石刁柏核质体DNA的生物信息学分析及染色体定位

doi:10.11983/CBB18117

摘要/Abstract

摘要： 在植物基因组中, 叶绿体DNA (cpDNA)序列可以向核基因组转移成为核质体DNA (NUPT)。NUPTs在植物染色体(包括性染色体)的演化过程中具有重要作用, 但目前相关研究比较缺乏。以雌雄异株植物石刁柏(Asparagus officinalis)为材料, 采用生物信息学方法对其核基因组NUPTs进行注释及分析, 并选取叶绿体基因组反向重复区(IR) 2个片段进行染色体定位。结果表明, 石刁柏核基因组中有2 239个NUPTs序列的插入, 总长度为565 970 bp, 占核基因组的0.047%。不同染色体上插入的NUPTs数量存在较大差异, Y染色体上的NUPTs数量、密度及总长度均高于其它染色体, 表明NUPTs在石刁柏性(Y)染色体上累积的更多。石刁柏叶绿体基因组中的IR区、大单拷贝区(LSC)和小单拷贝区(SSC)序列均能够向核基因组转移, 但IR区序列转移频率更高。此外, 对2个IR区的叶绿体序列进行荧光原位杂交, 其中AocpIR1主要分布在所有染色体的着丝粒部位, 而AocpIR2特异性分布在Y染色体上。研究结果为深入揭示石刁柏基因组的结构及其性染色体的演化奠定了坚实的基础。

关键词: 石刁柏, 生物信息学分析, 核质体DNA, NUPTs, 性染色体

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

程广前,贾克利,李娜,邓传良,李书粉,高武军. 石刁柏核质体DNA的生物信息学分析及染色体定位. 植物学报, 2019, 54(3): 328-334.

Guangqian Cheng,Keli Jia,Na Li,Chuanliang Deng,Shufen Li,Wujun Gao. Bioinformatics Analysis and Chromosome Location of Nuclear Integrants of Plastid DNA in Asparagus officinalis. Chinese Bulletin of Botany, 2019, 54(3): 328-334.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB18117

https://www.chinbullbotany.com/CN/Y2019/V54/I3/328

图/表 5

图1 石刁柏不同染色体核质体DNA (NUPTs)长度(A)和数目(B)

Figure 1 The length (A) and number (B) of nuclear integrants of plastid DNAs (NUPTs) in different chromosomes of Asparagus officinalis

图2 石刁柏基因组核质体DNA (NUPTs)在染色体上的分布模式

Figure 2 The chromosome distribution pattern of nuclear integrants of plastid DNAs (NUPTs) of Asparagus officinalis genome

表1 石刁柏核基因组核质体DNA (NUPTs)的叶绿体基因组来源分析

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

图3 石刁柏2个叶绿体反向重复区(IR)序列的PCR扩增1, 2分别代表AocplR1和AocplR2的扩增结果。

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.

图4 AocpIR1和AocpIR2在石刁柏有丝分裂中期染色体上的定位(A), (E) 45S rDNA杂交信号图; (B), (F) AocpIR1和AocpIR2杂交信号图; (C), (G) 合成图; (D), (H) 核型图。Bars=10 μm

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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