利用叶绿体基因探讨稻属BBCC基因组物种的系统起源

doi:10.11983/CBB15054

摘要/Abstract

摘要： 基于9个叶绿体基因片段(atpA、atpB、matK、petA、psaA、psbA、psbB、psbC和rbcL), 深入探讨了稻属(Oryza) 3个BBCC基因组异源四倍体和5个与之相关的BB或CC基因组二倍体物种间的谱系关系。进一步的系统发育分析表明: 3个具有相同BBCC基因组的四倍体物种并非同一次物种形成事件的产物, 而是在不同的分布区经历了至少3次分别的物种起源。其中, 四倍体Oryza punctata的母本可能来自同样分布在非洲并具有CC基因组的二倍体物种O. eichingeri; 而四倍体O. malampuzhaensis和O. minuta的母本则可能来自亚洲已经灭绝的具有BB基因组的不同二倍体。研究结果不但为追溯稻属异源四倍体的复杂网状进化提供了重要的分子证据, 而且拓展了我们对有花植物复杂物种形成的深入理解。

关键词: 二倍体, 异源四倍体, 谱系关系, 基因组

Abstract: With 9 maternal heritable chloroplast gene fragments (atpA, atpB, matK, petA, psaA, psbA, psbB, psbC, and rbcL), we explored the lineage relationships of 3 BBCC genome allotetraploids and 5 related BB or CC genome diploids in the Oryza genus. Further phylogenetic analyses indicated that the 3 allotetraploid species did not originate from a common speciation event but occurred at least 3 times in different distribution areas. The maternal parent of the tetraploid O. punctata was possibly the Africa CC genome diploid O. eichingeri, whereas the maternal parent of O. minuta and O. malampuzhaensis was possibly 2 extinct Asian BB genome diploids. Our results provided important molecular evidence to track complicated reticular evolutionary processes for the polyploids and also broaden our understanding of the puzzling speciation histories of flowering plants.

Key words: diploid, allotetraploid, lineage relationship, genome

杜家潇, 秦宗燕, 徐思, 景翔, 包颖. 利用叶绿体基因探讨稻属BBCC基因组物种的系统起源. 植物学报, 2016, 51(2): 175-183.

Jiaxiao Du, Zongyan Qin, Si Xu, Xiang Jing, Ying Bao. Phylogenetic Origin of BBCC Genome Allotetraploids in Oryza Revealed by Chloroplast Gene Sequences. Chinese Bulletin of Botany, 2016, 51(2): 175-183.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB15054

https://www.chinbullbotany.com/CN/Y2016/V51/I2/175

图/表 6

表1 稻属植物样品材料

Table 1 Plant materials of Oryza used in this study

Species	Genome	IRRI Acc. No.	Origin
Oryza punctata Kotechy ex Steud.	BB	103888	Tanzania
Oryza punctata Kotechy ex Steud.		101434	Tanzania
O. eichingeri A. Peter	CC	105159	Uganda
O. officinalis Wall. ex G. Watt.	CC	104973	China
O. rhizomatis D. A. Vaughan	CC	103410	Sri Lanka
O. malampuzhaensis Krish. et Chand.	BBCC	80764	India
O. malampuzhaensis Krish. et Chand.		105223	India
		105328	India
O. minuta J. S. Presl. ex C. B. Presl.	BBCC	104677	Philippines
O. minuta J. S. Presl. ex C. B. Presl.		105307	Philippines
		103880	Philippines
O. punctata	BBCC	105181	Uganda
		104059	Nigeria
		104975	Kenya
O. australiensis Domin	EE	103303	Australia
		105165	Australia

