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浮上する特質ベースのゲノミクスでモデル化された海洋生地化学

V J Coles1, M R Stukel2, M T Brooks3

  • 1Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Post Office Box 775, Cambridge, MD 21613, USA. vcoles@umces.edu.

Science (New York, N.Y.)
|December 2, 2017
PubMed
まとめ

海洋生態系モデルはメタゲノムとメタトランスクリプトームをシミュレートし コミュニティが

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科学分野:

  • 海の微生物生態学
  • 計算生物学
  • ゲノムとトランスクリプトミックのモデリング

背景:

  • 海洋生態系モデルは 代謝経路に関するゲノムデータを 統合しています
  • これらのモデルを経験的メタゲノミクスとメタトランスクリプトミクスデータと直接比較する際にはギャップが存在します.
  • 微生物の集合と機能のシミュレーションは 最初の原則から難しいものです

研究 の 目的:

  • メタゲノムとメタトランスクリプトームをシミュレートした新しいモデルを開発し,観測データと直接比較する.
  • モデル海洋生態系における微生物の集合と生地化学的グラデーションの原動力を調査する.
  • 生態系特性の形成におけるコミュニティ構成と遺伝子機能分布の役割を評価する.

主な方法:

  • メタゲノムとメタトランスクリプトームを直接シミュレートする計算モデルを開発した.
  • ランダムに割り当てられた遺伝子は 68種のコミュニティ内の微生物をモデル化するための 特殊な機能を持っています
  • 仮想大西洋の生態学的動態をシミュレートし,フィットネスに基づく生物の置換を含みます.

主要な成果:

  • モデルが自己組織化して コミュニティゲノムとトランスクリプトームを生成します
  • シミュレーションは一貫して栄養素,ゲノム,トランスクリプトームの リアルな垂直と水平のグラデーションを生成しました
  • これらの現実的なパターンは 微生物間の遺伝子機能の初期分布に関係なく 生まれました

結論:

  • 微生物コミュニティ内の遺伝子機能の集合図書館は,その組み立てと生地化学的機能の主要な原動力です.
  • 生体間の特定の分布ではなく コミュニティレベルでの遺伝子レパートリーが 生態系の構造とグラデーションを決定します
  • このモデリングアプローチは,海洋環境における生態系機能とゲノムの可能性を結びつけるための枠組みを提供します.