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BMC Genomics. 2018 Aug 14;19(1):614. doi: 10.1186/s12864-018-4991-4.

The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.

Dong S1,2, Zhao C1,3, Chen F4,5,6, Liu Y4,5,6, Zhang S1, Wu H2, Zhang L7,8,9, Liu Y10,11.

Author information

1
Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
2
College of Life Sciences, South China Agricultural University, Guangzhou, China.
3
Department of Biology, School of Life Sciences, East China Normal University, Shanghai, China.
4
State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China.
5
Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China.
6
Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China.
7
State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China. fafuzhang@163.com.
8
Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China. fafuzhang@163.com.
9
Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China. fafuzhang@163.com.
10
Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China. yang.liu0508@gmail.com.
11
BGI-Shenzhen, Shenzhen, 518083, China. yang.liu0508@gmail.com.

Abstract

BACKGROUND:

Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms.

RESULTS:

Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome.

CONCLUSIONS:

The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.

KEYWORDS:

Mitochondrial genome; Nymphaea; PacBio sequencing; Recombination; Repeats

PMID:
30107780
PMCID:
PMC6092842
DOI:
10.1186/s12864-018-4991-4
[Indexed for MEDLINE]
Free PMC Article

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