Abstract
BACKGROUND AND AIMS: The mitochondrial genomes of plants are large, with the majority ranging between 500 and 800 kb. However, the mitochondrial genomes of Cyperaceae (sedges) species were found to be much larger, exceeding 1 Mb in size. Here we aimed to investigate the gigantism of the mitochondrial genomes of three Rhynchospora (beak sedges) species and one related species of the sister family Juncaceae, the common rush (Juncus effusus). METHODS: Long PacBio HiFi reads were sequenced and assembled using hifiasm software. The mitochondrial genomes were annotated using Geneious and Mitofy software. Transposable elements were annotated using DANTE and RepeatModeler pipelines, and gene prediction in intergenic regions was conducted using Augustus. The predicted genes were annotated using BLAST and gene ontology terms. KEY RESULTS: The mitogenome of R. breviuscula was 2 222 920 bp, that of R. pubera was 2 064 773 bp, that of R. tenuis was 1 678 054 bp and that of J. effusus was 553 985 bp. The results revealed giant intergenic spaces in all three Rhynchospora species, containing predicted nuclear genes and LTR retrotransposons. BLASTn revealed a high migration of DNA from the nucleus to the mitogenome. CONCLUSIONS: Our findings show that the Rhynchospora mitogenome is the largest among the monocotyledons. These mitogenomes feature giant intergenic spaces, incorporation of chloroplast DNA and numerous rearrangements. Gigantism of the intergenic spaces is associated with the movement of nuclear DNA segments, suggesting a mechanism of DNA transfer from the nuclear genome to the mitochondrial genome.
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Claims 10
Claim · model-written summary
The R. breviuscula mitogenome is 2 222 920 bp
- Taxon
- R. breviusculaRhynchospora breviusculae0
- Material
- R. breviusculae0
- Outcome
- mitogenomee0
- Value
- 2 222 920 bpe0
Verbatim
e0“The mitogenome of R. breviuscula was 2 222 920 bp”
t0“Giant mitogenomes in Rhynchospora”
Claim · model-written summary
The R. pubera mitogenome is 2 064 773 bp
- Taxon
- R. puberaRhynchospora puberae0
- Outcome
- mitogenomee0
- Value
- 2 064 773 bpe0
Verbatim
e0“The mitogenome of R. breviuscula was 2 222 920 bp, that of R. pubera was 2 064 773 bp”
t0“Giant mitogenomes in Rhynchospora”
Claim · model-written summary
The R. tenuis mitogenome is 1 678 054 bp
- Taxon
- R. tenuisRhynchospora tenuise0
- Outcome
- mitogenomee0
- Value
- 1 678 054 bpe0
Verbatim
e0“The mitogenome of R. breviuscula was 2 222 920 bp, that of R. pubera was 2 064 773 bp, that of R. tenuis was 1 678 054 bp”
t0“Giant mitogenomes in Rhynchospora”
Claim · model-written summary
The Juncus effusus mitogenome is 553 985 bp
- Taxon
- J. effusus
Juncus effususe0 - Outcome
- mitogenomee0
- Value
- 553 985 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The mitogenome of R. breviuscula was 2 222 920 bp, that of R. pubera was 2 064 773 bp, that of R. tenuis was 1 678 054 bp and that of J. effusus was 553 985 bp”
Claim · model-written summary
The three Rhynchospora mitogenomes have giant intergenic spaces containing predicted nuclear genes and LTR retrotransposons
- Taxon
- Rhynchospora species
Rhynchosporae1 - Outcome
- giant intergenic spacese1
- Qualifier
- containing predicted nuclear genes and LTR retrotransposonse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The results revealed giant intergenic spaces in all three Rhynchospora species, containing predicted nuclear genes and LTR retrotransposons”
t0“Giant mitogenomes in Rhynchospora”
Claim · model-written summary
BLASTn revealed a high migration of DNA from the nucleus to the mitogenome
- Taxon
- RhynchosporaRhynchosporat0
- Outcome
- migration of DNA from the nucleus to the mitogenomee2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“BLASTn revealed a high migration of DNA from the nucleus to the mitogenome”
t0“Giant mitogenomes in Rhynchospora”
Claim · model-written summary
The Rhynchospora mitogenome is the largest among the monocotyledons
- Taxon
- RhynchosporaRhynchosporae3
- Outcome
- largest among the monocotyledonse3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e3“Our findings show that the Rhynchospora mitogenome is the largest among the monocotyledons”
Claim · model-written summary
These mitogenomes feature giant intergenic spaces, chloroplast DNA incorporation and numerous rearrangements
- Taxon
- RhynchosporaRhynchosporat0
- Outcome
- giant intergenic spaces, incorporation of chloroplast DNA and numerous rearrangementse4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“These mitogenomes feature giant intergenic spaces, incorporation of chloroplast DNA and numerous rearrangements”
t0“Giant mitogenomes in Rhynchospora”
Claim · model-written summary
Gigantism of the intergenic spaces is associated with the movement of nuclear DNA segments
- Taxon
- RhynchosporaRhynchosporat0
- Treatment
- movement of nuclear DNA segmentse5
- Outcome
- Gigantism of the intergenic spacese5
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“Gigantism of the intergenic spaces is associated with the movement of nuclear DNA segments”
t0“Giant mitogenomes in Rhynchospora”
Claim · model-written summary
Nuclear-to-mitochondrial DNA transfer is suggested as a mechanism of intergenic gigantism
- Taxon
- RhynchosporaRhynchosporat0
- Outcome
- DNA transfer from the nuclear genome to the mitochondrial genomee6
- Qualifier
- nuclear genomee6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e6“suggesting a mechanism of DNA transfer from the nuclear genome to the mitochondrial genome”
t0“Giant mitogenomes in Rhynchospora”