Functional & Integrative Genomics

, Volume 11, Issue 4, pp 599–609 | Cite as

Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage

  • Juncheng Zhang
  • Jizeng Jia
  • James Breen
  • Xiuying KongEmail author
Original Paper


The assembly of a 1.3-Mb size region of the wheat genome has provided the opportunity to study a recent nuclear mitochondrial DNA insertion (NUMT). In the present study, we have studied two bacterial artificial chromosomes (BACs) and characterized a 52-kb NUMT segment from the tetraploid and hexaploid wheat BAC libraries. The conserved orthologous NUMT regions from tetraploid and hexaploid wheat Langdon and Chinese Spring shared identical gene haplotypes even though mutations (insertions, deletions, and substitutions) had occurred. The 52-kb NUMT was present in hexaploid variety Chinese Spring, but absent in variety Hope, by sequence comparison of their corresponding region. Amplifying the NUMT junctions using a set of the wheat materials including diploid, tetraploid, and hexaploid lines showed that none of the diploid wheat carried the region and only some tetraploid and hexaploid wheat were positive for the NUMT. Age estimation of the NUMT displayed the mean ages of Langdon NUMT and Chinese Spring NUMT to be 378,000 and 416,000 years ago, respectively. Reverse transcription PCR and sequencing of the nad7 gene showed 28 C → U RNA editing sites and four partial editing sites, as expected for mitochondrial DNA expression. Specific SNPs discriminated between cDNA from the nucleus and the mitochondria and suggested that the nuclear copy was not expressed. The mitochondrial DNA studied was inserted into the genome quite recently within the wheat lineage and gave rise to the non-coding nuclear nad7 gene. The NUMT segment could be lost and acquired frequently during the wheat evolution.


Wheat NUMT nad7 gene RNA editing Evolution 



We thank Dr. Jing Wu for help in screening the high-density filters of tetraploid BAC library; Lingli Zheng, Lei Pan, and Guanhua Yang for their sequencing work; and Jiajie Wu and Qi Zuo for their sequence annotation assistance. The authors are grateful to Professor Rudi Appels for his contributions to the research in this manuscript. This research was supported by grants from the Ministry of Science and Technology of China (2006AA10A104) and Australia GRDC ET5.

Supplementary material

10142_2011_237_MOESM1_ESM.pdf (7 kb)
Supplementary Table S1 (PDF 7 kb)
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Supplementary Table S2 (PDF 8 kb)
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Supplementary Table S3 (PDF 7 kb)
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Supplementary Table S4 (PDF 8 kb)
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Supplementary Table S5 (PDF 7 kb)
10142_2011_237_MOESM6_ESM.pdf (92 kb)
Supplementary Table S6 (PDF 91 kb)
10142_2011_237_MOESM7_ESM.pdf (225 kb)
Supplementary Figure S1 Alignment of cDNA sequences of the nad7 gene. The left column represented the sequence names; the first three sequences were from mitochondria, Langdon, and Chinese Spring, respectively, which were manually spliced according to the gene annotation in the mitochondria genome by deleting the introns. The four sequences beginning with CS-cDNA were cDNA sequences from Chinese Spring; the letters following CS-cDNA represented the individual clones. Here, we only list the four representative sequences of the 16 sequenced clones due to limited space. Similarly, four sequences with names beginning with LDN-cDNA were nad7 cDNA sequences from Langdon. The sequences with the underlined black lines are the conserved primers used in the expression analysis. The vertical black lines represented the exon borders. The black arrows indicated the 28 C → U RNA editing sites, while the green arrows indicated the partial C → U RNA editing sites. The yellow quadrangle indicated the SNPs between NUMT and mitochondria of Langdon, and the yellow, double triangle, six-rayed star represented the SNPs between NUMT and mitochondria of Chinese Spring (PDF 224 kb)
10142_2011_237_MOESM8_ESM.pdf (534 kb)
Supplementary Figure S2 a Alignment of deletion sites in NUMT and mitochondrial region. Dashes indicate a 55-bp nucleotide fragment deletion. Black boxes indicate the target site duplication. b Chain slippage in replication of DNA resulting in the 55-bp nucleotide deletion. A and B indicated the two TTA direct repeats. The sequence between A and B is prone to form a stem-loop structure which could block the DNA polymerase combine with the DNA template (PDF 534 kb)
10142_2011_237_MOESM9_ESM.pdf (122 kb)
Supplementary Figure S3 a Schematic presentation of composition of wheat NUMT compared with the mitochondria. Red characters indicate the conserved rrn5–rrn18–trnfM three-gene cluster. b Generation and integration of wheat NUMT. “rrn5–rrn18–trnfM” haplotype of wheat NUMT originated from the recombination of the trnfM-1–nad1a and the rrn5–2-trnI haplotype of mitochondria meditated by IR repeat (copy 1 and copy 2; Ogihara et al. 2005) (PDF 121 kb)


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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Juncheng Zhang
    • 1
  • Jizeng Jia
    • 1
  • James Breen
    • 2
  • Xiuying Kong
    • 1
    • 3
    Email author
  1. 1.Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Science, CAAS/The Key Facility for Crop Gene Resources and Genetic ImprovementBeijingPeople’s Republic of China
  2. 2.Centre for Comparative GenomicsMurdoch UniversityMurdochAustralia
  3. 3.Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

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