Development of fish diversity studies by next-generation mitogenome sequencing: From Sanger method to massively parallel method

新一代线粒体基因组测序鱼类多样性研究进展：从桑格法到大规模并行法

• 批准号: 23370041
• 负责人: NISHIDA Mutsumi
• 金额: $ 11.81万
• 依托单位: University of the Ryukyus (2013)The University of Tokyo (2011-2012)
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2011
• 资助国家: 日本
• 起止时间: 2011-04-01 至 2014-03-31
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23370041/
• 关键词: 進化; 集団・種多様性; 遺伝的多様性

Whole mitochondrial genome (mitogenome) sequences are extremely useful for resolving phylogenies of animals including fishes. This study aims to establish efficient procedures to obtain mitogenome data from many samples including degraded ones by using "next-generation" massively parallel sequencing technologies. For samples in good condition, long-PCR amplification/purification and parallel tagged sequencing successfully provided mitogenome data from many samples simultaneously, suggesting that this is a rather easier method for such samples. For degraded samples, many segments from mitogenome were successfully captured by using the capture-on-beads method with double indexing. Thus, we conclude that efficient procedures have been established to have large mitogenome data from many samples including degraded ones by using next-generation sequencing technologies.

整个线粒体基因组（线粒体基因组）序列对于解析包括鱼类在内的动物的系统发育非常有用。本研究旨在建立有效的程序，通过使用“下一代”大规模并行测序技术从许多样本（包括降解样本）中获取线粒体基因组数据。对于状况良好的样品，长PCR扩增/纯化和平行标记测序成功地同时提供了来自许多样品的线粒体基因组数据，这表明对于此类样品来说这是一种相当简单的方法。 对于降解的样品，通过使用双索引的珠上捕获方法成功捕获了丝裂基因组的许多片段。 因此，我们得出的结论是，已经建立了有效的程序，可以通过使用下一代测序技术从许多样本（包括降解样本）中获取大量线粒体基因组数据。

项目成果

Molecular identification of species and ploidy of Carassius fishes in Lake Biwa, using mtDNA and microsatellite multiplex PCRs

• DOI: 10.1007/s10228-014-0388-9
• 发表时间: 2014
• 期刊: Ichthyological Research
• 影响因子: 1.2
• 作者: Tappei Mishina;Mikumi Takada;H. Takeshima;M. Nakano;Ryoichi Tabata;M. Nishida;Katsutoshi Watanabe

Remarkable consistency of exon-intron structure of hatching enzyme genes and molecular phylogenetic relationships of teleostean fishes

硬骨鱼类孵化酶基因外显子-内含子结构与分子系统发育关系的显着一致性

• DOI: 10.1007/s10641-011-9920-1
• 发表时间: 2012
• 期刊: Environmental Biology of Fishes
• 影响因子: 1.4
• 作者: Mari Kawaguchi;Sebastien Lavoue;Junya Hiroi;Hirofumi Hayano;Ichiro Iuchi;Shigeki Yasumasu;Mutsumi Nishida
• 通讯作者: Mutsumi Nishida

孵化酵素の環境適応～1つのアミノ酸変異による至適塩濃度の違い～

孵化酶的环境适应 ~ 一种氨基酸突变导致的最佳盐浓度差异 ~

• 发表时间: 2011
• 作者: Sano K;Kawaguchi M;Yoshikawa M;Kaneko T;Tanaka T;Iuchi I and Yasumasu S;野村健太郎・川口眞理・竹花佑介・成瀬清・安増茂樹;佐野香織・川口眞理・井内一郎・安増茂樹;川口眞理;川口眞理・井内一郎・西田睦・安増茂樹
• 通讯作者: 川口眞理・井内一郎・西田睦・安増茂樹

Phylogenetic analysis of syngnathoid fishes based on whole mitochondrial genome sequences:Limits and intrarelationships of the "Syngnathoidei".

基于线粒体全基因组序列的合颌鱼类系统发育分析：“合颌鱼类”的局限性和内部关系。

• 发表时间: 2012
• 作者: H. Song;K. Mabuchi;T. P. Satoh;M. Miya;M. Nishida
• 通讯作者: M. Nishida

ベトナムで採集された分布域最南端のアユの遺伝的特徴

越南最南端香鱼的遗传特征

• 发表时间: 2012
• 作者: Nguyen Thi Tu Anh;Maiko Nishitani;Shigeharu Harada;Masamitsu Yamaguchi;Kaeko;小林拓也;住田一真;武島弘彦・Hau D. TRAN・木下 泉・井口恵一朗・西田 睦
• 通讯作者: 武島弘彦・Hau D. TRAN・木下 泉・井口恵一朗・西田 睦