Data from: Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion

Linkage maps are important tools in evolutionary genetics and in studies of speciation. We performed a karyotyping study and constructed high-density linkage maps for two closely related killifish species, Lucania parva and Lucania goodei, that differ in salinity tolerance and still hybridize in their contact zone in Florida. Using SNPs from orthologous EST contigs, we compared synteny between the two species to determine how genomic architecture has shifted with divergence. Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes (1N) while L. parva possesses 23 chromosomes (1N), one of which is a large metacentric chromosome. Likewise, high-density SNP-based linkage maps indicated 24 linkage groups for L. goodei and 23 linkage groups for L. parva. Synteny mapping revealed two linkage groups in L. goodei that were highly syntenic with the largest linkage group in L. parva. Together, this evidence points to the largest linkage group in L. parva being the result of a chromosomal fusion. We further compared synteny between Lucania with the genome of a more distant teleost relative medaka (Oryzias latipes) and found good conservation of synteny at the chromosomal level. Each Lucania linkage group had a single best match with each medaka chromosome. These results provide the groundwork for future studies on the genetic architecture of reproductive isolation and salinity tolerance in Lucania and other Fundulidae.

连锁图谱（linkage map）是进化遗传学与物种形成研究中的重要工具。本研究针对两种亲缘关系密切的鳉鱼物种——卢卡尼亚副鳉（Lucania parva）与古德氏卢卡尼亚鳉（Lucania goodei）开展了核型分析，并构建了高密度连锁图谱。这两个物种的盐度耐受性存在显著差异，且在佛罗里达州的自然接触带中仍可发生杂交。我们利用同源表达序列标签重叠群（orthologous EST contigs）中的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，对两个物种的同线性（synteny）进行比较，以解析基因组结构随物种分化发生的演化改变。核型分析结果显示，古德氏卢卡尼亚鳉具有24条近端着丝粒染色体（单倍体染色体数1N），而卢卡尼亚副鳉的单倍体染色体数为23条，其中包含1条大型中着丝粒染色体。同样，基于SNP的高密度连锁图谱显示，古德氏卢卡尼亚鳉的连锁群数量为24个，卢卡尼亚副鳉则为23个。同线性分析揭示，古德氏卢卡尼亚鳉的2个连锁群与卢卡尼亚副鳉的最大连锁群呈现高度同线性。综上，上述证据表明卢卡尼亚副鳉的最大连锁群源自一次染色体融合事件。我们进一步将卢卡尼亚鳉属的同线性特征与亲缘关系更远的硬骨鱼（teleost）模式物种青鳉（Oryzias latipes）的基因组进行比较，发现二者在染色体水平上保留了较好的同线性。卢卡尼亚鳉属的每个连锁群均能与青鳉的每条染色体找到唯一的最佳匹配区段。本研究结果为后续解析卢卡尼亚鳉属及其他底鳉科（Fundulidae）物种的生殖隔离与盐度耐受性的遗传结构奠定了坚实基础。