ACTA THERIOLOGICA SINICA ›› 2023, Vol. 43 ›› Issue (2): 182-192.DOI: 10.16829/j.slxb.150724
• ORIGINAL PAPERS • Previous Articles Next Articles
Weiwei SHAO, Fen QIAO, Wei CAI, Zhihua LIN, Li WEI()
Received:
2022-08-13
Accepted:
2022-11-07
Online:
2023-03-30
Published:
2023-03-23
Contact:
Li WEI
通讯作者:
韦力
作者简介:
邵伟伟 (1981- ),女,硕士,主要从事动物学研究.
基金资助:
CLC Number:
Weiwei SHAO, Fen QIAO, Wei CAI, Zhihua LIN, Li WEI. Characteristics of microsatellite distributions in genomes of Hipposideros armiger (Chiroptera)[J]. ACTA THERIOLOGICA SINICA, 2023, 43(2): 182-192.
邵伟伟, 乔芬, 蔡玮, 林植华, 韦力. 大蹄蝠全基因组微卫星分布特征分析[J]. 兽类学报, 2023, 43(2): 182-192.
微卫星类型 Type of SSR | 微卫星数量 Number of SSRs | 长度 Length (bp) | 丰度Abundance (loci/Mb) | 比例 Percentage (%) |
---|---|---|---|---|
单碱基 Mononucleotide | 173 953 | 2 451 423 | 77.78 | 34.94 |
二碱基 Dinucleotide | 222 591 | 6 114 126 | 99.52 | 44.71 |
三碱基 Trinucleotide | 37 566 | 800 058 | 16.8 | 7.55 |
四碱基 Tetranucleotide | 47 250 | 1 517 188 | 21.13 | 9.49 |
五碱基 Pentanucleotide | 13 134 | 310 285 | 5.87 | 2.64 |
六碱基 Hexanucleotide | 3 389 | 98 148 | 1.52 | 0.68 |
SSR总数 Total of SSRs | 497 883 | 11 291 228 | 222.61 | 100 |
总基因组大小 Whole genome length (bp) | 2 236 581 172 | |||
微卫星含量 SSR content of genome (%) | 0.50 |
Table 1 Distribution of microsatellites in the genomes of Hipposideros armiger
微卫星类型 Type of SSR | 微卫星数量 Number of SSRs | 长度 Length (bp) | 丰度Abundance (loci/Mb) | 比例 Percentage (%) |
---|---|---|---|---|
单碱基 Mononucleotide | 173 953 | 2 451 423 | 77.78 | 34.94 |
二碱基 Dinucleotide | 222 591 | 6 114 126 | 99.52 | 44.71 |
三碱基 Trinucleotide | 37 566 | 800 058 | 16.8 | 7.55 |
四碱基 Tetranucleotide | 47 250 | 1 517 188 | 21.13 | 9.49 |
五碱基 Pentanucleotide | 13 134 | 310 285 | 5.87 | 2.64 |
六碱基 Hexanucleotide | 3 389 | 98 148 | 1.52 | 0.68 |
SSR总数 Total of SSRs | 497 883 | 11 291 228 | 222.61 | 100 |
总基因组大小 Whole genome length (bp) | 2 236 581 172 | |||
微卫星含量 SSR content of genome (%) | 0.50 |
模体单元 Motif length | 重复单元 Repeat unit | 微卫星数量 Microsatellites | 比例 Percentage (%) |
---|---|---|---|
单碱基重复 Mononucleotide repeat | A | 165 494 | 95.14 |
G | 8 459 | 4.86 | |
二碱基重复 Dinucleotide repeat | AC | 122 977 | 55.25 |
CT | 42 659 | 19.16 | |
GC | 1 460 | 0.66 | |
TA | 55 495 | 24.93 | |
三碱基重复 Trinucleotide repeat | TAT | 14 429 | 38.41 |
CAA | 7 164 | 19.07 | |
ACC | 3 653 | 9.72 | |
CAT | 3 408 | 9.07 | |
四碱基重复 Tetranucleotide repeat | TTTA | 10 475 | 22.17 |
AAAC | 8 049 | 17.03 | |
ATAG | 7 078 | 14.98 | |
CATT | 4 959 | 10.50 | |
五碱基重复 Pentanucleotide repeat | AACAA | 6 393 | 48.68 |
TTATT | 2 544 | 19.37 | |
TTTCT | 795 | 6.05 | |
TATTA | 354 | 2.70 | |
六碱基重复 Hexanucleotide repeat | TATCTA | 688 | 20.30 |
AAACAA | 510 | 15.05 | |
GAGAGG | 284 | 8.38 | |
AATAAA | 133 | 3.92 |
Table 2 The most frequent microsatellite motifs found in genomes of Hipposideros armiger
模体单元 Motif length | 重复单元 Repeat unit | 微卫星数量 Microsatellites | 比例 Percentage (%) |
---|---|---|---|
单碱基重复 Mononucleotide repeat | A | 165 494 | 95.14 |
G | 8 459 | 4.86 | |
二碱基重复 Dinucleotide repeat | AC | 122 977 | 55.25 |
CT | 42 659 | 19.16 | |
GC | 1 460 | 0.66 | |
TA | 55 495 | 24.93 | |
三碱基重复 Trinucleotide repeat | TAT | 14 429 | 38.41 |
CAA | 7 164 | 19.07 | |
ACC | 3 653 | 9.72 | |
CAT | 3 408 | 9.07 | |
四碱基重复 Tetranucleotide repeat | TTTA | 10 475 | 22.17 |
AAAC | 8 049 | 17.03 | |
ATAG | 7 078 | 14.98 | |
CATT | 4 959 | 10.50 | |
五碱基重复 Pentanucleotide repeat | AACAA | 6 393 | 48.68 |
TTATT | 2 544 | 19.37 | |
TTTCT | 795 | 6.05 | |
