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Comparison of Complete Mitochondrial Genome and Structural Characteristics Analysis of Channa argus, Channa maculata, and Their Reciprocal Species
DAIHan, CHENJing, YAOJiayun, YUANXuemei, HUANGLei, JIAOJinbiao, HUANGFei, SHENShuie, SUShengqi, ZHANGHaiqi
Chin Agric Sci Bull ›› 2026, Vol. 42 ›› Issue (16) : 209-218.
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Abbreviation (ISO4): Chin Agric Sci Bull
Editor in chief: Yulong YIN
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Comparison of Complete Mitochondrial Genome and Structural Characteristics Analysis of Channa argus, Channa maculata, and Their Reciprocal Species
Channa argus and Channa maculata are important indigenous fish species in China, and their orthogonal (C. maculata ♀×C. argus ♂) and backcross species (C. argus ♀×C. maculata ♂) also exhibit good hybrid advantages in actual production. In this study, Illumina sequencing technology was used to assemble the whole mitochondrial genomes of C. argus, C. maculata and their orthogonal and backcross species, and the mitochondrial genome structural characteristics and phylogenetic relationships of these four species were compared and analyzed. The results showed that the mitochondrial genomes of these four fish species were all 16425 bp in size and contained 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNA), and 1 displacement-loop region (D-loop). Except for ND6, tRNAGln, tRNAAla,tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu, andtRNAPro located on the light chain, the remaining component were located on the heavy chain. The nucleotide composition of the mitochondrial genomes of these four fish species exhibited strong A+T bias. Phylogenetic analysis based on the maximum likelihood method showed that, due to the matrilineal inheritance of the mitochondrial genome, Channa argusare most related to C. argus ♀×C. maculata ♂, followed by C. maculata ♀×C. argus ♂, and a little farther away from Channa maculata; Channa were clustered together as a branch, and are closer to the Gobiidae in the Perciformes; and most distantly related to the Cyprinidae, Blenniidae and Gobiesocidae. This study has built a certain theoretical foundation for the conservation of germplasm resources and the breeding of new varieties of Channa fish.
Channa argus / Channa maculata / reciprocal cross / mitochondrial genome / phylogenetic analysis
| [1] |
|
| [2] |
郭新红, 刘少军, 刘巧, 等. 鱼类线粒体DNA研究新进展[J]. 遗传学报, 2004, 31(9):983-1000.
|
| [3] |
陈四海, 区又君, 李加儿. 鱼类线粒体DNA及其研究进展[J]. 生物技术通报, 2011(3):13-20.
|
| [4] |
黄鑫, 余海军, 王茜. 常见基因序列在鱼类系统发育研究中的应用[J]. 天津农学院学报, 2021, 28(2):89-93.
本文通过总结细胞色素C氧化酶亚基I（COI）、细胞色素C氧化酶亚基II（COII）、16S rDNA、12S rDNA、线粒体细胞色素b基因（Cytb）、线粒体基因组、内部转录间隔区（ITS）以及18S rDNA在鱼类系统发育中的相关文献,探究常用基因序列在鱼类系统发育研究中的应用情况。
|
| [5] |
田美, 申欣, 孟学平, 等. 7个海星动物线粒体基因组比较及基因变异位点分析[J]. 台湾海峡, 2012, 31(2):189-194.
|
| [6] |
上官清. 鳢科鱼类物种鉴定及斑鳢种群遗传研究[D]. 上海: 上海海洋大学, 2020.
|
| [7] |
江小斌. 斑鳢Channa.maculata (♀)×乌鳢C.argus (♂)杂交子代及其亲本的遗传关系分析与鉴定[J]. 福建水产, 2013, 35(2):93-99.
|
| [8] |
罗青, 陈昆慈, 赵建, 等. 乌鳢、斑鳢及其杂交F1代肌肉营养成分和含肉率的比较分析[J]. 大连海洋大学学报, 2015, 30(2):175-180.
|
| [9] |
薛丹, 章群, 郜星晨, 等. 基于线粒体控制区的云南澜沧江和海南岛主要水系宽额鳢遗传变异分析[J]. 水生生物学报, 2015, 39(6):1107-1116.
|
| [10] |
|
| [11] |
|
| [12] |
|
| [13] |
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
|
| [14] |
About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.Copyright © 2012 Elsevier Inc. All rights reserved.
|
| [15] |
The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the form of GFF (General Feature Format) files. The server uses BLAST to compare the primary sequence to up to three comparison genomes or sequence sets. The BLAST results and feature information are converted to a graphical map showing the entire sequence, or an expanded and more detailed view of a region of interest. Several options are included to control which types of features are displayed and how the features are drawn. The CGView Server can be used to visualize features associated with any bacterial, plasmid, chloroplast or mitochondrial genome, and can aid in the identification of conserved genome segments, instances of horizontal gene transfer, and differences in gene copy number. Because a collection of sequences can be used in place of a comparison genome, maps can also be used to visualize regions of a known genome covered by newly obtained sequence reads. The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/
|
| [16] |
|
| [17] |
贾永义, 蒋文枰, 顾志敏. 温州光唇鱼线粒体基因组结构及系统发育分析[J]. 上海海洋大学学报, 2014, 23(1):22-30.
