Sequencing and analysis of the complete mitochondrial genome of green abalone (Haliotis fulgens)
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摘要: 为高效鉴别鲍属物种和更好地管理和保护鲍种质资源，本研究通过高通量测序获得了养殖绿鲍（Haliotis fulgens）稚贝的线粒体基因组全序列，并对其序列和结构特征进行分析。结果表明，绿鲍线粒体基因组全长17 041 bp，含有37个编码基因，其中蛋白质编码基因13个、tRNA基因22个、rRNA基因2个。13个蛋白质编码基因均以AUG为起始密码子，以UAG或UAA为终止密码子。除tRNA-Ser(AGN)外的21个tRNA基因可折叠成典型三叶草结构。分析发现tRNA-Glu和COX3间存在富含A+T的非编码区，其内含有2个带回文序列的发卡结构。基于已报道的10个鲍属线粒体基因组全序列构建系统发育树，发现绿鲍与皱纹盘鲍（Haliotis discus hannai）、红鲍（Haliotis rufescens）、黑鲍（Haliotis cracherodii）聚为一支。将绿鲍与皱纹盘鲍13个线粒体编码蛋白的结构域比较，发现二者ND2、ND4的跨膜结构域数量存在差异，这是否与二者的高温耐受性差异有关，有待进一步研究。总之，绿鲍线粒体基因组全序列的首次获取和分析，丰富了鲍类细胞遗传信息，为分类、种质鉴定与种质资源保护提供了基础数据和参考。Abstract: To identify abalone species effectively for better management and protection of abalone germplasm resources, we have obtained the complete mitochondrial genome of juvenile green abalone (Haliotis fulgens) through high-throughput sequencing, and its sequences and structural characteristics are analyzed accordingly. The results show that the mitogenome of H. fulgens is 17 041 bp in total length and encoded 37 genes, including 13 protein coding genes, 22 transfer RNA (tRNA) genes and 2 ribosomal RNA (rRNA) genes. The 13 protein coding genes used AUG as the starting codon and UAA or UAG as the termination codon. Twenty-one tRNA genes other than tRNA-Ser(AGN) could be folded into a typical cloverleaf structure. There is a rich A+T non-coding region between tRNA-Glu and COX3, with two hairpin structures containing palindromes in it. A phylogenetic tree was constructed based on the reported complete mitochondrial genome sequences of Haliotis genus species, and phylogenetic analysis shows that H. fulgens is clustered with H. discus hannai, H. rufescens and H. cracherodii. Comparing the domains of 13 proteins of mitogenome of H. fulgens and H. discus hannai, we found the number of transmembrane domains of ND2 or ND4 dehydrogenase subunits were different in them. Whether this is related to the difference of high temperature tolerance between them needs further study. In brief, the first acquisition and analysis of the complete mitochondrial genome of H. fulgens has enriched the abalone cellular genetic information, and provided basic data and references for abalone species classification, germplasm identification, and protection of germplasm resources of H. fulgens as well.
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Key words:
- Haliotis fulgens /
- mitochondrial genome /
- genome composition /
- phylogeny /
- domain
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图 1 鲍属cytB基因NJ系统发育树
Fig. 1 Phylogenetic tree based on the neighbor-joining （NJ） analysis of the cytB genes of Haliotis spp.
