McLysaght A, Enright A J, Skrabanek L, Wolfe K H
Department of Genetics, University of Dublin, Trinity College, Ireland.
Yeast. 2000 Apr;17(1):22-36. doi: 10.1002/(SICI)1097-0061(200004)17:1<22::AID-YEA5>3.0.CO;2-S.
Knowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergence. The vertebrate Fugu rubripes (pufferfish) has a small genome with little repetitive sequence which makes it attractive as a model genome. Genome compaction and synteny conservation between human and Fugu were studied using data from public databases.
Intron length and map positions of human and Fugu orthologues were compared to analyse relative genome compaction and synteny conservation respectively. The divergence of these two genomes by genome rearrangement was simulated and the results were compared to the real data.
Analysis of 199 introns in 22 orthologous genes showed an eight-fold average size reduction in Fugu, consistent with the ratio of total genome sizes. There was no consistent pattern relating the size reduction in individual introns or genes to gene base composition in either species. For genes that are neighbours in Fugu (genes from the same cosmid or GenBank entry), 40-50% have conserved synteny with a human chromosome. This figure may be underestimated by as much as two-fold, due to problems caused by incomplete human genome sequence data and the existence of dispersed gene families. Some genes that are neighbours in Fugu have human orthologues that are several megabases and tens of genes apart. This is probably caused by small inversions or other intrachromosomal rearrangements.
Comparison of observed data to computer simulations suggests that 4000-16 000 chromosomal rearrangements have occurred since Fugu and human shared a common ancestor, implying a faster rate of rearrangement than seen in human/mouse comparisons.
了解两个物种之间基因顺序和同线性保守的程度有助于洞察物种分化的程度和机制。脊椎动物红鳍东方鲀（河豚）具有小基因组且重复序列少，这使其成为有吸引力的模式基因组。利用公共数据库中的数据研究了人类与河豚之间的基因组压缩和同线性保守情况。
比较人类和河豚直系同源基因的内含子长度和图谱位置，分别分析相对基因组压缩和同线性保守情况。模拟了这两个基因组因基因组重排而产生的分化，并将结果与实际数据进行比较。
对22个直系同源基因中的199个内含子进行分析表明，河豚的内含子平均大小减少了8倍，这与总基因组大小的比例一致。在任何一个物种中，单个内含子或基因的大小减少与基因碱基组成之间都没有一致的模式。对于在河豚中相邻的基因（来自同一黏粒或GenBank条目的基因），40%-50%与人类染色体具有保守的同线性。由于人类基因组序列数据不完整以及分散基因家族的存在所导致的问题，这个数字可能被低估了多达两倍。一些在河豚中相邻的基因，其人类直系同源基因相隔几个兆碱基和数十个基因。这可能是由小的倒位或其他染色体内重排引起的。
将观察到的数据与计算机模拟结果进行比较表明，自河豚和人类拥有共同祖先以来，已经发生了4000-16000次染色体重排，这意味着重排速度比人类/小鼠比较中观察到的要快。
