DOI: 10.5061/dryad.634d24h
title: Data from: The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics

description: Background: Chloroplast genomes provide insufficient phylogenetic
 information to distinguish between closely related sugarcane cultivars,
 due to the recent origin of many cultivars and the conserved sequence of
 the chloroplast. In comparison, the mitochondrial genome of plants is much
 larger and more plastic and could contain increased phylogenetic signals.
 We assembled a consensus reference mitochondrion with Illumina TruSeq
 synthetic long reads and ONT MinION long reads. Based on this assembly we
 also analyzed the mitochondrial transcriptomes of sugarcane and sorghum
 and improved the annotation of the sugarcane mitochondrion as compared
 with other species. Methods: Mitochondrial genomes were assembled
 from genomic read pools using a bait and assemble methodology. The
 mitogenome was exhaustively annotated using BLAST and transcript datasets
 were mapped with HISAT2 prior to analysis with the Integrated Genome
 Viewer. Results: The sugarcane mitochondrion is comprised of two
 independent chromosomes, for which there is no evidence of recombination.
 Based on the reference assembly from the sugarcane cultivar SP80-3280 the
 mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and
 SP70-1143) were assembled (with the SP70-1143 assembly utilizing both
 genomic and transcriptomic data and the R570 data based on MinION
 assembly). We demonstrate that the sugarcane plastome is completely
 transcribed and we assembled the chloroplast genome of SP80-3280 using
 transcriptomic data only. Phylogenomic analysis using mitogenomes allow
 closely related sugarcane cultivars to be distinguished and supports the
 discrimination between Saccharum officinarum and Saccharum cultum as
 modern sugarcane’s female parent. From whole chloroplast comparisons, we
 demonstrate that modern sugarcane arose from a limited number of S. cultum
 female founders. Transcriptomic and spliceosomal analyses reveal that the
 two chromosomes of the sugarcane mitochondrion are combined at the
 transcript level and that splice sites occur more frequently within gene
 coding regions than without. We reveal one confirmed and one potential
 cytoplasmic male sterility factor in the sugarcane mitochondrion, both of
 which are transcribed Conclusion: Transcript processing in the
 sugarcane mitochondrion is highly complex with diverse splice events, the
 majority of which span the two chromosomes. PolyA baited transcripts are
 consistent with the use of polyadenylation for transcript degradation. For
 the first time we annotate two cytoplasmic male sterility factors within
 the sugarcane mitochondrion and demonstrate that sugarcane possesses all
 the molecular machinery required for cytoplasmic male sterility and
 rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is
 proposed. We also demonstrate that mitogenomes can be used to perform
 phylogenomic studies on sugarcane cultivars.
description: Phylogenetic analyses
 and raw alignments for the paper This compressed
 directory contains all the base phylogenies performed on the sugarcane
 mitochondrial assemblies. Folders contained within are: mt1 alignment and
 maximum likelihood of all the sugarcane mitochondrial chromosome 1
 assemblies, along with outgroups. mt2 alignment and maximum likelihood of
 all the sugarcane mitochondrial chromosome 2 assemblies, along with
 outgroups. This is the reference dataset on which subsequent analyses were
 performed. merged alignment and maximum likelihood of all the combined
 sugarcane mitochondrial chromosome 1 and 2 assemblies along with
 outgroups. Phylos.zip
 
 Sequences from
 third party data presented in the paper Assemblies within the
 compressed directory are detailed below: Complete assemblies of the
 Saccharum hybrid SP70-1143 and SP80-3280 sugarcane cultivar chloroplasts
 produced with transcriptomic data only: SP80-tc.embl
 Saccharum_hybrid_SP70-1143-tc.embl Complete assembly of the Saccharum
 hybrid SP70-1143 mitochondrial genome produced with combined
 transcriptomic and nuclear DNA datasets: Saccharum_hybrid_SP70-1143-mt1.fa
 Saccharum_hybrid_SP70-1143-mt2.fa Partial assembly of the Saccharum
 officinarum IJ76-514 cultivar mitochondrial genome:
 Saccharum_officinarum_IJ76-514-mt1.fa
 Saccharum_officinarum_IJ76-514-mt2.fa Mappings of the partial assemblies
 of Saccharum spontaneum SES234B mitochondrial genome and Miscanthus
 sinensis cv Andante mitochondrial genomes to the reference SP80-3280
 sugarcane mitogenome Saccharum_spontaneum_SES234B-mt1.fa
 Saccharum_spontaneum_SES234B-mt2.fa Miscanthus_sinensis_cv_Andante-mt1.fa
 Miscanthus_sinensis_cv_Andante-mt2.fa Partial assembly of mitogenomes
 containing CMS2 Chrysopogon_zizanoides-cms.fa (transcriptomic data)
 Sarga_versicolor-CMS2.fa Tripsacum_dactyloides-tc.fa (transcriptomic data)
 Assembly of mitochondrial nad6 from transcriptomic data
 Chrysopogon_zizanoides-nad6-mt.fa Sequences.zip
 
 Copies of EMBL
 formatted files submitted to ENA Copies of EMBL formatted
 files submitted to ENA for review. Directories are named after the
 reference ENA projects that the files have been submitted under.
 PRJEB26367-mt Complete mitochondrial assemblies of the sugarcane cultivars
 LCP85-3840, RB72454 and SP80-3260 in EMBL format PRJEB26685-cp Complete
 assembly of the sugarcane cultivar SP80-3280 chloroplast genome from
 Illumina synthetic long reads in EMBL format. PRJEB31395-tc Complete
 assemblies of the R570 mitochondrial chromosomes and chloroplasts based on
 genome capture and MinIN long read assembly along with the associated
 MinION reads. Complete assemblies of the mitochondrial genome restorer of
 function transcripts GRP162, DSK2 and RF1 from the sugarcane cultivars N22
 and SP80-3280 from transcriptomic data in EMBL format. In addition,
 assemblies of the two mitochondral genome sequence stabilizing transcripts
 RECA1 and RECG from SP80-3280 ar presented. PRJEB31395-cms Partial
 mitochondral sequences covering the potential second CMS factor in
 sugarcane from Andropogon virginicus, Coix lacryma-jobi, Miscanthus
 sinensis cv Andante and Saccharum spontaneum cv SES234B
 ENA_submission_files.zip