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

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.

Download Full-text

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

Genes ◽

10.3390/genes12071017 ◽

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.

Download Full-text

Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Life ◽

10.3390/life10110300 ◽

2020 ◽

Vol 10 (11) ◽

pp. 300

Author(s):

Leyland Fraser ◽

Łukasz Paukszto ◽

Anna Mańkowska ◽

Paweł Brym ◽

Przemysław Gilun ◽

...

Keyword(s):

Target Genes ◽

De Novo ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Differentially Expressed ◽

Biological Processes ◽

Protein Coding ◽

Protein Coding Genes ◽

Potential Target ◽

Non Coding Rnas

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm’s response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

Download Full-text

Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys)

Data in Brief ◽

10.1016/j.dib.2021.107267 ◽

2021 ◽

pp. 107267

Author(s):

Michael G.C. Brown ◽

Jeff Bowman ◽

Paul J. Wilson

Keyword(s):

North American ◽

De Novo ◽

Transcriptome Assembly ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Flying Squirrels

Download Full-text

The brain transcriptome of the wolf spider, Schizocosa ocreata

BMC Research Notes ◽

10.1186/s13104-021-05648-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Daniel Stribling ◽

Peter L. Chang ◽

Justin E. Dalton ◽

Christopher A. Conow ◽

Malcolm Rosenthal ◽

...

Keyword(s):

Gene Expression ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Wolf Spiders ◽

Schizocosa Ocreata ◽

Genomic Studies ◽

The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

Download Full-text

Sub-Chronic Effects of Slight PAH- and PCB-Contaminated Mesocosms in Paracentrotus lividus Lmk: A Multi-Endpoint Approach and De Novo Transcriptomic

International Journal of Molecular Sciences ◽

10.3390/ijms22136674 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6674

Author(s):

Luisa Albarano ◽

Valerio Zupo ◽

Davide Caramiello ◽

Maria Toscanesi ◽

Marco Trifuoggi ◽

...

Keyword(s):

De Novo ◽

Sea Urchins ◽

Transcriptome Assembly ◽

Paracentrotus Lividus ◽

Marine Biota ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Limit Values ◽

The Impact ◽

Endpoint Approach

Sediment pollution is a major issue in coastal areas, potentially endangering human health and the marine environments. We investigated the short-term sublethal effects of sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on the sea urchin Paracentrotus lividus for two months. Spiking occurred at concentrations below threshold limit values permitted by the law (TLVPAHs = 900 µg/L, TLVPCBs = 8 µg/L, Legislative Italian Decree 173/2016). A multi-endpoint approach was adopted, considering both adults (mortality, bioaccumulation and gonadal index) and embryos (embryotoxicity, genotoxicity and de novo transcriptome assembly). The slight concentrations of PAHs and PCBs added to the mesocosms were observed to readily compartmentalize in adults, resulting below the detection limits just one week after their addition. Reconstructed sediment and seawater, as negative controls, did not affect sea urchins. PAH- and PCB-spiked mesocosms were observed to impair P. lividus at various endpoints, including bioaccumulation and embryo development (mainly PAHs) and genotoxicity (PAHs and PCBs). In particular, genotoxicity tests revealed that PAHs and PCBs affected the development of P. lividus embryos deriving from exposed adults. Negative effects were also detected by generating a de novo transcriptome assembly and its annotation, as well as by real-time qPCR performed to identify genes differentially expressed in adults exposed to the two contaminants. The effects on sea urchins (both adults and embryos) at background concentrations of PAHs and PCBs below TLV suggest a need for further investigations on the impact of slight concentrations of such contaminants on marine biota.

Download Full-text

De novo Transcriptome Assembly of a Chinese Locoweed (Oxytropis ochrocephala) Species Provides Insights into Genes Associated with Drought, Salinity, and Cold Tolerance

Frontiers in Plant Science ◽

10.3389/fpls.2015.01086 ◽

2015 ◽

Vol 6 ◽

Cited By ~ 6

Author(s):

Wei He ◽

Huihui Zhuang ◽

Yanping Fu ◽

Linwei Guo ◽

Bin Guo ◽

...

Keyword(s):

Cold Tolerance ◽

De Novo ◽

Transcriptome Assembly ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome

Download Full-text

Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

Plant Genetic Resources ◽

10.1017/s147926211400032x ◽

2014 ◽

Vol 12 (S1) ◽

pp. S83-S86 ◽

Cited By ~ 1

Author(s):

Yul-Kyun Ahn ◽

Swati Tripathi ◽

Young-Il Cho ◽

Jeong-Ho Kim ◽

Hye-Eun Lee ◽

...

Keyword(s):

Molecular Markers ◽

Next Generation Sequencing ◽

De Novo ◽

Transcriptome Assembly ◽

Sequence Variant ◽

Nucleotide Polymorphisms ◽

Next Generation ◽

Chilli Pepper ◽

Next Generation Sequencing Technology ◽

Generation Sequencing

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

Download Full-text