Structural characteristics of di-nucleotide/tetra-nucleotide repeat microsatellite DNA in Pachyhynobius shangchengensisgenomes and its effect on isolation

doi:10.3724/SP.J.1003.2012.08168

Abstract

Abstract:

A low success ratio is often encountered in the microsatellite isolation from the species of Caudata. In the present study, di-nucleotide/tetra-nucleotide repeat microsatellite loci were isolated following the FLASCO (fast isolation by AFLP of sequences containing repeats) approach and the sequences were analyzed for the purpose of learning how microsatellite structure impacted on isolation efficiency. We found that most di-nucleotide repeat microsatellite loci were involved in the microsatellite DNA family, which resulted in low isolation efficiency. In contrast, no microsatellite DNA family members were found in the tetra-nucleotide repeat microsatellite loci. On the basis of analysis of the three microsatellite DNA families found in the present study, there were significant differences in the extent of variation between the upstream and downstream flanking sequences in same microsatellite DNA family. This variation was the highest in the sequence sections adjacent to the core repeated units, but more conservative in other regions, which might reflect the complexity of the microsatellite DNA family evolution. These results suggest that in the process of microsatellite development for Caudata, we must pay attention to interference from microsatellite DNA family evolution. The choice of appropriate nucleotide repeats is key to obtaining a high isolation efficiency.

Key words: microsatellite, structure characteristics, microsatellite DNA family, Pachyhynobius shangchengensis, isolation efficiency

Hui Wang, Baowei Zhang, Wenbo Shi, Xia Luo, Lizhi Zhou, Demin Han, Qing Chang. Structural characteristics of di-nucleotide/tetra-nucleotide repeat microsatellite DNA in Pachyhynobius shangchengensisgenomes and its effect on isolation[J]. Biodiv Sci, 2012, 20(1): 51-58.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2012.08168

https://www.biodiversity-science.net/EN/Y2012/V20/I1/51

Figures/Tables 3

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序列组 Sequence set	包含的序列数目 Sequence number	长度范围 Size range	序列间的遗传距离范围 Range of genetic distance among sequence	序列间平均的遗传距离 Average genetic distance among sequence
Psmf1上游侧翼序列 Upstream flanking sequence ofPsmf1	11	165-438	0.016-0.084	0.042
Psmf1下游侧翼序列 Downstream flanking sequence ofPsmf1	11	52-482	-	-
Psmf2上游侧翼序列 Upstream flanking sequence ofPsmf2	4	277-297	0.109-0.253	0.174
Psmf2下游侧翼序列 Downstream flanking sequence ofPsmf2	4	79-140	0.090-0.295	0.159
Psmf3上游侧翼序列 Upstream flanking sequence ofPsmf3	26	314-500	0.021-0.416	0.168
Psmf3下游侧翼序列 Downstream flanking sequence ofPsmf3	26	60-85	0-0.210	0.091

序列组 Sequence set	包含的序列数目 Sequence number	长度范围 Size range	序列间的遗传距离范围 Range of genetic distance among sequence	序列间平均的遗传距离 Average genetic distance among sequence
Psmf1上游侧翼序列 Upstream flanking sequence ofPsmf1	11	165-438	0.016-0.084	0.042
Psmf1下游侧翼序列 Downstream flanking sequence ofPsmf1	11	52-482	-	-
Psmf2上游侧翼序列 Upstream flanking sequence ofPsmf2	4	277-297	0.109-0.253	0.174
Psmf2下游侧翼序列 Downstream flanking sequence ofPsmf2	4	79-140	0.090-0.295	0.159
Psmf3上游侧翼序列 Upstream flanking sequence ofPsmf3	26	314-500	0.021-0.416	0.168
Psmf3下游侧翼序列 Downstream flanking sequence ofPsmf3	26	60-85	0-0.210	0.091

