De novo transcriptome assembly of four organs of Collichthys lucidus and identification of genes involved in sex determination and reproduction

2019 ◽  
Author(s):  
Wei Song ◽  
Yi-Bing Zhang ◽  
Xiao-Juan Zhang ◽  
Jianfang Gui
Keyword(s):  
Sex Determination ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Sex Differentiation ◽  
Molecular Regulation ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Sexual Characteristics ◽  
Collichthys Lucidus

Abstract Background Spinyhead croaker (Collichthys lucidus) is an important kind of fish for commercial fishery because of its delicious meat and abundant resource. However, the resource has been declining with the overfishing and environmental disruption. Unfortunately, the mechanism of sex determination and reproduction in Collichthys lucidus is still confusing, which has largely hindered molecular regulation and reproduction studies. Results Based on transcripts sequencing in brain, liver, ovary and testis, a de novo transcriptome assembly of Collichthys lucidus was performed. Totally, 131,168 non-redundant unigenes with an average length of 644 bp and an N50 value of 1033 bp, among which 2,143, 304, 333 and 556 were found specifically expressing in brain, liver, ovary and testis, respectively. Importantly, 1288 genes were differently expressed between ovary and testis, including 442 up- and 846 down-regulated in ovary. The differently expressed genes were involved in function of sexual reproduction, sex differentiation, development of primary male sexual characteristics, female gamete generation, and male sex differentiation. HYAL and SYCP3, two genes which were reported to play dominant roles in reproduction, may regulated the key of fertilization and meiosis in Collichthys lucidus. Meanwhile, 35,476 simple sequence repeats (SSRs) were identified, which would contribute to further genetic and mechanism researches. Conclusions The studies of genetic information, molecular regulation and reproduction of Collichthys lucidus would be expand due to the sequencing and de novo assembling on the transcripts of major organs. In addition, the identification of candidate genes involved in reproduction will be useful for protecting the resource of Collichthys lucidus.

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

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.

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

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.

scholarly journals De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e96855 ◽  
Author(s):  
Samuel E. Fox ◽  
Matthew Geniza ◽  
Mamatha Hanumappa ◽  
Sushma Naithani ◽  
Chris Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Triticum Monococcum ◽  
Diploid Wheat ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome

scholarly journals Sequencing and De Novo Transcriptome Assembly ofBrachypodium sylvaticum(Poaceae)

2013 ◽  
Vol 1 (3) ◽  
pp. 1200011 ◽  
Author(s):  
Samuel E. Fox ◽  
Justin Preece ◽  
Jeffrey A. Kimbrel ◽  
Gina L. Marchini ◽  
Abigail Sage ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome

scholarly journals RNA-Seq Based De Novo Transcriptome Assembly and Gene Discovery of Cistanche deserticola Fleshy Stem

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0125722 ◽  
Author(s):  
Yuli Li ◽  
Xiliang Wang ◽  
Tingting Chen ◽  
Fuwen Yao ◽  
Cuiping Li ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Gene Discovery ◽  
De Novo Transcriptome Assembly ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Cistanche Deserticola
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