rps4作为苔藓植物候选条形码的可行性: 基于GenBank数据的分析

doi:10.3724/SP.J.1003.2011.08239

生物多样性 ›› 2011, Vol. 19 ›› Issue (3): 311-318. DOI: 10.3724/SP.J.1003.2011.08239

所属专题：物种形成与系统进化

rps4作为苔藓植物候选条形码的可行性: 基于GenBank数据的分析

刘艳¹, 王建秀², 葛学军³^,^*(), 曹同⁴^,^*()

1 (重庆师范大学生命科学学院, 重庆 401331)
2 (中国科学院植物研究所系统与进化植物学国家重点实验室, 北京 100093)
3 (中国科学院华南植物园植物资源保护与可持续利用重点实验室, 广州 510650)
4 (上海师范大学生命与环境科学学院, 上海 200234)

收稿日期:2010-11-01 接受日期:2011-02-05 出版日期:2011-05-20 发布日期:2013-12-10
通讯作者: 葛学军,曹同
作者简介:ct1946@263.net
*E-mail:xjge@scbg.ac.cn;
基金资助:
中国科学院依托国家大科学装置-种质资源库的植物DNA条形码研究项目(2009-LSF-GBOWS-01);中国科学院知识创新工程重要方向性项目(KSCX2-YW-N-0807);重庆师范大学校立博士启动基金项目(10XLB018)

The rps4 locus as an alternative marker for barcoding bryophytes: eva- luation based on data mining from GenBank

Yan Liu¹, Jianxiu Wang², Xuejun Ge³^,^*(), Tong Cao⁴^,^*()

1 College of Life Sciences, Chongqing Normal University, Chongqing 401331
2 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093
3 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650
4 College of Life & Environment Sciences, Shanghai Normal University, Shanghai 200234

Received:2010-11-01 Accepted:2011-02-05 Online:2011-05-20 Published:2013-12-10
Contact: Xuejun Ge,Tong Cao

摘要/Abstract

摘要：

对于苔藓植物DNA条形码研究来说, 目前已提议的可用片段只有rbcL和trnH-psbA, 并且均具有一定局限性。本文基于GenBank中3,365条rps4序列, 利用遗传距离法和分子系统学方法评价它作为苔藓植物候选条形码的可行性。结果显示: (1)rps4序列覆盖了藓纲96%的科和苔纲88%的科, 具有通用性; (2)rps4物种分辨能力为73.0%, 并且它在6个序列最丰富的苔藓植物属(Plagiochila, Tortula, Plagiomnium, Pyrrhobryum, Pogonatum, Grimmia)内的物种识别能力均高于rbcL-a在同属中的分辨能力; (3)GenBank中已经积累了大量已知物种来源的rps4序列, 可为DNA条形码物种鉴定提供一个参考数据库。因此, 本文建议将rps4作为苔藓植物候选DNA条形码。尤其是当rbcL和trnH-psbA在某个具体类群中无法取得理想的物种识别效果时, rps4可作为补充。

关键词: 隐花植物, 陆生植物条形码, 叶绿体DNA, 物种鉴定

Abstract

Among the candidate DNA barcoding loci suggested for land plants, only rbcL and trnH-psbA are available for barcoding bryophytes. However, both loci have limitations in discriminating among species. The present study evaluated the feasibility of using the cpDNA rps4 locus as an additional marker to complement other candidate barcodes for bryophytes. We analyzed 3,365 rps4 sequences retrieved from GenBank using pair-wise distance and phylogenetic methods. Our results demonstrated the universality of rps4 in bryophytes; the locus covers 96% of moss families and 88% of liverwort families. The rps4 locus resolved 73.0% of the species we tested. The discriminatory ability of rps4 is better than that of rbcL-a in each of the six bryophyte genera (i.e. Plagiochila, Tortula, Plagiomnium, Pyrrhobryum, Pogonatum, Grimmia) most commonly represented in the database. Moreover, large numbers of rps4 sequences from individuals of known bryophyte identities have been compiled in GenBank, thereby providing a reference for species identification. Therefore, we propose rps4 as an additional barcode, especially when rbcL and trnH-psbA do not perform well in certain bryophyte taxa.

Key words: cryptogamic plants, land plant barcoding, plastid DNA, species identification

刘艳, 王建秀, 葛学军, 曹同 (2011) rps4作为苔藓植物候选条形码的可行性: 基于GenBank数据的分析. 生物多样性, 19, 311-318. DOI: 10.3724/SP.J.1003.2011.08239.