位点名称 Loci	核心序列重复单元 Repeated core units	引物序列(上游/下游) Primer sequence (Upper primer/down primer)	扩增结果 PCR result
Psh110	AC₁₆	5′-CACCGCTGACCTGGACACTT-3′ ∕ 5′-GTGACTGACAGCTAGGGAAG-3′	单带 Single band
Psh116	AC₂₁	5′-CAAGAGGCAATGAATGTGAG-3′ ∕ 5′-TACTATGTCCCATCTTC-3′	单带 Single band
Psh118	AC₁₂	5′-GGTGGTTCTCTGGAGTGTTG-3′ ∕ 5′-TGGTCCTCCAGTCTCACAGC-3′	单带 Single band
Psh124	AC₁₅	5′-CACGGATCTCGGAAGCT-3′ ∕ 5′-AGAATAAAGTAACCTCAATG-3′	单带 Single band
Psh131	AC₁₆	5′-TATTCCCTTTCCTACTCCT-3′ ∕ 5′-AACAGACCCATGATAAGAGC-3′	单带 Single band
Psh135	AC₂₂	5′-AGGAAAGAGCTCCACCAAG-3′ ∕ 5′-GTGAAAGAAGAGAAGCAGAG-3′	单带 Single band
Psh138	AC₂₉	5′-CTCCTATTTCCTCCTCAGAC-3′ ∕ 5′-AAGGGTGTAGGCTGAGAG-3′	弥散带 Smear
Psh143	AC₂₁	5′-TGTGTGGGCTCTGCATTTAC-3′ ∕ 5′-CAGGATGGGGGAAAATATAC-3′	单带 Single band
Psh209	AG₁₉	5′-CACATTTATACGGACACCAC-3′ ∕ 5′-TCCACATTTTTACAGCCAGG-3′	单带 Single band
Psh211	AG₂₈	5′-TGAGGAGTTCCCCTAAGCAC-3′ ∕ 5′-GGTGAACGGAAAAGGATTAC-3′	多带 Multi-band
Psh216	AG₂₇	5′-AACAGAGGCAATGTCCACAC-3′ ∕ 5′-CAACAGTCTGCATGTGAAAG-3′	单带 Single band
Psh229	AG₄₃	5′-TTTTTGGGACTCTGCCTCTC-3′ ∕ 5′-CTATAGGGCTATGAAG-3′	无法扩增 No band
Psh230	AG₂₇	5′-ACAGGGTAGGAAGGCAGTAG-3′ ∕ 5′-AGTAAGGGAGAGAAAAAAGC-3′	弥散带 Smear
Psh238	AG₂₈	5′-TCGCTCGCTCACCCATTCAC-3′ ∕ 5′-GCAGGGGATTGAGATAGTTG-3′	多带 Single band
Psh245	AG₅₃	5′-CTGTTTCTTTAGAGTGAGTG-3′ ∕ 5′-GGTAGCAAGTTTGATAAGTG-3′	单带 Single band
Psh246	AG₃₄	5′-TAGGCATCAACTAAGGGGAC-3′ ∕ 5′-TGTTCCATATTTGGGACTGG-3′	单带 Single band
Psh248	AG₃₇	5′-AGGTATTGTGCGGAACGATC-3′ ∕ 5′-TGGACTGTTTTTGCCACCAG-3′	单带 Single band
Psh228	AG₄₀	5′-GAAAATGGAGAGGGATGAAC-3′ ∕ 5′-ACAGTCTGCATGAGAAAGGC-3′	单带 Single band
Psh150	AC₃₀	5′-TAAATGTGAGTCCAGCAAAC-3′ ∕ 5′-CGATTTGAGTATTTGGGTAG-3′	单带 Single band
Psh274	AG₅₂	5′-GGTGAGCCCTTGAGTTTGAG-3′ ∕ 5′-GCCGCTTCACATTAGTTTTC-3′	无法扩增 No band
Psh207	AG₂₄	5′-TCTTTGTTGAGACTCGGGAC-3′ ∕ 5′-AAAGCAAAAGGCAAACC-3′	弥散带 Smear

