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Reproductive switching analysis of Daphnia similoides between sexual female and parthenogenetic female by transcriptome comparison

View Article: PubMed Central - PubMed

ABSTRACT

The water flea Daphnia are planktonic crustaceans commonly found in freshwater environment that can switch their reproduction mode from parthenogenesis to sexual reproduction to adapt to the external environment. As such, Daphnia are great model organisms to study the mechanism of reproductive switching, the underlying mechanism of reproduction and development in cladocerans and other animals. However, little is known about the Daphnia’s reproductive behaviour at a molecular level. We constructed a genetic database of the genes expressed in a sexual female (SF) and a parthenogenetic female (PF) of D. similoides using Illumina HiSeq 2500. A total of 1,763 differentially expressed genes (865 up- and 898 down-regulated) were detected in SF. Of the top 30 up-regulated SF unigenes, the top 4 unigenes belonged to the Chitin_bind_4 family. In contrast, of the top down-regulated SF unigenes, the top 3 unigenes belonged to the Vitellogenin_N family. This is the first study to indicate genes that may have a crucial role in reproductive switching of D. similoides, which could be used as candidate genes for further functional studies. Thus, this study provides a rich resource for investigation and elucidation of reproductive switching in D. similoides.

No MeSH data available.


Distribution of unigene size in the D. similoides transcriptome assembly.
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f2: Distribution of unigene size in the D. similoides transcriptome assembly.

Mentions: We carried out a next-generation sequencing project on a cDNA library constructed from D. similoides (Fig. 1) using an Illumina HiSeq™ 2500 platform. Low quality raw reads and reads with adapters and N content of more than 10% were excluded. The number of clean reads obtained from SF and PF of D. similoides was 62,395,405 and 52,037,554, respectively. All clean reads were assembled into transcripts by Trinity software; the longest copy of redundant transcripts was regarded a unigene1617. In total, 61,047 transcripts were obtained and assembled into 37,385 unigenes. Of the 37,385 unigenes, those with a sequence length more than 500 bp accounted for 41.43% of the transcriptome assembly (Fig. 2). All the clean reads of SF and PF are deposited and available from the NCBI/SRA data base (SRA experiment accession number: PF: SRX1645097, SF: SRX1645182).


Reproductive switching analysis of Daphnia similoides between sexual female and parthenogenetic female by transcriptome comparison
Distribution of unigene size in the D. similoides transcriptome assembly.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037449&req=5

f2: Distribution of unigene size in the D. similoides transcriptome assembly.
Mentions: We carried out a next-generation sequencing project on a cDNA library constructed from D. similoides (Fig. 1) using an Illumina HiSeq™ 2500 platform. Low quality raw reads and reads with adapters and N content of more than 10% were excluded. The number of clean reads obtained from SF and PF of D. similoides was 62,395,405 and 52,037,554, respectively. All clean reads were assembled into transcripts by Trinity software; the longest copy of redundant transcripts was regarded a unigene1617. In total, 61,047 transcripts were obtained and assembled into 37,385 unigenes. Of the 37,385 unigenes, those with a sequence length more than 500 bp accounted for 41.43% of the transcriptome assembly (Fig. 2). All the clean reads of SF and PF are deposited and available from the NCBI/SRA data base (SRA experiment accession number: PF: SRX1645097, SF: SRX1645182).

View Article: PubMed Central - PubMed

ABSTRACT

The water flea Daphnia are planktonic crustaceans commonly found in freshwater environment that can switch their reproduction mode from parthenogenesis to sexual reproduction to adapt to the external environment. As such, Daphnia are great model organisms to study the mechanism of reproductive switching, the underlying mechanism of reproduction and development in cladocerans and other animals. However, little is known about the Daphnia’s reproductive behaviour at a molecular level. We constructed a genetic database of the genes expressed in a sexual female (SF) and a parthenogenetic female (PF) of D. similoides using Illumina HiSeq 2500. A total of 1,763 differentially expressed genes (865 up- and 898 down-regulated) were detected in SF. Of the top 30 up-regulated SF unigenes, the top 4 unigenes belonged to the Chitin_bind_4 family. In contrast, of the top down-regulated SF unigenes, the top 3 unigenes belonged to the Vitellogenin_N family. This is the first study to indicate genes that may have a crucial role in reproductive switching of D. similoides, which could be used as candidate genes for further functional studies. Thus, this study provides a rich resource for investigation and elucidation of reproductive switching in D. similoides.

No MeSH data available.