterization of the species. Here, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assembly (NCBI TSA ICRV01) of a large number of high-quality short-read sequences, and the functional annotation of predicted genes. Based on our transcriptome, we confirmed that the organism possesses genes that were predicted to function in phagocytosis, supporting the earlier observations of H. akashiwo bacterivory. Along with its capability for photosynthesis, the mixotrophy of H. akashiwo may partially explain its high adaptability to various environmental conditions. Our study here will provide an important toehold to decipher H. akashiwo ecophysiology at a molecular level.

Comparative transcriptome analysis of five Medicago varieties reveals the genetic signals underlying freezing tolerance

2019 ◽  
Vol 70 (3) ◽  
pp. 273
Author(s):  
Lijun Xu ◽  
Xuejuan Tang ◽  
Bo Wang ◽  
Xiaoping Xin ◽  
Qizhong Sun ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Freezing Tolerance ◽  
Calcium Binding ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Synonymous Substitution ◽  
Biological Processes ◽  
Medicago Species ◽  
Go Terms ◽  
Binding Cell

Medicago plants such as M. sativa (lucerne, alfalfa) are important forage all over the world. Freezing-tolerance capacity is one of the key determinants of the survival and production of Medicago. In order to explore the molecular basis underlying freezing tolerance, we sequenced the root transcriptomes of five Medicago varieties belonging to two species, M. sativa and M. varia, and compared their gene expression and molecular evolution. A range of 19.5–23.8 Gb clean bases was obtained, and de novo transcriptome assembly generated 205238–268520 unigenes. The GO (Gene Ontology) terms of basic biological processes such as binding, cell and metabolism were most represented for the unigenes. In addition, a large number of unigenes related to GO terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways of membrane, signalling, transcription and response to stimulus were identified in functional annotation. In total, 12455 orthologs were identified among the five Medicago varieties. Among the orthologs, many unigenes that directly related to freezing tolerance were highly expressed in all five varieties, including genes for WRKY transcription factors, calcium-binding factors, and antioxidant enzymes such as catalase and ascorbate peroxidase. Molecular evolution testing showed that the unigenes involved in membrane shared high Ka/Ks (non-synonymous/synonymous substitution rate) across all the five Medicago varieties. Positively selected genes were mainly involved in transcription regulation, metabolism and signal transduction. Our study provides a large transcriptome dataset in the Medicago genus and brings new insights into the freezing tolerance for Medicago species.

scholarly journals De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Diana D. Moreno-Santillán ◽  
Carlos Machain-Williams ◽  
Georgina Hernández-Montes ◽  
Jorge Ortega
Keyword(s):  
Functional Annotation ◽  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome

scholarly journals De novo transcriptome assembly and functional annotation of cobia (Rachycentron canadum): molecular approach as a base to nutritional studies

2020 ◽  
Author(s):  
David Aciole Barbosa ◽  
Bruno C. Araújo ◽  
Giovana S. Branco ◽  
Alexandre W. S. Hilsdorf ◽  
Luiz R. Nunes ◽  
...  
Keyword(s):  
Functional Annotation ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Fish Farming ◽  
Relevant Information ◽  
Commercial Fish ◽  
Rachycentron Canadum ◽  
Productive Potential ◽  
Nutritional Studies

ABSTRACTCobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. This lack of information hinders gene expression assessments, which could bring forward novel insights into the physiology, ecology, evolution, and genetics of this aquaculture species. In this study, we report the first de novo transcriptome assembly of cobia liver to improve the availability of gene sequences from this important commercial fish. Thus, Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1617.34 nt, respectively. Comparisons against six different databases resulted in functional annotation for 125,993 of these elements (77.3%), providing relevant information regarding the genomic content of R. canadum. We trust that the availability of these functionally annotated cobia elements will likely assist future nutrigenomics and breeding programs, involving this important fish farming species.

scholarly journals De Novo Transcriptome Assembly of Two Microsorum Fern Species Identifies Enzymes Required for Two Upstream Pathways of Phytoecdysteroids

2021 ◽  
Vol 22 (4) ◽  
pp. 2085
Author(s):  
Siriporn Sripinyowanich ◽  
Eui-Joon Kil ◽  
Sahanat Petchsri ◽  
Yeonhwa Jo ◽  
Hoseong Choi ◽  
...  
Keyword(s):  
High Performance ◽  
Pacific Islands ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Phylogenetic Analyses ◽  
Orthologous Group ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Protein Database ◽  
Fern Species

Microsorum species produce a high amount of phytoecdysteroids (PEs), which are widely used in traditional medicine in the Pacific islands. The PEs in two different Microsorum species, M. punctatum (MP) and M. scolopendria (MS), were examined using high-performance liquid chromatography (HPLC). In particular, MS produces a high amount of 20-hydroxyecdysone, which is the main active compound in PEs. To identify genes for PE biosynthesis, we generated reference transcriptomes from sterile frond tissues using the NovaSeq 6000 system. De novo transcriptome assembly after deleting contaminants resulted in 57,252 and 54,618 clean transcripts for MP and MS, respectively. The clean Microsorum transcripts for each species were annotated according to gene ontology terms, UniProt pathways, and the clusters of the orthologous group protein database using the MEGAN6 and Sma3s programs. In total, 1852 and 1980 transcription factors were identified for MP and MS, respectively. We obtained transcripts encoding for 38 and 32 enzymes for MP and MS, respectively, potentially involved in mevalonate and sterol biosynthetic pathways, which produce precursors for PE biosynthesis. Phylogenetic analyses revealed many redundant and unique enzymes between the two species. Overall, this study provides two Microsorum reference transcriptomes that might be useful for further studies regarding PE biosynthesis in Microsorum species.

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