Yan Liu, Jianxiu Wang, Xuejun Ge, Tong Cao (2011) The rps4 locus as an alternative marker for barcoding bryophytes: eva- luation based on data mining from GenBank. Biodiversity Science, 19, 311-318. DOI: 10.3724/SP.J.1003.2011.08239.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2011.08239

https://www.biodiversity-science.net/CN/Y2011/V19/I3/311

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	种数 No. of species	属数 No. of genera	科数 No. of families	目数 No. of orders	序列数目 No. of accessions
藓纲 Bryophyta	1,580	692	108	30	2,604
苔纲 Marchantiophyta	498	184	74	15	756
角苔纲 Anthocerotophyta	4	3	2	2	5
总计 Total	2,082	879	184	47	3,365

	种数 No. of species	属数 No. of genera	科数 No. of families	目数 No. of orders	序列数目 No. of accessions
藓纲 Bryophyta	1,580	692	108	30	2,604
苔纲 Marchantiophyta	498	184	74	15	756
角苔纲 Anthocerotophyta	4	3	2	2	5
总计 Total	2,082	879	184	47	3,365

	种内、种间遗传距离数值的数目 Total no. of pair-wise comparisons	物种识别率 Species resolution (%)	无法识别的物种比例 Species unresolved (%)
	种内、种间遗传距离数值的数目 Total no. of pair-wise comparisons	物种识别率 Species resolution (%)	无种间变异 No inter-specific divergence (%)	种内距离≥种间距离 Intra-specific distance ≥ inter-specific distance (%)	种内变异> 0.2%^* Intra-specific variations > 0.2%^* (%)
藓纲 Bryophyta	19,664	70.7 (876/1,239)	17.8 (221/1,239)	7.6 (94/1,239)	3.9 (48/1,239)
苔纲 Marchantiophyta	12,896	79.9 (333/417)	9.6 (40/417)	8.4 (35/417)	2.2 (9/417)
总计 Total	3,2560	73.0 (1,209/1,656)	15.8 (261/1,656)	7.8 (129/1,656)	3.4 (57/1,656)

	种内、种间遗传距离数值的数目 Total no. of pair-wise comparisons	物种识别率 Species resolution (%)	无法识别的物种比例 Species unresolved (%)
	种内、种间遗传距离数值的数目 Total no. of pair-wise comparisons	物种识别率 Species resolution (%)	无种间变异 No inter-specific divergence (%)	种内距离≥种间距离 Intra-specific distance ≥ inter-specific distance (%)	种内变异> 0.2%^* Intra-specific variations > 0.2%^* (%)
藓纲 Bryophyta	19,664	70.7 (876/1,239)	17.8 (221/1,239)	7.6 (94/1,239)	3.9 (48/1,239)
苔纲 Marchantiophyta	12,896	79.9 (333/417)	9.6 (40/417)	8.4 (35/417)	2.2 (9/417)
总计 Total	3,2560	73.0 (1,209/1,656)	15.8 (261/1,656)	7.8 (129/1,656)	3.4 (57/1,656)

	种数 No. of species		序列数 No. of accessions		物种识别率 Species resolution (%)		种间无变异 No inter-specific divergence (%)		种内距离≥种间距离 Intra-specific distance ≥ inter-specific distance (%)
	rps4	rbcL-a	rps4	rbcL-a	rps4	rbcL-a	rps4	rbcL-a	rps4	rbcL-a
羽苔属 Plagiochila	128	111	147	125	82	77.5	8.6	20.7	9.4	1.8
墙藓属 Tortula	18	4	97	5	61.1	-	11.1	-	27.8	-
匍灯藓属 Plagiomnium	24	5	87	17	66.7	40	0	60	33.3	0
桧藓属 Pyrrhobryum	10	9	55	16	60	44.4	20	44.4	20	11.1
小金发藓属 Pogonatum	32	18	50	32	68.8	55.6	21.9	11.1	9.4	33.3
紫萼藓属 Grimmia*	35	29	49	71	71.4	58.6	22.9	20.7	5.7	20.7

rps4作为苔藓植物候选条形码的可行性: 基于GenBank数据的分析

The rps4 locus as an alternative marker for barcoding bryophytes: eva- luation based on data mining from GenBank

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