DNA Barcodes Study of Echinochloa

doi:10.11924/j.issn.1000-6850.casb2020-0372

Abstract

Abstract:

To evaluate the effectiveness of DNA barcodes in the identification of the genus Echinochloa, two candidate DNA barcodes from nuclear genome (ITS, ETS) and three candidate DNA barcodes from chloroplast genome (psbA, trnL-F, matK) were analyzed. The study amplified and sequenced the five candidate DNA barcodes from four Echinochloa species (E. crus-galli var. mitis, E. crus-galli var. crus-galli, E. caudate and E. crus-galli var. praticola), and analyzed the characteristics of each DNA barcode. The results show that matK has the highest proportion of variable sites (3.6%), and ETS has the lowest (1.7%); psbA has the largest interspecific distance, while matK has the largest intraspecific distance. The neighbor-joining (NJ) tree shows that all five candidate DNA barcodes have the ability to identify E. caudata, and their support rates are all higher than 80%. Furthermore, ITS could distinguish E. crus-galli var. praticola from E. crus-galli var. mitis and E. crus-galli var. crus-galli species. Therefore, it is recommended to use ITS as the potential DNA barcode for identifying Echinochloa.

Key words: Echinochloa spp., field weed, DNA barcodes, molecular identification, ITS, ETS, psbA, trnL-F, matK

CLC Number:

S451

Yuan Guohui, Tian Zhihui, Li Tao, Qian Zhenguan, Shen Guohui. DNA Barcodes Study of Echinochloa[J]. Chinese Agricultural Science Bulletin, 2021, 37(15): 106-111.

Figures/Tables 4

References 28

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条形码序列	引物名称	引物序列(5’-3’)	退火温度/℃
ITS	ITS4	TCCTCCGCTTATTGATATGC	56
ITS	ITS-Y5	TAGAGGAAGGAGAAGTCGTAACAA	56
ETS	RETS4_F	TGGCTACGCGAGCGCATGAG	56
ETS	18S_R	AGACAAGCATATGACTACTGGCAGG	56
psbA	#1-F	GTGCCTACTCGGCATTTCAC	56
psbA	#1-R	GTTGATAGCCAAGGTCGCGT	56
trnL-F	trn-F	ATTTGAACTGGTGACACGAG	54
trnL-F	trn-C	CGAAATCGGTAGACGCTACG	54
matK	W	TACCCTATCCTATCCAT	55~50 touch down
matK	trnK-2R	AACTAGTCGGATGGAGTAG	55~50 touch down

条形码序列	引物名称	引物序列(5’-3’)	退火温度/℃
ITS	ITS4	TCCTCCGCTTATTGATATGC	56
ITS	ITS-Y5	TAGAGGAAGGAGAAGTCGTAACAA	56
ETS	RETS4_F	TGGCTACGCGAGCGCATGAG	56
ETS	18S_R	AGACAAGCATATGACTACTGGCAGG	56
psbA	#1-F	GTGCCTACTCGGCATTTCAC	56
psbA	#1-R	GTTGATAGCCAAGGTCGCGT	56
trnL-F	trn-F	ATTTGAACTGGTGACACGAG	54
trnL-F	trn-C	CGAAATCGGTAGACGCTACG	54
matK	W	TACCCTATCCTATCCAT	55~50 touch down
matK	trnK-2R	AACTAGTCGGATGGAGTAG	55~50 touch down

条形码序列	序列长度/bp	G+C含量/%	变异位点/%	种内变异	种间变异	变异分辨率/%
ITS	704~705	58.7~59.1	2.0	0.0012±0.0002	0.0036±0.0015	50.0
ETS	472	58.9~59.3	1.7	0.0011±0.0008	0.0032±0.0025	48.8
psbA	337	38.3~38.9	2.7	0.0015±0.0011	0.0060±0.0044	60.0
trnL-F	951~956	35.0~35.4	3.0	0.0022±0.0009	0.0048±0.0026	37.1
matK	1330~1331	33.7~34.1	3.6	0.0029±0.0007	0.0048±0.0016	24.7

条形码序列	序列长度/bp	G+C含量/%	变异位点/%	种内变异	种间变异	变异分辨率/%
ITS	704~705	58.7~59.1	2.0	0.0012±0.0002	0.0036±0.0015	50.0
ETS	472	58.9~59.3	1.7	0.0011±0.0008	0.0032±0.0025	48.8
psbA	337	38.3~38.9	2.7	0.0015±0.0011	0.0060±0.0044	60.0
trnL-F	951~956	35.0~35.4	3.0	0.0022±0.0009	0.0048±0.0026	37.1
matK	1330~1331	33.7~34.1	3.6	0.0029±0.0007	0.0048±0.0016	24.7