|
| [18] |
张方, 米志勇. 动物线粒体DNA的分子生物学研究进展[J]. 生物工程进展, 1998(3):25-31.
|
| [19] |
廖贤晖. 中国近海黄魴鮄科鱼类分类及系统发育研究[D]. 舟山: 浙江海洋大学, 2024.
|
| [20] |
王开杰, 姜燕, 徐永江, 等. 黄带拟鲹线粒体基因组测序及鲹科鱼类系统发育分析[J]. 水产学报, 2022, 46(11):2017-2027.
|
| [21] |
蒙雨, 宋一清, 谢青颖, 等. 海南万泉河口尖鳍鲤线粒体基因组测序与结构特征分析[J]. 海洋科学, 2023, 47(11):66-78.
|
| [22] |
张亚颖, 何慧, 马海霞, 等. 小头高原鱼和骨唇黄河鱼线粒体基因组比较及系统发育分析[J]. 动物学杂志, 2024, 59(5):743-753.
|
| [23] |
钟东, 赵贵军, 张振书, 等. 基因组内碱基分布整体均衡与局部不均衡的研究进展[J]. 遗传, 2002(3):351-355.
|
| [24] |
王开杰, 徐永江, 崔爱君, 等. 高体(鱼师)(Seriola dumerili)线粒体全基因组测定及结构特征分析[J]. 海洋与湖沼, 2022, 53(1):120-132.
|
| [25] |
周传江, 马爱喆, 汪曦, 等. 鱼类线粒体基因组研究进展[J]. 河南师范大学学报(自然科学版), 2019, 47(2):74-82.
|
| [26] |
孟乾, 张志勇, 张志伟, 等. 斑石鲷和条石鲷线粒体基因组密码子使用分析[J]. 水产科学, 2020, 39(5):702-709.
|
| [27] |
蒋宗良, 张明, 林勇, 等. 奥利亚罗非鱼线粒体基因组全序列测定与系统进化分析[J]. 中国水产科学, 2011, 18(4):790-800.
|
| [28] |
黄小林, 杨育凯, 林黑着, 等. 篮子鱼属线粒体基因组序列系统发育信息分析[J]. 生物学杂志, 2018, 35(5):33-36.
|
| [29] |
黄小林, 李文俊, 林黑着, 等. 基于线粒体DNA D-loop序列的黄斑篮子鱼群体遗传多样性分析[J]. 热带海洋学报, 2018, 37(4):45-51.
对中国华南沿海不同地理群体的黄斑篮子鱼(Siganus oramin)进行遗传多样性分析, 测定了漳州东山湾(DS)、深圳大亚湾(DY)、深圳大鹏湾(DP)、阳江沙扒湾(SB) 4个群体共计100尾黄斑篮子鱼线粒体DNA D-loop序列。结果显示: 序列长度约828bp, 包含72个变异位点, 50个单倍型, A、T、C、G含量平均为31.2%、31.1%、20.8%和16.9%; 单倍型多样性指数为0.893±0.053~0.957±0.030, 核苷酸多样性指数为0.0105±0.0031~0.0179±0.0031, 表现为高单倍型多样性而低核苷酸多样性的特点; 群体内的遗传距离0.0107~0.0184, 群体间的遗传距离0.0112~0.0172, AMOVA分析显示群体间的分子变异占0.66%, 群体内占99.34%; 中性检验结果表明Fu’s Fs检验值为显著的负值(-16.7079, p<0.01); 核苷酸不配对分布图呈单峰, 表明黄斑篮子鱼演化过程中经历过种群扩张事件, 推测扩张时间约在1.38~4.60万年前。综上, 华南沿海岸4个黄斑篮子鱼群体间不存在显著的遗传分化, 可划归一个管理单元, 而沙扒湾(SB)群体遗传多样性水平相对较高, 应优先加以保护。
|
| [30] |
王攀攀, 谢姝敏, 于世豪, 等. 日本囊对虾两种表型差异类型线粒体的全基因组比较[J]. 水产学报, 2023, 47(3):49-65.
|
| [31] |
袁冬皓, 杨天燕, 孟玮, 等. 四种鱚属鱼类线粒体Cyt b基因的序列变异及系统发育研究[J]. 浙江农业学报, 2020, 32(1):35-42.
测定和分析了4种鱚属(Sillago)鱼类:斑鱚(Sillago aeolus)、亚洲鱚(S. asiatica)、多鳞鱚(S. sihama)和少鳞鱚(S. japonica)线粒体细胞色素b基因序列片段,比较了不同鱚属鱼类种间的序列差异,探讨了彼此间系统发育关系和分类地位。结果显示,4种鱼类平均核苷酸组成为T 29.9%、C 29.2%、A 21.5%、G 19.3%,种间平均净遗传距离在0.157到0.280之间。最大似然法构建的系统树显示,少鳞鱚和亚洲鱚首先聚类、再与多鳞鱚和斑鱚相聚,斑鱚是最晚分化出的鱼类。基于Cyt b基因序列核苷酸分歧速率计算得出4种鱼类发生遗传分化时间在距今785—1400年前的第三纪中新世(Miocene)。
|
| [32] |
|
| [33] |
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