Chin Bull Bot ›› 2019, Vol. 54 ›› Issue (3): 328-334.doi: 10.11983/CBB18117

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

Bioinformatics Analysis and Chromosome Location of Nuclear Integrants of Plastid DNA in Asparagus officinalis

Cheng Guangqian1,†,Jia Keli1,2,†,Li Na1,Deng Chuanliang1,Li Shufen1,Gao Wujun1,*   

  1. 1. College of Life Sciences, Henan Normal University, Xinxiang 453007, China
    2.SanQuan College, Xinxiang Medical University, Xinxiang 453003, China
  • Received:2018-05-11 Accepted:2018-08-06 Online:2019-11-24 Published:2019-05-01
  • Contact: Gao Wujun

Abstract:

Chloroplast DNA (cpDNA) can transfer into the plant nuclear genome to form nuclear integrants of plastid DNA (NUPTs). NUPTs may play a role in plant sex chromosome evolution. However, few studies have focused on this research area. In this study, we annotated and analyzed NUPTs in the genome of dioecious Asparagus officinalis and located two cpDNA fragments on chromosomes. The nuclear genome of A. officinalis contains 2 239 NUPT insertions, with total length 565 970 bp, accounting for 0.047% of the genome. The amount of NUPTs differs among chromosomes; the number, density, and the average length of NUPTs on the Y chromosome were all higher than those on the other chromosomes, which indicates more accumulation of NUPTs on sex chromosomes. All regions of inverted repeats (IRs) and small and large single copy regions of cpDNA could transfer into nuclear DNA; however, the IR region showed the highest transfer frequency. Furthermore, FISH analysis of two cpDNA sequences from IR regions showed that AocpIR1 distributed mainly on the centromeres of all chromosomes, whereas AocpIR2 specifically located on sex chromosomes of A. officinalis. The data provide an important foundation for determining the genome structure and sex chromosome evolution of A. officinalis.

Key words: Asparagus officinalis, bioinformatic analysis, nuclear integrants of plastid DNA, NUPTs, sex chromosome

Figure 1

The length (A) and number (B) of nuclear integrants of plastid DNAs (NUPTs) in different chromosomes of Asparagus officinalis"

Figure 2

The chromosome distribution pattern of nuclear integrants of plastid DNAs (NUPTs) of Asparagus officinalis genome"

Table 1

Origin analysis of nuclear integrants of plastid DNAs (NUPTs) sequences on the chloroplast genome of Asparagus officinalis"

IR LSC SSC
Total sequence length (bp) 26471 83821 17904
Number of NUPTs 726 1227 286
Average density (No./kb) 27.9 14.6 15.9
Average length of NUPTs (bp) 241 258 246
The length of NUPTs (bp) 175215 316626 70394

Figure 3

PCR amplification of inverted repeat region (IR) two sequences of region in Asparagus officinalis 1, 2 respresents the amplification results of AocplR1 and AocplR2, respectively."

Figure 4

Mitosis metaphase chromosome locations of AocpIR1 and AocpIR2 of Asparagus officinalis (A), (E) FISH result of 45S rDNA; (B), (F) FISH result of AocpIR1 and AocpIR2; (C), (G) Merged picture; (D), (H) Karyotype analysis. Bars=10 μm"

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