位点名称 Loci	核心序列重复单元 Repeated core units	引物序列(上游/下游) Primer sequence (Upper primer/down primer)	扩增结果 PCR result
Psh110	AC₁₆	5′-CACCGCTGACCTGGACACTT-3′ ∕ 5′-GTGACTGACAGCTAGGGAAG-3′	单带 Single band
Psh116	AC₂₁	5′-CAAGAGGCAATGAATGTGAG-3′ ∕ 5′-TACTATGTCCCATCTTC-3′	单带 Single band
Psh118	AC₁₂	5′-GGTGGTTCTCTGGAGTGTTG-3′ ∕ 5′-TGGTCCTCCAGTCTCACAGC-3′	单带 Single band
Psh124	AC₁₅	5′-CACGGATCTCGGAAGCT-3′ ∕ 5′-AGAATAAAGTAACCTCAATG-3′	单带 Single band
Psh131	AC₁₆	5′-TATTCCCTTTCCTACTCCT-3′ ∕ 5′-AACAGACCCATGATAAGAGC-3′	单带 Single band
Psh135	AC₂₂	5′-AGGAAAGAGCTCCACCAAG-3′ ∕ 5′-GTGAAAGAAGAGAAGCAGAG-3′	单带 Single band
Psh138	AC₂₉	5′-CTCCTATTTCCTCCTCAGAC-3′ ∕ 5′-AAGGGTGTAGGCTGAGAG-3′	弥散带 Smear
Psh143	AC₂₁	5′-TGTGTGGGCTCTGCATTTAC-3′ ∕ 5′-CAGGATGGGGGAAAATATAC-3′	单带 Single band
Psh209	AG₁₉	5′-CACATTTATACGGACACCAC-3′ ∕ 5′-TCCACATTTTTACAGCCAGG-3′	单带 Single band
Psh211	AG₂₈	5′-TGAGGAGTTCCCCTAAGCAC-3′ ∕ 5′-GGTGAACGGAAAAGGATTAC-3′	多带 Multi-band
Psh216	AG₂₇	5′-AACAGAGGCAATGTCCACAC-3′ ∕ 5′-CAACAGTCTGCATGTGAAAG-3′	单带 Single band
Psh229	AG₄₃	5′-TTTTTGGGACTCTGCCTCTC-3′ ∕ 5′-CTATAGGGCTATGAAG-3′	无法扩增 No band
Psh230	AG₂₇	5′-ACAGGGTAGGAAGGCAGTAG-3′ ∕ 5′-AGTAAGGGAGAGAAAAAAGC-3′	弥散带 Smear
Psh238	AG₂₈	5′-TCGCTCGCTCACCCATTCAC-3′ ∕ 5′-GCAGGGGATTGAGATAGTTG-3′	多带 Single band
Psh245	AG₅₃	5′-CTGTTTCTTTAGAGTGAGTG-3′ ∕ 5′-GGTAGCAAGTTTGATAAGTG-3′	单带 Single band
Psh246	AG₃₄	5′-TAGGCATCAACTAAGGGGAC-3′ ∕ 5′-TGTTCCATATTTGGGACTGG-3′	单带 Single band
Psh248	AG₃₇	5′-AGGTATTGTGCGGAACGATC-3′ ∕ 5′-TGGACTGTTTTTGCCACCAG-3′	单带 Single band
Psh228	AG₄₀	5′-GAAAATGGAGAGGGATGAAC-3′ ∕ 5′-ACAGTCTGCATGAGAAAGGC-3′	单带 Single band
Psh150	AC₃₀	5′-TAAATGTGAGTCCAGCAAAC-3′ ∕ 5′-CGATTTGAGTATTTGGGTAG-3′	单带 Single band
Psh274	AG₅₂	5′-GGTGAGCCCTTGAGTTTGAG-3′ ∕ 5′-GCCGCTTCACATTAGTTTTC-3′	无法扩增 No band
Psh207	AG₂₄	5′-TCTTTGTTGAGACTCGGGAC-3′ ∕ 5′-AAAGCAAAAGGCAAACC-3′	弥散带 Smear