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Generation of Expressed Sequence Tags and development of microsatellite markers for Castanopsis sieboldii var. sieboldii (Fagaceae)

Generation de marqueurs de séquences exprimées et développement de marqueurs microsatellites pour Castanopsis sieboldii var. sieboldii (Fagaceae)

Abstract

  • Castanopsis sieboldii var. sieboldii is an evergreen broadleaved canopy tree that grows on Honshu, Shikoku and Kyushu Islands in Japan. A closely-related, hybridizing, congener species, C. cuspidata var. cuspidata, has different leaf epidermis structure and different seed nuts morphology compared to C. sieboldii var. sieboldii. Furthermore, the habitats in which the two species grow often indicate different water requirements.

  • • Analysis of genetic diversity, using transcribed sequences, will provide a sound basis for the management of this species, allowing successful reforestation, incorporating phylogeographic conservation. In order to obtain transcripts sequences for the species and to develop transcript-based markers, we constructed and analyzed a cDNA library, surveyed microsatellite sequences within it and designed PCR primers for the microsatellites.

  • • The cDNA library was constructed using tissue from the inner bark of C. sieboldii var. sieboldii; 3 354 Expressed Sequence Tags (ESTs) were identified. We constructed 2 417 putative unigenes and assigned putative functions to 1 856 of them. Three hundred and fourteen microsatellites were found within the putative unigenes and 16 EST-SSR (Simple Sequence Repeat) markers were developed. The EST-SSR markers developpe in this study should facilitate future analysis of the genetic diversity of this and related species.

Résumé

  • Castanopsis sieboldii var. sieboldii est un feuillu sempervirent qui pousse sur les îles japonaises de Honshu, Shikoku et Kyushu. C. cuspidata var. cuspidata une espèce congénère, étroitement liée, hybridée, a une structure de l’épiderme des feuilles différente et une morphologie différente des noix semences par rapport à C. sieboldii var. sieboldii. En outre, les habitats dans lesquels les deux espèces poussent indiquent souvent des besoins en eau différents.

  • • L’analyse de la diversité génétique, en utilisant des séquences transcrites, fournira une base solide pour la gestion de cette espèce, ce qui permettra le succès des reboisements, en intégrant une conservation phylogéographique. Afin d’obtenir les transcriptions des séquences de l’espèce et de mettre au point des marqueurs à base de transcription, nous avons construit et analysé une banque d’ADNc, étudié des séquences microsatellites et conçu des amorces PCR pour les microsatellites.

  • • La banque d’ADNc a été construite en utilisant les tissus de l’écorce interne de C. sieboldii var. sieboldii, 3 354 marqueurs de séquences exprimées (EST) ont été identifiés. Nous avons construit 2 417 unigènes putatifs et assigné des fonctions putatives à 1 856 d’entre eux. Trois cents quatorze microsatellites ont été trouvés à l’intérieur des unigènes putatifs et 16 EST-SSR (Simple Sequence Repeat) marqueurs ont été développés. Les marqueurs EST-SSR développés dans cette étude devraient faciliter l’analyse future de la diversité génétique de cette espèce et des espèces apparentées.

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Ueno, S., Aoki, K. & Tsumura, Y. Generation of Expressed Sequence Tags and development of microsatellite markers for Castanopsis sieboldii var. sieboldii (Fagaceae). Ann. For. Sci. 66, 509 (2009). https://doi.org/10.1051/forest/2009037

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Keywords

  • broadleaved tree
  • gene ontology
  • Castanopsis cuspidata var. cuspidata
  • Castanopsis sieboldii var. lutchuensis
  • Castanopsis sieboldii var. carlesii

Mots-clés

  • arbre feuillu sempervirent
  • Castanopsis cuspidata var. cuspidata
  • Castanopsis sieboldii var. lutchuensis
  • Castanopsis sieboldii var. carlesii