Putta Srikrishna, Smith Jeramiah J, Walker John A, Rondet Mathieu, Weisrock David W, Monaghan James, Samuels Amy K, Kump Kevin, King David C, Maness Nicholas J, Habermann Bianca, Tanaka Elly, Bryant Susan V, Gardiner David M, Parichy David M, Voss S Randal
Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
BMC Genomics. 2004 Aug 13;5(1):54. doi: 10.1186/1471-2164-5-54.
Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories.
Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human - Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species.
Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research.
为亲缘关系密切的物种建立基因组资源将提供比较性见解，这对于理解生物组织多个层面的多样性和变异性至关重要。我们为墨西哥钝口螈（Ambystoma mexicanum）和东部虎螈（A. tigrinum tigrinum）开发了ESTs，这两个物种有着深厚且多样的研究历史。
从包括再生肢体和尾巴在内的各种组织中为这些物种分离出了约40,000条高质量cDNA序列。这些序列以及现有的一组16,030条墨西哥钝口螈cDNA序列经过处理后，分别为墨西哥钝口螈和东部虎螈产生了35,413条和20,599条高质量ESTs。由于东部虎螈的ESTs主要来自一个标准化文库，因此每个物种获得的重叠群数量大致相等，总共鉴定出21,091个独特重叠群。与人类RefSeq数据库序列显示出显著相似性的10,592个重叠群反映了一系列多样的分子功能和生物学过程，其中许多对应于大鼠脊髓损伤和斑马鱼鳍再生过程中表达的基因。为了证明这些EST资源的实用性，我们搜索数据库以鉴定用于再生研究的探针，表征种内和种间核苷酸多态性，用标记基因座饱和一个人类 - 钝口螈同线群，并将为墨西哥钝口螈/东部虎螈直系同源物设计的PCR引物组扩展到一个相关的虎螈物种。
我们的研究突出了在传统模型系统中开发资源的价值，在这些系统中信息转移到多个亲缘关系密切的分类群的可能性很高，从而同时促进实验室研究和自然历史研究。