图 3 绿鲍线粒体编码基因及非编码基因排列图
Fig. 3 The mitochondrial coding and non-coding genes arrangement diagram of Haliotis fulgens
图 4 绿鲍特殊tRNA基因二级结构
Fig. 4 The unusual secondary structures of the tRNA genes in Haliotis fulgens
图 5 绿鲍线粒体控制区序列及结构特征示意图
下划线表示存在回文序列的两个发卡结构序列，下方为对应的发卡结构
Fig. 5 Schematic map of the control region sequences and characteristics of Haliotis fulgens
Underline shows the sequences of two hairpin structures containing palindromes and bottom is the corresponding hairpin structures
图 6 鲍属线粒体基因组NJ系统发育树
Fig. 6 Phylogenetic tree based on the neighbor-joining (NJ) analysis of Haliotis genus whole mitochondrial genomes
图 7 绿鲍与皱纹盘鲍线粒体蛋白质氨基酸序列相似性及二级结构比较
Fig. 7 Comparison of amino acid sequence identity and secondary structure of mitochondrial proteins between Haliotis fulgens and Haliotis discus hannai
表 1 已报道鲍属贝类线粒体基因组
Tab. 1 The complete mitochondrial genomes reported of Haliotis genus for analysis
物种 长度/bp GC含量/% GenBank登录号 皱纹盘鲍（Haliotis discus hannai） 16 886 39.6 KF724723.1 黑足鲍（Haliotis iris） 17 131 40.2 KU310895.1 黑唇鲍（Haliotis rubra） 16 907 40.9 AY588938.1 绿唇鲍（Haliotis laevigata） 16 545 42.2 KJ472483.1 欧洲疣鲍（Haliotis tuberculata） 15 938 39.5 FJ605488.1 杂色鲍（Haliotis diversicolor） 16 543 40.1 MZ465525.1 羊鲍（Haliotis ovina） 16 531 40.7 NC056350.1 红鲍（Haliotis rufescens） 16 646 39.7 NC036928.1 黑鲍（Haliotis cracherodii） 18 391 37.7 CM039063.1 
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表 2 绿鲍线粒体基因组注释结果
Tab. 2 The results of the complete mitochondrial genome annotation for Haliotis fulgens
基因 长度/bp 定位 间隔区/bp 反密码子 密码子 编码链 起始位点 终止位点 起始密码子 终止密码子 COX3 780 1 780 0 − AUG UAA H trnD 73 812 884 31 GUC − − H trnK 72 884 955 −1 UUU − − H trnA 69 951 1 019 −5 UGC − − H trnR 66 1 021 1 086 1 UCG − − H trnI 70 1 099 1 168 12 GAU − − H ND3 354 1 171 1 524 2 − AUG UAA H trnN 71 1 537 1 607 12 GUU − − H trnS 67 1 611 1 677 3 GCU − − H ND2 1 095 1 681 2 775 3 − AUG UAA H COX1 1 542 2 795 4 336 19 − AUG UAA H COX2 696 4 375 5 070 38 − AUG UAG H ATP8 165 5 155 5 319 84 − AUG UAA H ATP6 696 5 374 6 069 54 − AUG UAA H trnF 68 6 113 6 180 43 GAA − − L ND5 1 740 6 195 7 934 14 − AUG UAA L trnH 68 7 935 8 002 0 GUG − − L ND4 1 233 8 050 9 282 47 − AUG UAA L ND4L 300 9 438 9 737 155 − AUG UAG L trnT 70 9 762 9 831 24 UGU − − H trnS 67 9 858 9 924 26 UGA − − L CYTB 1 140 9 937 11 076 12 − AUG UAG L ND6 507 11 114 11 620 37 − AUG UAG L trnP 67 11 621 11 687 0 UGG − − L ND1 945 11 710 12 654 22 − AUG UAG L trnL 68 12 656 12 723 1 UAA − − L trnL 68 12 814 12 881 90 UAG − − L 16S 1 400 12 898 14 297 