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Related Experiment Video

Updated: Jan 6, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics.

Dyfed Lloyd Evans^1,2,3, Thandekile Thandiwe Hlongwane¹, Shailesh V Joshi^1,4

¹Plant Breeding, South African Sugarcane Research Institute, Durban, KwaZulu-Natal, South Africa.

|October 4, 2019

Summary

This summary is machine-generated.

Mitochondrial genomes, unlike chloroplast genomes, offer sufficient phylogenetic signals for distinguishing sugarcane cultivars. This study reveals complex mitochondrial transcript processing and identifies two cytoplasmic male sterility factors in sugarcane.

Keywords:

Cytoplasmic male sterility Mitochondria Phylogenetics Plastomes RNA splicing Saccharum cultum Sugarcane Sugarcane origins

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Published on: July 27, 2018

Area of Science:

Plant genomics
Molecular biology
Phylogenetics

Background:

Chloroplast genomes lack sufficient phylogenetic information for closely related sugarcane cultivars due to recent origins and conserved sequences.
Plant mitochondrial genomes are larger, more plastic, and potentially hold greater phylogenetic signals.

Purpose of the Study:

To assemble a reference mitochondrion for sugarcane using long-read sequencing technologies.
To analyze sugarcane and sorghum mitochondrial transcriptomes and improve sugarcane mitochondrion annotation.
To investigate the phylogenetic utility of mitochondrial genomes for sugarcane cultivar discrimination.

Main Methods:

Mitochondrial genomes were assembled using a bait and assemble methodology with Illumina TruSeq and Oxford Nanopore Technologies MinION long reads.
Mitochondrial genomes were exhaustively annotated using BLAST; transcript datasets were mapped with HISAT2.
Phylogenomic analysis was performed using assembled mitogenomes.

Main Results:

The sugarcane mitochondrion consists of two non-recombining chromosomes.
Phylogenomic analysis using mitogenomes successfully distinguished closely related sugarcane cultivars and clarified the ancestry of modern sugarcane.
Two cytoplasmic male sterility (CMS) factors were identified within the sugarcane mitochondrion, both of which are transcribed.

Conclusions:

Sugarcane mitochondrial transcript processing is complex, involving extensive cross-chromosomal splicing events.
The study provides the first annotation of two CMS factors in the sugarcane mitochondrion, indicating the presence of necessary molecular machinery for CMS.
Mitogenomes are demonstrated to be valuable tools for phylogenomic studies in sugarcane.