A genetic map of Xenopus tropicalis.
A genetic map of Xenopus tropicalis.
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DOI：
10.1016/j.ydbio.2011.03.022
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发表时间：
2011-06-01
影响因子：
2.7
通讯作者：
Sater AK
中科院分区：
文献类型：
--
作者：
Wells DE;Gutierrez L;Xu Z;Krylov V;Macha J;Blankenburg KP;Hitchens M;Bellot LJ;Spivey M;Stemple DL;Kowis A;Ye Y;Pasternak S;Owen J;Tran T;Slavikova R;Tumova L;Tlapakova T;Seifertova E;Scherer SE;Sater AK
我们提出了一个由2886个简单序列长度多态(SSLP)标记组成的热带爪哇遗传图谱。利用基于生物信息学的策略，我们在热带疟原虫基因组中确定了独特的SSLP。对热带X线虫基因组组装2.0(JGI)的支架进行简单序列重复(SSR)扫描；然后使用尼日利亚和象牙海岸近交系个体的DNA测试独特的SSR的扩增和多态。因此，SSLP根据来自190个F2个体的DNA样本的图谱交叉板进行了基因分型。对近4000个SSLP进行了基因分型，得到了一个2886个标记的遗传图谱，其中包括10个长度在73-132 cM之间的主要连锁群，以及4个7-40 cM之间的较小连锁群。图谱的总有效大小为1658 cM，每个连锁群的平均标记间距离为0.27~0.75 cM。利用定位于标记支架上的基因探针进行荧光原位杂交(FISH)，为染色体分配连锁群。将该图谱与热带志贺氏菌基因组组装4.1(JGI)进行比较，表明该图谱至少代表了热带志贺氏菌基因组的66%，包含了超过10万个碱基对的大约1300个支架中的758个。遗传图谱和SSLP标记数据库是热带管圆线虫遗传和基因组分析的重要资源。►热带非洲爪哇2886个简单序列长度多态的遗传图谱。►10条染色体对应的10个主连锁群，加上4个小连锁群。►连锁群通过荧光原位杂交法定位于染色体。
We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132 cM in length, and 4 smaller linkage groups between 7 and 40 cM. The total effective size of the map is 1658 cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75 cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000 bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis. ► A genetic map of 2886 Simple Sequence Length Polymorphisms for Xenopus tropicalis. ► 10 major linkage groups corresponding to the 10 chromosomes, plus 4 minor linkage groups. ► Linkage groups are cytogenetically mapped to chromosomes by Fluorescence In Situ Hybridization.
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影响因子：
1.7
作者：
Krylov, V.;Tlapakova, T.;Macha, J.
通讯作者：
Macha, J.
影响因子：
14.9
作者：
Sparrow, D B;Latinkic, B;Mohun, T J
通讯作者：
Mohun, T J
影响因子：
4.5
作者：
Goda, Tadahiro;Abu-Daya, Anita;Zimmerman, Lyle B.
通讯作者：
Zimmerman, Lyle B.
影响因子：
4.5
作者：
Olmstead, Allen W.;Lindberg-Livingston, Annelle;Degitz, Sigmund J.
通讯作者：
Degitz, Sigmund J.
影响因子：
14.9
作者：
Benson, G
通讯作者：
Benson, G