表2 引物序列

Table 2 The sequences of primers

Gene	Primer sequences (5'-3')
atpA	AGGCTTACTTGGGTCGTGTT TCCTCGGTGAATGTCTTGCT
atpB	ATCCTACTACTTCTCGTCCC AATTGCGATAATGTCCTGAA
petA	TTGGGTAAAGGAACAGATGA AATAACGGATGCGAAGAAGA
psaA	TAGCAGGGTTATTAGGACTTG ATGCGTGAATGTGATGGACT
psbA	TCGGATGGTTCGGTGTTTTGA AGGGAAGTTGTGAGCATTACG
psbB	GGGTTTGCCTTGGTATCGTG GGCTGTCTCCCTGTAGTTGG
psbC	GGGTTGATTTTACTTCCGCAC GAAGGTCCCAAAAACGCATAG
rbcL	TATCTTGGCAGCATTCCGAGTAA ATTTGATCGCTTTCCATATTTC

表3 9个稻属叶绿体基因片段的序列特点

Table 3 Sequence characteristics for 9 chloroplast gene fragments of Oryza

Gene name	Length (bp)	SNP	GC (%)
atpA	997	3	42
atpB	673	3	43
matK	1552	16	34
petA	770	0	43
psaA	511	1	44
psbA	662	3	42
psbB	628	1	45
psbC	648	5	41
rbcL	1019	6	43
Total	7460	41	42

表4 9个稻属叶绿体基因片段的变异核苷酸位点

Table 4 Variable nucleotide sites of 9 chloroplast gene fragments of Oryza

Species (genome)	Variable nucleotide sites
Species (genome)	atpA	atpB	matK	psaA	psbA	psbB	psbC	rbcL
O. punctata (BB)	GGA	GGC	CTATATAATTCTTTCT	C	ACC	G	GAAA	CTTGTC
O. punctata (BB)	...	...	................	.	...	.	....	......
O. minuta (BBCC)	A..	...	................	.	...	.	....	......
O. malampuzhaensis (BBCC)	A..	A..	.......C........	.	...	.	....	......
O. eichingeri (CC)	AAC	AAT	TAGCGCCATCAACTTA	T	GTT	A	GGCG	ACGACG
O. officinalis (CC)	...	...	........A....C..	.	...	.	C.A.	......
O. rhizomatis (CC)	...	...	................	.	...	.	..A.	......
O. punctata (BBCC)	...	...	................	.	...	.	....	......

图1 BBCC基因组四倍体和其相关二倍体的对遗传距离 (A)-(H) 分别代表atpA、atpB、matK、psaA、psbA、psbB、psbC和rbcL基因片段。横坐标puBB、eiCC、ofCC和rhCC分别代表BB基因组的二倍体O. punctata和CC基因组的二倍体O. eichingeri、O. officinalis和O. rhizomatis; 纵坐标为遗传距离。

Figure 1 Pairwise genetic distances of the BBCC genomic tetraploids and their related diploids (A)-(H) Pairwise genetic distances of atpA, atpB, matK, psaA, psbA, psbB, psbC, and rbcL, respectively. x axis: puBB, eiCC, ofCC, and rhCC represents diploid O. punctata with genome BB, and O. eichingeri, O. officinalis, and O. rhizomatis with genome CC, respectively; y axis: Genetic distances

图2 叶绿体基因的最大似然树 (A)-(H) 分别基于个体基因atpA、atpB、matK、psaA、psbA、psbB、psbC和rbcL构建的最大似然性系统发育关系树; (I) 基于5个基因(atpA、atpB、matK、psbA和psbC)合并数据的最大似然树; 分支上的数字表示大于50%的自展支持率; BBCC基因组异源四倍体用粗体表示。

Figure 2 The maximum likelihood trees based on 8 and combined chloroplast genes (A)-(H) The ML tree based on atpA, atpB, matK, psaA, psbA, psbB, psbC, and rbcL gene, respectively; (I) The ML tree based on 5 combined genes (atpA, atpB, matK, psbA, and psbC). Numbers near branches indicate bootstrap values above 50%, Boldface indicates allotetraploid species with BBCC genome.

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