Plastome sequences of Lygodium japonicum and Marsilea crenata reveal the genome organization transformation from basal ferns to core leptosporangiates.
Plastome sequences of Lygodium japonicum and Marsilea crenata reveal the genome organization transformation from basal ferns to core leptosporangiates.
复制标题
海金沙和马西藻的质体序列揭示了从基底蕨类植物到核心细孢子囊藻的基因组组织转变
DOI：
10.1093/gbe/evt099
复制
发表时间：
2013
影响因子：
3.3
通讯作者：
Wang T
中科院分区：
文献类型：
--
作者：
Gao L;Wang B;Wang ZW;Zhou Y;Su YJ;Wang T
先前的研究表明，核心细孢子植物是现存蕨类植物中物种最丰富的一类（单生植物），与基生蕨类植物谱系具有不同的质体基因组（质体组）组织模式。然而，由于现有的质体体数据有限，从祖先蕨类植物到核心细孢子植物的基因组结构转变的细节仍不清楚。在此，我们测定了裂类蕨类（Schizaeales）的成员Lygodium japonicum （Lygodiaceae）和异孢子蕨类（saliniales）的代表Marsilea crenatata （Marsilea Marsilea）的叶绿体全基因组序列。这两个物种分别代表核心细孢子虫的姐妹系和基系，它们的质体体序列目前还无法获得。对所有已测序的蕨类植物质体的比较基因组分析表明，日本菖蒲质体的基因序列位于基部蕨类植物和核心细孢子囊植物之间的中间位置。蕨类植物ndhB基因的两个外显子具有独特的基因内拷贝数变异模式。具体来说，两个外显子之间的替代率异质性与其拷贝数变化一致，证实了反向重复可能对叶绿体基因序列的替代率起约束作用。
Previous studies have shown that core leptosporangiates, the most species-rich group of extant ferns (monilophytes), have a distinct plastid genome (plastome) organization pattern from basal fern lineages. However, the details of genome structure transformation from ancestral ferns to core leptosporangiates remain unclear because of limited plastome data available. Here, we have determined the complete chloroplast genome sequences of Lygodium japonicum (Lygodiaceae), a member of schizaeoid ferns (Schizaeales), and Marsilea crenata (Marsileaceae), a representative of heterosporous ferns (Salviniales). The two species represent the sister and the basal lineages of core leptosporangiates, respectively, for which the plastome sequences are currently unavailable. Comparative genomic analysis of all sequenced fern plastomes reveals that the gene order of L. japonicum plastome occupies an intermediate position between that of basal ferns and core leptosporangiates. The two exons of the fern ndhB gene have a unique pattern of intragenic copy number variances. Specifically, the substitution rate heterogeneity between the two exons is congruent with their copy number changes, confirming the constraint role that inverted repeats may play on the substitution rate of chloroplast gene sequences.