SSR Loci in Transcriptome of Moringa oleifera Lam
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摘要: 采用MISA对15 824条长度大于1 kb的辣木Unigene进行SSR位点分布频率和基本特征的分析，共检测到8 272个SSR位点，分布于6 003条Unigene，SSR位点出现频率为52.28%，共包含114种重复单元。辣木转录组的SSR以单核苷酸重复为主，占总SSR的55.69%。其次是二、三核苷酸重复，分别占总SSR的32.34%和11.24%。A/T、AG/CT和AAG/CTT是单核苷酸、二核苷酸和三核苷酸中的优势重复基元。辣木转录组SSR以10~20次重复为主，基序长度主要集中于12~19 bp。结果表明辣木转录组中含有大量SSR，且类型丰富，可为辣木SSR引物开发提供候选序列。Abstract: MISA software was employed to analyze the distribution and basic characteristics of SSR loci of 15 824 unigenes, which were longer than 1 kb, from the transcriptome of Moringa oleifera Lam leaves at different development stages. A total of 8 272 SSR loci consisting of 114 motifs were detected in 6 003 unigenes, i.e., a frequency of 52.28%. The most abundant repeating motif was a single nucleotide (55.69%), which was followed by dinucleotide (32.34%) and trinucleotide (11.24%); and, their SSRs were A/T, AG/CT and AAG/CTT, respectively. The most commonly found SSRs had 10-20 tandem repeats (30.35%) with their motif lengths ranging from 12 bp to 19 bp. It appeared that there were numerous SSRs in the transcriptomes with high distribution frequencies and many varieties. The results obtained from this study provided valuable information for developing SSR markers.
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Key words:
- Moringa oleifera /
- transcriptome /
- SSR
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表 1 辣木转录组SSR不同基序长度和重复次数的数量分布
Table 1. Distribution of SSRs with different motif types and repeating numbers in transcriptome of M. oleifera
基序长度/bp 重复次数 总计 比例/% 5 6 7 8 9 10~20 >20 1 0 0 0 0 0 4522 85 4607 55.69 2 0 769 501 452 429 524 0 2675 32.34 3 579 217 108 21 3 2 0 930 11.24 4 37 6 2 0 0 0 0 45 0.54 5 4 1 0 0 0 0 0 5 0.06 6 1 5 3 0 0 1 0 10 0.12 总计 621 998 614 473 432 5049 85 8272 比例/% 7.51 12.06 7.42 5.72 5.22 61.04 1.03 
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表 2 辣木转录组SSR基序类型分布
Table 2. Distribution of SSR types in transcriptome of M. oleifera
SSR基序 数量 A/T 4452 C/G 155 AG/CT 2214 AT/AT 306 AC/GT 150 CG/CG 5 AAG/CTT 298 ATC/ATG 132 AGC/CTG 138 AGG/CCT 94 AAT/ATT 93 ACC/GGT 93 AAC/GTT 46 ACG/CGT 19 AAAAG/CTTTT 2 AAACC/GGTTT 1 AACAAG/CTTGTT 1 AAGCAG/CTGCTT 1 ACCATC/ATGGTG 1 ACCCTG/AGGGTC 1 ACTAGC/AGTGCT 1 ACT/AGT 3 CCG/CGG 14 AAAG/CTTT 13 AAAT/ATTT 17 AAGC/CTTG 1 AAGG/CCTT 2 AATT/AATT 1 ACAG/CTGT 1 ACAT/ATGT 3 AGCC/CTGG 1 AGCG/CGCT 1 AGGC/CCTG 1 AGGG/CCCT 3 ATCC/ATGG 1 AAAAC/GTTTT 1 AAATC/ATTTG 1 AACTGC/AGTTGC 1 ACCAGC/CTGGTG 1 ACCATG/ATGGTC 1 ACGATC/ATCGTG 1 AGCAGG/CCTGCT 1
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