The Dugesia ryukyuensis Database as a Molecular Resource for Studying Switching of the Reproductive System

Ishizuka, Hideyuki; Maezawa, Takanobu; Kawauchi, Junpei; Nodono, Hanae; Hirao, Yukako; Nishimura, Osamu; Nakagawa, Hiroo; Sekii, Kiyono; Tasaka, Kenta; Tarui, Hiroshi; Agata, Kiyokazu; Hoshi, Motonori; Kobayashi, Kazuya; Sakakibara, Yasubumi; Matsumoto, Midori

doi:10.2108/zsj.24.31

Cited by 28 publications

(25 citation statements)

References 20 publications

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“…The development of research tools to study gene expression and function in planarians, which include genome (Nishimura et al, 2015; Robb et al, 2015, 2008) and transcriptome (Brandl et al, 2016; Ishizuka et al, 2007; Nishimura et al, 2012; Sanchez Alvarado et al, 2002; Sasidharan et al, 2013; Zayas et al, 2005) sequences, as well as protocols for whole-mount in situ hybridization (King and Newmark, 2013; Pearson et al, 2009; Umesono et al, 1997) and RNA-interference (RNAi) (Newmark et al, 2003; Orii et al, 2003; Rouhana et al, 2013; Sanchez Alvarado and Newmark, 1999), have revitalized the use planarians as a model for molecular studies of stem cell-driven developmental processes (reviewed by Elliott and Sanchez Alvarado (2013), Newmark and Sanchez Alvarado (2002), Reddien and Sanchez Alvarado (2004), Rink (2013), Salo et al (2009) and Shibata et al (2010)). Planarians have also been the subject of recent work in toxicology, as well as behavioral, ecological, and evolutionary biology research (Alvarez-Presas et al, 2008; Hagstrom et al, 2016, 2015; Hicks et al, 2006; Inoue et al, 2015; Levin et al, 2016; Lombardo et al, 2011; Majdi et al, 2014; Shomrat and Levin, 2013), broadening their use as a model beyond fields related to developmental biology.…”

Section: Introductionmentioning

confidence: 99%

Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

Almazan

Lesko

Markey

et al. 2018

Developmental Biology

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Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities. In order to circumvent these limitations and increase the genetic information available for comparative studies, we sequenced the transcriptome of Girardia dorotocephala, a planarian species pandemic and commercially available in North America. A total of 254,802,670 paired sequence reads were obtained from RNA extracted from intact individuals, regenerating fragments, as well as freshly excised auricles of a clonal line of G. dorotocephala (MA-C2), and used for de novo assembly of its transcriptome. The resulting transcriptome draft was validated through functional analysis of genetic markers of stem cells and their progeny in G. dorotocephala. Akin to orthologs in other planarian species, G. dorotocephala Piwi1 (GdPiwi1) was found to be a robust marker of the planarian stem cell population and GdPiwi2 an essential component for stem cell-driven regeneration. Identification of G. dorotocephala homologs of the early stem cell descendent marker PROG-1 revealed a family of lysine-rich proteins expressed during epithelial cell differentiation. Sequences from the MA-C2 transcriptome were found to be 98–99% identical to nucleotide sequences from G. dorotocephala populations with different chromosomal number, demonstrating strong conservation regardless of karyotype evolution. Altogether, this work establishes G. dorotocephala as a viable and accessible option for analysis of gene function in North America.

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Section: Introductionmentioning

confidence: 99%

Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

Almazan

Lesko

Markey

et al. 2018

Developmental Biology

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“…These new tools include whole-mount immunostaining and confocal microscopy (Cebrià et al 1997;Reuter et al 1995b;Reuter et al 1996a), wholemount in situ hybridization (Umesono et al 1997), RNA interference (RNAi; Newmark et al 2003;Reddien et al 2005;Sánchez Alvarado and Newmark 1999), BrdU labeling of neoblasts (Newmark and Sánchez Alvarado 2000), expressed sequence tag (EST) collections (Ishizuka et al 2007;Sánchez Alvarado et al 2002;Zayas et al 2005), and a genome sequencing project (further information on the white paper proposal can be obtained from http://www.genome.gov/12512286). The use of these tools should allow us to improve our understanding of the regenerative process in planarians.…”

Section: Introductionmentioning

confidence: 99%

Regenerating the central nervous system: how easy for planarians!

2007

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The regenerative capabilities of freshwater planarians (Platyhelminthes) are very difficult to match. A fragment as tiny as 1/279th of the planarian body is able to regenerate a whole animal within very few days [Morgan. Arch Entwm 7:364-397 (1898)]. Although the planarian central nervous system (CNS) may appear quite morphologically simple, recent studies have shown it to be more complex at the molecular level, revealing a high degree of molecular compartmentalization in planarian cephalic ganglia. Planarian neural genes include homologues of well-known transcription factors and genes involved in human diseases, neurotransmission, axon guidance, signaling pathways, and RNA metabolism. The availability of hundreds of genes expressed in planarian neurons coupled with the ability to silence them through the use of RNA interference makes it possible to start unraveling the molecular mechanisms underlying CNS regeneration. In this review, I discuss current knowledge on the planarian nervous system and the genes involved in its regeneration, and I discuss some of the important questions that remain to be answered.

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“…Clones of the nanos homolog, Dr_sW_003_K04 and Dr_sW_028_K12 in the D. ryukyuensis ESTs (Ishizuka et al, 2007), included the complete Dr-nanos open reading frame. The full-length sequences of Dr-nanos were obtained using 3′ and 5′ rapid amplification of cDNA ends (RACE) using a SMART™ RACE cDNA Amplification Kit (Clontech, Mountain View, CA, USA).…”

Section: Identification and Cloning Of Dr-nanos Genesmentioning

confidence: 99%

The Dr-nanos gene is essential for germ cell specification in the planarian Dugesia ryukyuensis

Nakagawa

Ishizu²,

Chinone³

et al. 2012

Int. J. Dev. Biol.

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Homologs of nanos are required for the formation and maintenance of germline stem cell (GSC) systems and for gametogenesis in many metazoans. Planarians can change their reproductive mode seasonally, alternating between asexual and sexual reproduction; they develop and maintain their somatic stem cells (SSCs) and GCSs from pluripotent stem cells known as neoblasts. We isolated a nanos homolog, Dr-nanos, from the expressed sequence tags (ESTs) of the sexualized form of Dugesia ryukyuensis. We examined the expression of Dr-nanos in asexual and sexualized planarians by in situ hybridization and analyzed its function using RNA interference (RNAi) together with a planarian sexualization assay. A nanos homolog, Dr-nanos, was identified in the planarian D. ryukyuensis. Dr-nanos expression was observed in the ovarian primordial cells of the asexual worms. This expression increased in proportion to sexualization and was localized in the early germline cells of the ovaries and testes. In X-ray-irradiated worms, the expression of Dr-nanos decreased to a large extent, indicating that Dr-nanos is expressed in some subpopulations of stem cells, especially in GSCs. During the sexualization process, worms in which Dr-nanos was knocked down by RNAi exhibited decreased numbers of oogonia in the ovaries and failed to develop testes, whereas the somatic sexual organs were not affected. We conclude that Dr-nanos is essential for the development of germ cells in the ovaries and testes and may have a function in the early stages of germ cell specification, but not in the development of somatic sexual organs.

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The Dugesia ryukyuensis Database as a Molecular Resource for Studying Switching of the Reproductive System

Cited by 28 publications

References 20 publications

Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

Regenerating the central nervous system: how easy for planarians!

The Dr-nanos gene is essential for germ cell specification in the planarian Dugesia ryukyuensis

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