TATTA | 354 | 2.70 | |
六碱基重复 Hexanucleotide repeat | TATCTA | 688 | 20.30 |
AAACAA | 510 | 15.05 | |
GAGAGG | 284 | 8.38 | |
AATAAA | 133 | 3.92 |
指标 Index | 基因区Genetic region | 基因间区 Intergenic region | |||
---|---|---|---|---|---|
编码区 CDS | 非翻译区 Untranslated | 外显子 Exon | 内含子 Intron | ||
数量 Number | 1 461 | 5 081 | 7 416 | 199 340 | 322 666 |
丰度 Abundance(loci/Mb) | 461.98 | 1 647.13 | 1 188.18 | 2 204.77 | 2 541.57 |
Table 3 The number and abundance of microsatellites in different genomic regions of Hipposideros armiger
指标 Index | 基因区Genetic region | 基因间区 Intergenic region | |||
---|---|---|---|---|---|
编码区 CDS | 非翻译区 Untranslated | 外显子 Exon | 内含子 Intron | ||
数量 Number | 1 461 | 5 081 | 7 416 | 199 340 | 322 666 |
丰度 Abundance(loci/Mb) | 461.98 | 1 647.13 | 1 188.18 | 2 204.77 | 2 541.57 |
Fig. 2 The distribution of microsatellite types in different genomic regions.Genome (A), CDS (B), Exon (C) and Intergenetic (D) of Hipposideros armiger. 1 - 6 indicated mono-, di-, tri-, tetra-, penta-, hexa-nucleotide respectively
Fig. 3 The microsatellite abundance in gene regions and their upstream and downstream regions of Hipposideros armiger. Number 1 - 13 indicated upstream 500 bp, exon 1, intron1, exon 2, intron 2, mid left exon, mid intron, mid right exon,intron reverse 2, exon reverse 2, intron reverse 1, exon reverse 1, downstream 500 bp, respectively
Fig. 4 GO classifications of coding sequencings with microsatellites in the genomes of Hipposideros armiger. 1: Reproduction; 2: Cell killing; 3: Immune system process; 4: Behavior; 5: Metabolic process; 6: Cell proliferation; 7: Carbohydrate utilization; 8: Cellular process; 9: Nitrogen utilization; 10: Reproductive process; 11: Biological adhesion; 12: Signaling; 13: Multicellular organismal process; 14: Developmental process; 15: Growth; 16: Locomotion; 17: Pigmentation; 18: Biological phase; 19: Rhythmic process; 20: Positive regulation of biological process; 21: Negative regulation of biological process; 22: Regulation of biological process; 23: Response to stimulus; 24: Localization; 25: Multi-organism process; 26: Biological regulation; 27: Cellular component organization or biogenesis; 28: Cell aggregation; 29: Detoxification; 30: Presynaptic process involved in chemical synaptic transmission; 31: Extracellular region; 32: Cell; 33: Nucleoid; 34: Membrane; 35: Virion; 36: Cell junction; 37: Membrane-enclosed lumen; 38: Protein-containing complex; 39: Organelle; 40: Other organism; 41: Other organism part; 42: Extracellular region part; 43: Organelle part; 44: Virion part; 45: Membrane part; 46: Synapse part; 47: Cell part; 48: Synapse; 49: Symplast; 50: Supramolecular complex; 51: Catalytic activity; 52: Signal transducer activity; 53: Structural molecule activity; 54: Transporter activity; 55: Binding; 56: Antioxidant activity; 57: Cargo receptor activity; 58: Translation regulator activity; 59: Toxin activity; 60: Molecular function regulator; 61: Hijacked molecular function; 62: Molecular carrier activity; 63: Transcription regulator activity. The black, stripe and white area indicated biological process, cellular component and molecular function, respectively
Fig. 5 The KEGG enrichment of exon microsatellites in Hipposideros armiger. A: Metabolism; B: Environmental information processing; C: Genetic information processing; D: Cell process; E: Organismal systems; F: Human diseases and drug development
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