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

doi:10.3724/SP.J.1003.2011.08239

Abstract

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

Yan Liu, Jianxiu Wang, Xuejun Ge, Tong Cao. The rps4 locus as an alternative marker for barcoding bryophytes: eva- luation based on data mining from GenBank[J]. Biodiv Sci, 2011, 19(3): 311-318.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2011.08239

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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