Rapid evolution of piRNA pathway and its transposon targets in Japanese flounder (Paralichthys olivaceus)

Song, Haofei; Xing, Changjin; Lü, Wei; Liu, Zeyu; Wang, Xubo; Cheng, Jie; Zhang, Quanqi

doi:10.1016/j.cbd.2019.100609

Cited by 12 publications

(20 citation statements)

References 35 publications

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“…Other limitations are that inter-family ambiguities still occur, the number of loci expressed is unknown, and most reads remain unmapped, complicating normalization and sample-to-sample comparisons. Nevertheless, when studying species for which a reference genome or transcriptome is not available, they may be the only options for obtaining a first glimpse of the TE transcriptome [137][138][139] .…”

Section: Mappabilitymentioning

confidence: 99%

Measuring and interpreting transposable element expression

2020

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Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur, but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA-sequencing include transposon-derived transcripts, the majority of computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from gene-TE chimeric transcripts or pervasive transcription. Here, we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.

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Section: Mappabilitymentioning

confidence: 99%

Measuring and interpreting transposable element expression

2020

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“…After two rounds of WGD in vertebrates, there is a third round in the evolution of the teleost lineage, termed as teleost-specific (TS)-WGD, which could provide a large amount of raw information for adaptive evolution and innovation (Glasauer and Neuhauss 2014;Sato and Nishida 2010). In this manner, several studies have reported that adaptive evolution could influence the piRNA pathway in teleost lineages consistent with the diversity of TEs in teleost genomes (Parhad and Theurkauf 2019), which supported the association of TE diversity with the piRNA pathway evolution in teleost fish, such as in Japanese flounder (Paralichthys olivaceus) (Song et al 2019) and swamp eel (Monopterus albus) (Yi et al 2014).…”

Section: Introductionmentioning

confidence: 81%

“…Many piRNA pathway genes may have undergone evolutionary adaptation reported dominantly in human (e.g., Piwil1-4), Drosophila (e.g., Piwi, Ago3, and Aubergene) and C. elegans (e.g., PRG1-2). They are all under evolutionary pressure with piRNA-dependent transposon silencing (Gan et al 2019;Parhad and Theurkauf 2019;Simkin et al 2013;Song et al 2019;Wynant et al 2017). With high reproductive diversity in teleosts, which are subject to challenges from dynamic aquatic environments, the reproduction-related genes have previously been deemed to be under stronger adaptive evolution in teleosts than their orthologous counterparts in mammals (Yi et al 2014).…”

Section: Rapid Evolution Of Tdrd Genes In Teleosts Than In Mammalsmentioning

confidence: 99%

“…Therefore, the piRNA pathway in teleosts, as a protector of the genome in silencing TEs, is suggested to be under intensive evolutionary selection, probably coping with the higher abundance and diversity of transposons (Chalopin et al 2015). For example, the rapid evolution of PIWI proteins in several fish, such as in swamp eel (Yi et al 2014), Japanese flounder (Song et al 2019) and tilapia (Tao et al 2016) was reported. With the molecular evolution analysis, we highlighted that adaptive evolution was likely also to be present in the Tdrd family genes of teleost lineages, which could interact with PIWI proteins during the pingpong cycle.…”

Section: Rapid Evolution Of Tdrd Genes In Teleosts Than In Mammalsmentioning

confidence: 99%

“…The coding nucleotide sequences of each Tdrd were aligned using Clustal W with option -codons to make a codon alignment, and the ML tree was built with MEGA 7.0 to provide their evolutionary relationships (Supplementary Material S1). The codon based model tests were performed with the package PAML v4.9 (Yang 2007;Yang et al 2005) as explained in detail by Song et al (2019).…”

Section: Paml Analysismentioning

confidence: 99%

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Evolutionary dynamics and conserved function of the Tudor domain-containing (TDRD) proteins in teleost fish

Liu

Guo

et al. 2021

Mar Life Sci Technol

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Tudor domain-containing (TDRD) proteins, the germline enriched protein family, play essential roles in the process of gametogenesis and genome stability through their interaction with the PIWI-interacting RNA (piRNA) pathway. Several studies have suggested the rapid evolution of the piRNA pathway in teleost lineages with striking reproductive diversity. However, there is still limited information about the function and evolution of Tdrd genes in teleost species. In this study, through genome wide screening, 13 Tdrd family genes were identified in economically important aquaculture fish, including spotted sea bass (Lateolabrax maculatus), Asian sea bass (Lates calcarifer), and tongue sole (Cynoglossus semilaevis). With copy number, structure, phylogeny, and synteny analysis, duplication of Tdrd6 and Tdrd7, as well as loss of Stk31 and Tdrd10, were characterized in teleost lineages. Codon based molecular evolution analysis indicated faster evolution of teleost Tdrd genes than that in mammals, potentially associated with the accelerated evolution of the piRNA pathway in teleost lineages. The evolutionary diversity of Tdrd genes was also detected between different teleost lineages. RNA-seq analysis showed that most teleost Tdrd genes were dominantly expressed in gonads, particularly highly expressed in testis, such as Tdrd6, Tdrd7a, Tdrd9, Ecat8, and Tdrd15. The varied expression and evolutionary pattern between the duplicated Tdrd6 and Tdrd7 in teleosts may indicate their functional diversification. All these results suggest a conserved function of teleost Tdrd family in gametogenesis and the piRNA pathway, which could lay a foundation for the evolution of Tdrd genes and be helpful for further deciphering of Tdrd functions in teleosts.

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Comparative piRNAs Profiles Give a Clue to Transgenerational Inheritance of Sex-Biased piRNAs in Cynoglossus semilaevis

Zhao

Deng

et al. 2022

Mar Biotechnol

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Rapid evolution of piRNA pathway and its transposon targets in Japanese flounder (Paralichthys olivaceus)

Cited by 12 publications

References 35 publications

Measuring and interpreting transposable element expression

Measuring and interpreting transposable element expression

Evolutionary dynamics and conserved function of the Tudor domain-containing (TDRD) proteins in teleost fish

Comparative piRNAs Profiles Give a Clue to Transgenerational Inheritance of Sex-Biased piRNAs in Cynoglossus semilaevis

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