Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico.
Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Jalisco, Mexico.
Methods Mol Biol. 2022;2512:199-215. doi: 10.1007/978-1-0716-2429-6_12.
In comparative genomics, the study of synteny can be a powerful method for exploring genome rearrangements, inferring genomic ancestry, defining orthology relationships, determining gene and genome duplications, and inferring gene positional conservation patterns across taxa. In this chapter, we present a step-by-step protocol for microsynteny network (SynNet) analysis, as an alternative to traditional methods of synteny comparison, where nodes in the network represent protein-coding genes and edges represent the pairwise syntenic relationships. The SynNet pipeline consists of six main steps: (1) pairwise genome comparisons between all the genomes being analyzed, (2) detection of inter- and intrasynteny blocks, (3) generation of an entire synteny database (i.e., edgelist), (4) network clustering, (5) phylogenomic profiling of the gene family of interest, and (6) evolutionary inference. The SynNet approach facilitates the rapid analysis and visualization of synteny relationships (from specific genes, specific gene families up to all genes) across a large number of genomes.
在比较基因组学中，研究同线性可以成为探索基因组重排、推断基因组祖先、定义同源关系、确定基因和基因组复制以及推断跨分类单元的基因位置保守模式的有力方法。在本章中，我们提出了一种分步微同线性网络（SynNet）分析协议，作为传统同线性比较方法的替代方法，其中网络中的节点表示编码蛋白质的基因，边缘表示两两同线性关系。SynNet 分析流程包括六个主要步骤：（1）对所有正在分析的基因组进行两两基因组比较；（2）检测内外同线性块；（3）生成完整的同线性数据库（即边列表）；（4）网络聚类；（5）感兴趣基因家族的系统发生分析；（6）进化推断。SynNet 方法有助于快速分析和可视化大量基因组中同线性关系（从特定基因、特定基因家族到所有基因）。
