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Genome Annotation and Assembly03:36

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Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...
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Fungi are a diverse group of eukaryotes more closely related to animals than other eukaryotes. Fungal cell walls comprise chitin, a polysaccharide that provides structural strength, and glucans, which contribute to flexibility and integrity. Other polysaccharides, such as mannans and galactosans, may supplement or replace chitin in some fungi. These adaptations, along with their preference for acidic environments and tolerance for high osmotic pressure, enable fungi to thrive in various...
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T2T Colletotrichum liniゲノムとHifiasm：真菌のためのONT R9およびR10リード処理とアセンブリガイドライン

Elizaveta A Ivankina1, Ekaterina M Dvorianinova1, Alexander A Arkhipov1,2

  • 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.

Journal of fungi (Basel, Switzerland)
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まとめ

最適化されたOxford Nanopore Technologies（ONT）シーケンシングとHifiasmアセンブリパラメータは、Colletotrichum liniのような病原菌の完全なテロメア間（T2T）ゲノムアセンブリを可能にします。これは、ゲノム研究と亜麻炭疽病の理解を促進します。

キーワード:
Colletotrichum liniナノポアR9.4.1およびR10.4.1フローセルT2Tゲノムアセンブリ炭疽病塩基呼び出しツール亜麻病原菌リード処理

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科学分野:

  • ゲノミクス
  • バイオインフォマティクス
  • 菌学

背景:

  • テロメア間（T2T）ゲノムアセンブリは、複雑な真菌病原菌ゲノムを理解するために重要です。
  • Colletotrichum liniは、重大な亜麻炭疽病を引き起こし、詳細なゲノム解析を必要とします。

研究 の 目的:

  • Oxford Nanopore Technologies（ONT）シーケンシングデータを使用したT2Tゲノムアセンブリのガイドラインを最適化すること。
  • アセンブリ品質の向上のために、異なる塩基呼び出しツール、リードフィルタリング戦略、およびゲノムカバレッジレベルを評価すること。

主な方法:

  • 4つのC. lini株からのONT R9.4.1およびR10.4.1シーケンシングデータを解析しました。
  • GuppyおよびDorado塩基呼び出し、品質/長さリードフィルタリング（Q10/Q15、5kb/10kb）、およびカバレッジ（5x-160x）を比較しました。
  • ゲノムアセンブリには、Hifiasm 0.25.0アセンブラーと--ontモジュールを使用しました。

主要な成果:

  • Dorado塩基呼び出しは、特にR10.4.1データで、リードの品質とテロメアの解像度を向上させました。
  • 最適なアセンブリは、中程度のカバレッジ（40-65x）と特定のフィルタリング（R10.4.1の場合はQ15/5kb、R9.4.1の場合はQ10/5kb）で達成されました。
  • T2T/ほぼT2Tアセンブリ（53.7-56.1 Mb）、12-13染色体、完全なミトコンドリアゲノム、および98.5%以上のBUSCO完全性を達成しました。

結論:

  • 最適化されたONTデータ前処理とHifiasmアセンブリは、C. liniの高品位T2Tゲノムをもたらします。
  • ONT技術を使用した真菌ゲノムアセンブリのための堅牢なフレームワークを確立しました。
  • 本研究の結果は、Colletotrichum属のゲノム変異と病原性に関する将来の研究を支持します。