BACKGROUND Mitochondrial (mt) gene arrangement is highly variable among molluscs and especially among bivalves. Of the 30 complete molluscan mt-genomes published to date, only one is of a heterodont bivalve, although this is the most diverse taxon in terms of species numbers. We determined the complete sequence of the mitochondrial genomes of Acanthocardia tuberculata and Hiatella arctica, (Mollusca, Bivalvia, Heterodonta) and describe their gene contents and genome organisations to assess the variability of these features among the Bivalvia and their value for phylogenetic inference. RESULTS The size of the mt-genome in Acanthocardia tuberculata is 16.104 basepairs (bp), and in Hiatella arctica 18.244 bp. The Acanthocardia mt-genome contains 12 of the typical protein coding genes, lacking the Atpase subunit 8 (atp8) gene, as all published marine bivalves. In contrast, a complete atp8 gene is present in Hiatella arctica. In addition, we found a putative truncated atp8 gene when re-annotating the mt-genome of Venerupis philippinarum. Both mt-genomes reported here encode all genes on the same strand and have an additional trnM. In Acanthocardia several large non-coding regions are present. One of these contains 3.5 nearly identical copies of a 167 bp motive. In Hiatella, the 3' end of the NADH dehydrogenase subunit (nad)6 gene is duplicated together with the adjacent non-coding region. The gene arrangement of Hiatella is markedly different from all other known molluscan mt-genomes, that of Acanthocardia shows few identities with the Venerupis philippinarum. Phylogenetic analyses on amino acid and nucleotide levels robustly support the Heterodonta and the sister group relationship of Acanthocardia and Venerupis. Monophyletic Bivalvia are resolved only by a Bayesian inference of the nucleotide data set. In all other analyses the two unionid species, being to only ones with genes located on both strands, do not group with the remaining bivalves. CONCLUSION The two mt-genomes reported here add to and underline the high variability of gene order and presence of duplications in bivalve and molluscan taxa. Some genomic traits like the loss of the atp8 gene or the encoding of all genes on the same strand are homoplastic among the Bivalvia. These characters, gene order, and the nucleotide sequence data show considerable potential of resolving phylogenetic patterns at lower taxonomic levels.

中文翻译：

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异齿双壳类动物棘皮动物Acanthocardia tuberculata和Hiatella arctica的线粒体基因组的完整序列和基因组织-以及海洋双壳类动物中推定的Atpase亚基8基因的第一个记录。

背景线粒体（mt）基因的排列在软体动物之间，尤其是在双壳类动物之间是高度可变的。迄今为止，已发表的30个完整的软体动物mt基因组中，只有一个属于异齿双壳类，尽管就物种数量而言这是最多样化的分类群。我们确定了结核棘皮动物和北极Hiatella arctica（软体动物，Bivalvia，Heterodonta）的线粒体基因组的完整序列，并描述了它们的基因含量和基因组组织，以评估Bivalvia中这些特征的变异性及其在系统发育推断中的价值。结果：结核棘皮草mt基因组的大小为16.104个碱基对（bp），而Hiatella arctica中为18.244bp。Acanthocardia mt基因组包含12种典型的蛋白质编码基因，缺少Atpase亚基8（atp8）基因，就像所有出版的海洋双壳类动物一样 相反，完整的atp8基因存在于Hiatella arctica中。此外，当我们重新注释菲律宾金星鱼的mt基因组时，我们发现了一个推定的atp8基因被截断。此处报道的两个mt基因组均在同一链上编码所有基因，并具有一个额外的trnM。在Acanthocardia中，存在几个较大的非编码区域。其中一个包含3.5个几乎相同的167 bp动机副本。在Hiatella中，NADH脱氢酶亚基（nad）6基因的3'末端与相邻的非编码区一起复制。Hiatella的基因排列与所有其他已知的软体动物mt基因组明显不同，Acanthocardia的基因排列与菲律宾Venerupis几乎没有同一性。氨基酸和核苷酸水平的系统发育分析有力地支持了杂齿齿畸形和棘心病与Venerupis的姐妹群关系。仅通过对核苷酸数据集的贝叶斯推断就可以解决单亲双壳纲。在所有其他分析中，只有两个基因都位于两条链上的两个类，才没有与剩下的双壳类一起分组。结论本文报道的两个mt基因组增加并强调了双壳类和软体动物类群中基因顺序的高度可变性以及重复的存在。一些基因组特征，例如atp8基因的缺失或同一链上所有基因的编码，在双壳纲动物中是同型的。这些特征，基因顺序和核苷酸序列数据显示出在较低分类学水平上解决系统发育模式的巨大潜力。