斑马芬奇基因组中着丝粒特异性重复序列的鉴定

IF 1.7 4区 生物学 Q4 CELL BIOLOGY
Olga Takki, A. Komissarov, M. Kulak, S. Galkina
{"title":"斑马芬奇基因组中着丝粒特异性重复序列的鉴定","authors":"Olga Takki, A. Komissarov, M. Kulak, S. Galkina","doi":"10.1159/000521716","DOIUrl":null,"url":null,"abstract":"Tandem repetitive sequences represent a significant part of many genomes but remain poorly characterized due to various methodological difficulties. Here, we describe the tandem repeat composition in the genome of zebra finch, Taeniopygia guttata, a species that has long served as an animal model, primarily in neurobiology and comparative genomics. Using available genome sequencing raw read datasets, we bioinformatically reconstructed consensus sequences of several tandem repeats and proved that the most abundant ones, Tgut191A and Tgut716A, are centromere-associated in chromosomes. Each centromeric region can have a different number of copies of each repeat, with Tgut716A enrichment in almost all microchromosomes and sex chromosomes. Sequences similar to Tgut191A and Tgut716A found in other Estrildidae and Viduidae species can be considered as candidate centromeric sequences, but this requires further cytogenetic verification.","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7000,"publicationDate":"2022-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Identification of Centromere-Specific Repeats in the Zebra Finch Genome\",\"authors\":\"Olga Takki, A. Komissarov, M. Kulak, S. Galkina\",\"doi\":\"10.1159/000521716\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Tandem repetitive sequences represent a significant part of many genomes but remain poorly characterized due to various methodological difficulties. Here, we describe the tandem repeat composition in the genome of zebra finch, Taeniopygia guttata, a species that has long served as an animal model, primarily in neurobiology and comparative genomics. Using available genome sequencing raw read datasets, we bioinformatically reconstructed consensus sequences of several tandem repeats and proved that the most abundant ones, Tgut191A and Tgut716A, are centromere-associated in chromosomes. Each centromeric region can have a different number of copies of each repeat, with Tgut716A enrichment in almost all microchromosomes and sex chromosomes. Sequences similar to Tgut191A and Tgut716A found in other Estrildidae and Viduidae species can be considered as candidate centromeric sequences, but this requires further cytogenetic verification.\",\"PeriodicalId\":11206,\"journal\":{\"name\":\"Cytogenetic and Genome Research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.7000,\"publicationDate\":\"2022-03-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Cytogenetic and Genome Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1159/000521716\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"CELL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cytogenetic and Genome Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1159/000521716","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"CELL BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

串联重复序列代表了许多基因组的重要组成部分,但由于各种方法上的困难,其特征仍然很差。在这里,我们描述了斑胸带颈雀基因组中的串联重复组成,该物种长期以来一直是动物模型,主要用于神经生物学和比较基因组学。使用可用的基因组测序原始读取数据集,我们生物信息学地重建了几个串联重复序列的一致序列,并证明了最丰富的Tgut191A和Tgut716A是染色体中的着丝粒相关序列。每个着丝粒区域的每个重复序列可以有不同数量的拷贝,Tgut716A在几乎所有的微染色体和性染色体中富集。类似于在其他雌蛛科和Viduidae物种中发现的Tgut191A和Tgut716A的序列可以被认为是候选着丝粒序列,但这需要进一步的细胞遗传学验证。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Identification of Centromere-Specific Repeats in the Zebra Finch Genome
Tandem repetitive sequences represent a significant part of many genomes but remain poorly characterized due to various methodological difficulties. Here, we describe the tandem repeat composition in the genome of zebra finch, Taeniopygia guttata, a species that has long served as an animal model, primarily in neurobiology and comparative genomics. Using available genome sequencing raw read datasets, we bioinformatically reconstructed consensus sequences of several tandem repeats and proved that the most abundant ones, Tgut191A and Tgut716A, are centromere-associated in chromosomes. Each centromeric region can have a different number of copies of each repeat, with Tgut716A enrichment in almost all microchromosomes and sex chromosomes. Sequences similar to Tgut191A and Tgut716A found in other Estrildidae and Viduidae species can be considered as candidate centromeric sequences, but this requires further cytogenetic verification.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Cytogenetic and Genome Research
Cytogenetic and Genome Research 生物-细胞生物学
CiteScore
3.10
自引率
5.90%
发文量
25
审稿时长
1 months
期刊介绍: During the last decades, ''Cytogenetic and Genome Research'' has been the leading forum for original reports and reviews in human and animal cytogenetics, including molecular, clinical and comparative cytogenetics. In recent years, most of its papers have centered on genome research, including gene cloning and sequencing, gene mapping, gene regulation and expression, cancer genetics, comparative genetics, gene linkage and related areas. The journal also publishes key papers on chromosome aberrations in somatic, meiotic and malignant cells. Its scope has expanded to include studies on invertebrate and plant cytogenetics and genomics. Also featured are the vast majority of the reports of the International Workshops on Human Chromosome Mapping, the reports of international human and animal chromosome nomenclature committees, and proceedings of the American and European cytogenetic conferences and other events. In addition to regular issues, the journal has been publishing since 2002 a series of topical issues on a broad variety of themes from cytogenetic and genome research.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信