PDF(Pubmed)
Abstract：
BACKGROUND: Floating bamboo (Hygroryza aristata) is an endangered species with a narrow native distribution and is renowned for its unique aesthetic qualities, which holds significant ecological and ornamental value. However, the lack of genetic information research, with only one complete plastome available, significantly hampers conservation efforts and further research for this species.
RESULTS: In this research, we sequenced and assembled the organelle genomes of floating bamboo, including the mitogenome (587,847 bp) and plastome (135,675 bp). The mitogenome can recombine into various configurations, which are mediated by 25 repeat pairs (13 SRs, 6 MRs, 1 LR, and 5 CRs). LR1 and SR5 are particularly notable as they have the ability to combine with other contigs, forming complex repeat units that facilitate further homologous recombination. The rate of homologous recombination varies significantly among species, yet there is still a pronounced positive correlation observed between the length of these repeat pairs and the rate of recombination they mediate. The mitogenome integrates seven intact protein-coding genes from the chloroplast. The codon usage patterns in both organelles are similar, with a noticeable bias towards C and T on the third codon. The gene map of Poales shows the entire loss of rpl6, succinate dehydrogenase subunits (sdh3 and sdh4). Additionally, the BOP clade retained more variable genes compared to the PACMAD clade.
CONCLUSIONS: We provided a high-quality and well-annotated mitogenome for floating bamboo and demonstrated the presence of diverse configurations. Our study has revealed the correlation between repeat length and their corresponding recombination rate despite variations among species. Although the mitogenome can potentially exist in the form of a unicircular in vivo, this occurrence is rare and may not be stable.
RESULTS: In this research, we sequenced and assembled the organelle genomes of floating bamboo, including the mitogenome (587,847 bp) and plastome (135,675 bp). The mitogenome can recombine into various configurations, which are mediated by 25 repeat pairs (13 SRs, 6 MRs, 1 LR, and 5 CRs). LR1 and SR5 are particularly notable as they have the ability to combine with other contigs, forming complex repeat units that facilitate further homologous recombination. The rate of homologous recombination varies significantly among species, yet there is still a pronounced positive correlation observed between the length of these repeat pairs and the rate of recombination they mediate. The mitogenome integrates seven intact protein-coding genes from the chloroplast. The codon usage patterns in both organelles are similar, with a noticeable bias towards C and T on the third codon. The gene map of Poales shows the entire loss of rpl6, succinate dehydrogenase subunits (sdh3 and sdh4). Additionally, the BOP clade retained more variable genes compared to the PACMAD clade.
CONCLUSIONS: We provided a high-quality and well-annotated mitogenome for floating bamboo and demonstrated the presence of diverse configurations. Our study has revealed the correlation between repeat length and their corresponding recombination rate despite variations among species. Although the mitogenome can potentially exist in the form of a unicircular in vivo, this occurrence is rare and may not be stable.
摘要：
背景：浮竹（Hygroryzaaristata）是一种濒危物种，其本地分布狭窄，以其独特的美学品质而闻名，具有重要的生态和观赏价值。然而,缺乏遗传信息研究，只有一个完整的塑性体，大大阻碍了该物种的保护工作和进一步研究。
结果：在这项研究中，我们对漂浮竹子的细胞器基因组进行了测序和组装，包括有丝分裂基因组(587,847bp)和质体(135,675bp)。有丝分裂体可以重组成各种构型，由25个重复对介导(13个SR，6MR,1LR,和5个CR)。LR1和SR5特别值得注意，因为它们能够与其他重叠群结合，形成促进进一步同源重组的复杂重复单元。物种之间的同源重组率差异很大，然而，在这些重复序列对的长度和它们介导的重组率之间仍然存在明显的正相关。有丝分裂基因组整合了来自叶绿体的七个完整的蛋白质编码基因。两个细胞器中的密码子使用模式相似，在第三个密码子上明显偏向C和T。Poales的基因图谱显示rpl6，琥珀酸脱氢酶亚基（sdh3和sdh4）的全部丢失。此外,与PACMAD进化枝相比，BOP进化枝保留了更多的可变基因。
结论：我们为漂浮竹子提供了高质量且注释良好的有丝分裂细胞，并证明了存在多种构型。尽管物种之间存在差异，但我们的研究揭示了重复长度与其相应重组率之间的相关性。尽管有丝分裂基因组可能以体内单核的形式存在，这种情况很少见，可能不稳定。
结果：在这项研究中，我们对漂浮竹子的细胞器基因组进行了测序和组装，包括有丝分裂基因组(587,847bp)和质体(135,675bp)。有丝分裂体可以重组成各种构型，由25个重复对介导(13个SR，6MR,1LR,和5个CR)。LR1和SR5特别值得注意，因为它们能够与其他重叠群结合，形成促进进一步同源重组的复杂重复单元。物种之间的同源重组率差异很大，然而，在这些重复序列对的长度和它们介导的重组率之间仍然存在明显的正相关。有丝分裂基因组整合了来自叶绿体的七个完整的蛋白质编码基因。两个细胞器中的密码子使用模式相似，在第三个密码子上明显偏向C和T。Poales的基因图谱显示rpl6，琥珀酸脱氢酶亚基（sdh3和sdh4）的全部丢失。此外,与PACMAD进化枝相比，BOP进化枝保留了更多的可变基因。
结论：我们为漂浮竹子提供了高质量且注释良好的有丝分裂细胞，并证明了存在多种构型。尽管物种之间存在差异，但我们的研究揭示了重复长度与其相应重组率之间的相关性。尽管有丝分裂基因组可能以体内单核的形式存在，这种情况很少见，可能不稳定。