16 − − − L trnV 66 14 390 14 455 92 AAC − − L 12S 1 033 14 469 15 501 13 − − − L trnM 70 15 516 15 585 14 CAU − − L trnY 68 15 588 15 655 2 GUA − − L trnC 70 15 664 15 733 8 GCA − − L trnW 73 15 737 15 809 3 UCA − − L trnQ 70 15 820 15 889 10 UUG − − L trnG 68 15 892 15 959 2 UCC − − L trnE 68 15 964 16 031 4 UUC − − L 注：trn表示rRNA，后面的大写字母表示该tRNA转运的氨基酸；16S和12S为rRNA基因；−代表无密码子。
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表 3 鲍属线粒体基因组碱基组成
Tab. 3 Composition and skewness in the mitochondrial genomes of Haliotis genus species
物种 碱基组成/% AT偏移 GC偏移 A T C G A+T 线粒体全基因组 绿鲍 Haliotis fulgens 36.2 24.4 26.5 12.9 60.6 0.195 −0.345 皱纹盘鲍 Haliotis discus hannai 35.4 25.0 26.1 13.5 60.4 0.172 −0.318 黑足鲍 Haliotis iris 35.9 23.9 26.8 13.4 59.8 0.201 −0.333 黑唇鲍 Haliotis rubra 34.6 24.5 26.7 14.2 59.1 0.171 −0.306 绿唇鲍 Haliotis laevigata 23.9 33.9 14.9 27.3 57.8 −0.173 0.294 欧洲疣鲍 Haliotis tuberculata 34.8 25.7 25.8 13.6 60.5 0.150 −0.310 杂色鲍 Haliotis diversicolor 35.2 24.7 26.4 13.7 59.9 0.175 −0.317 羊鲍 Haliotis ovina 34.8 24.5 27.4 13.4 59.3 0.174 −0.343 红鲍 Haliotis rufescens 35.4 24.9 25.9 13.7 60.3 0.174 −0.308 黑鲍 Haliotis cracherodii 26.6 35.7 13.5 24.2 62.3 −0.146 0.284 蛋白质编码基因 绿鲍 Haliotis fulgens 23.4 36.3 19.1 21.2 59.7 −0.216 0.052 皱纹盘鲍 Haliotis discus hannai 23.4 36.3 19.2 21.1 59.7 −0.216 0.047 黑足鲍 Haliotis iris 22.5 36.0 19.6 21.9 58.5 −0.231 0.055 黑唇鲍 Haliotis rubra 22.3 35.1 19.9 22.6 57.4 −0.223 0.064 绿唇鲍 Haliotis laevigata 22.2 34.5 20.4 22.8 56.7 −0.217 0.056 欧洲疣鲍 Haliotis tuberculata 23.7 36.1 18.9 21.3 59.8 −0.207 0.060 杂色鲍 Haliotis diversicolor 23.2 35.9 19.1 21.8 59.1 −0.215 0.066 羊鲍 Haliotis ovina 22.6 35.8 19.3 22.2 58.4 −0.226 0.070 红鲍 Haliotis rufescens 23.5 36.0 19.3 21.2 59.5 −0.210 0.047 黑鲍 Haliotis cracherodii 23.2 35.9 19.4 21.6 59.1 −0.215 0.054 tRNA基因 绿鲍 Haliotis fulgens 28.1 31.0 16.9 24.0 59.1 −0.050 0.174 皱纹盘鲍 Haliotis discus hannai 28.2 30.5 17.3 24.0 58.7 −0.039 0.162 黑足鲍 Haliotis iris 27.6 30.6 17.5 24.3 58.2 −0.052 0.163 黑唇鲍 Haliotis rubra 27.5 30.4 17.4 24.8 57.9 −0.050 0.175 绿唇鲍 Haliotis laevigata 27.3 30.7 17.1 24.9 58.0 −0.059 0.186 欧洲疣鲍 Haliotis tuberculata 28.7 31.0 17.0 23.3 59.7 −0.039 0.156 杂色鲍 Haliotis diversicolor 27.2 30.8 17.2 24.9 58.0 −0.062 0.183 羊鲍 Haliotis ovina 27.5 31.2 17.0 24.4 58.7 −0.063 0.179 红鲍 Haliotis rufescens 28.3 30.5 17.4 23.8 58.8 −0.037 0.155 黑鲍 Haliotis cracherodii 28.0 30.8 17.1 24.1 58.8 −0.048 0.170 rRNA基因 绿鲍 Haliotis fulgens 26.1 35.1 13.4 25.4 61.2 −0.147 0.309 皱纹盘鲍 Haliotis discus hannai 27.2 35.2 13.1 24.5 62.4 −0.128 0.303 黑足鲍 Haliotis iris 25.8 35.7 12.9 25.6 61.5 −0.161 0.330 黑唇鲍 Haliotis rubra 26.2 34.9 13.6 25.3 61.1 −0.142 0.301 绿唇鲍 Haliotis laevigata 26.3 33.9 14.3 25.6 60.2 −0.126 0.283 欧洲疣鲍 Haliotis tuberculata 28.0 34.4 13.2 24.4 62.4 −0.103 0.298 杂色鲍 Haliotis diversicolor 27.1 35.1 13.2 24.5 62.2 −0.129 0.300 羊鲍 Haliotis ovina 25.8 34.6 13.5 26.1 60.4 −0.146 0.318 红鲍 Haliotis rufescens 27.3 34.9 13.3 24.5 62.2 −0.122 0.296 黑鲍 Haliotis cracherodii 27.1 35.0 13.3 24.6 62.1 −0.127 0.298 假定控制区 绿鲍 Haliotis fulgens 37.6 29.4 24.6 8.4 67.0 0.122 −0.491
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表 4 绿鲍13个蛋白质编码基因密码子平均使用频率
Tab. 4 Total codon average usage in the thirteen protein coding genes for Haliotis fulgens
密码子 数量 使用率 密码子 数量 使用率 密码子 数量 使用率 密码子 数量 使用率 UCU（S） 95 2.11 GUU（V） 127 1.60 ACU（T） 67 1.48 CAA（Q） 44 1.19 UCC（S） 58 1.29 GUA（V） 75 0.94 ACA（T） 66 1.46 CAG（Q） 30 0.81 UCA（S） 52 1.15 GUG（V） 74 0.93 ACC（T） 36 0.80 CAU（H） 46 1.15 AGU（S） 50 1.11 GUC（V） 42 0.53 ACG（T） 12 0.27 CAC（H） 34 0.85 AGG（S） 38 0.84 UUA（L） 151 1.56 UUU（T） 216 1.38 AAA（K） 46 1.12 AGA（S） 34 0.75 UUG（L） 148 1.53 UUC（T） 98 0.62 AAG（K） 36 0.88 AGC（S） 18 0.40 CUA（L） 115 1.19 UAU（Y） 86 1.33 UGA（W） 60 1.10 UCG（S） 16 0.35 CUU（L） 74 0.77 UAC（Y） 43 0.67 UGG（W） 49 0.90 CGA（R） 29 1.81 CUC（L） 59 0.61 GGA（G） 92 1.31 GAA（E） 50 1.10 CGU（R） 19 1.19 CUG（L） 33 0.34 GGG（G） 92 1.31 GAG（E） 41 0.90 CGG（R） 9 0.56 GCU（A） 94 1.55 GGU（G） 69 0.99 GAC（D） 40 1.08 CGC（R） 7 0.44 GCC（A） 63 1.04 GGC（G） 27 0.39 GAU（D） 34 0.92 CCA（P） 61 1.64 GCA（A） 58 0.96 AAU（N） 77 1.29 AUG（M） 88 1.05 CCU（P） 52 1.40 GCG（A） 27 0.45 AAC（N） 42 0.71 AUA（M） 80 0.95 CCG（P） 20 0.54 UGU（C） 45 1.50 AUU（I） 145 1.19 UAA 8 1.23 CCC（P） 16 0.43 UGC（C） 15 0.50 AUC（I） 98 0.81 UAG 5 0.77 注：黑体表示偏好密码子。
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表 5 基于线粒体全序列的10种鲍种间核酸相似性
Tab. 5 Nucleotide sequence identity among 10 species of abalone based on whole mitochondrial genome
物种 核酸相似性/% 绿鲍 Haliotis fulgens 100 皱纹盘鲍 Haliotis discus hannai 89.15 100 黑足鲍 Haliotis iris 82.86 83.41 100 黑唇鲍 Haliotis rubra 80.94 80.97 80.73 100 绿唇鲍 Haliotis laevigata 80.80 80.66 80.23 91.89 100 欧洲疣鲍 Haliotis tuberculata 81.51 81.39 81.32 83.84 83.37 100 杂色鲍 Haliotis diversicolor 81.03 80.77 80.16 83.09 82.80 82.59 100 羊鲍 Haliotis ovina 80.10 79.95 79.06 82.14 81.92 81.36 81.54 100 红鲍 Haliotis rufescens 88.16 90.94 83.41 81.51 81.12 81.61 81.59 80.75 100 黑鲍 Haliotis cracherodii 87.90 90.03 83.46 81.25 80.98 81.19 80.64 80.55 91.62 100
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