Genome Analysis Project– Paper 4

First things first: Data Organization

All data is organized into three main directories:

• code/
  Contains all scripts/code for each tool and process.

• data/
  Stores outcomes, statistics, and plots in formats like .html, .txt, .csv, and .pdf.

• images/
  Exclusively for plots in .png format (GitHub wiki-friendly).

  • Note: R-generated plots are found only here, while other plots (for example .pdf) are also available in Data/.

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Paper: Chromosome-level genome assembly of Niphotrichum japonicum provides new insights into heat stress responses in mosses

Authors: Xuping Zhou, Tao Peng, Yuying Zeng, Yuqing Cai, Qin Zuo, Li Zhang, Shanshan Dong, Yang Liu

Project Overview

This paper presents a high-quality de novo chromosome-level genome assembly of the moss Niphotrichum japonicum to understand heat defense mechanisms induced by gene activity. Nanopore long reads combined with Hi-C scaffolding produced 14 pseudochromosomes, followed by comparative genomics. Both previously known and species-specific genes showed differential expression under 12 hours of heat stress exposure. These discoveries are crucial for understanding resilient plant responses to extreme conditions.

In this project, I will attempt to recreate the results by:

1. Building chromosome 3 of Niphotrichum japonicum
2. Performing differential expression analysis

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Pipeline Steps & Tools

Main Workflow:

1. Reads Pre-processing

   • FastQC
   • Trimmomatic

2. Genome Assembly

   • FLYE

3. Assembly Quality Assessment

   • BUSCO
   • QUAST

4. DNA Mapping

   • BWA

5. Genome Polishing

   • Pilon

6. Polish Quality Assessment

   • QUAST

7. Polished DNA Mapping

   • BWA

8. Duplicate Marking

   • Samtools

9. Hi-C Scaffolding (extra analysis)

   • YAHS
   • Juicer

10. Scaffold Quality Assessment

    • QUAST

11. Repeat Masking

    • RepeatMasker

12. RNA Mapping

    • hisat2

13. Structural Annotation

    • BRAKER2

14. Functional Annotation

    • eggNOGmapper

15. Differential Expression Analysis

    • featureCounts
    • DESeq2

16. Chloroplast Assembly & Analysis (extra analysis)

    • GetOrganelle
    • QUAST