石杉树是一种传统的中草药植物,近年来因其产品HupA可用作乙酰胆碱酯酶抑制剂(AChEI)而受到特别关注。尽管已经研究了H.crispata的叶绿体(cp)基因组,由于先前报道的H.squarrosa已被修订为Phlegmariurussquarrosus,因此没有关于Humperzia线粒体(mt)基因组的报道。使用长读数纳米孔和Illumina测序平台的组合对H.crispata的mt基因组进行测序。整个H.crispatamt基因组被组装成一个长度为412,594bp的圆形,共有91个基因,包括45个tRNA,6个rRNAs,37个蛋白质编码基因(PCGs),还有3个伪基因.值得注意的是,rps8基因存在于squarrosus中,而假基因rps8存在于刺梨中,这是大多数蕨类植物和裸子植物所缺乏的。内含子编码的成熟酶(mat-atp9i85和mat-cobi787)基因存在于沙棘和沙棘中。但是在其他检查过的鱼黄植物中丢失了,蕨类植物,和裸子植物。共线性分析表明,与其他蕨类植物相比,鳞片和四叶草的mt基因组高度保守。相对同义密码子使用(RSCU)分析表明,最常见的氨基酸是苯丙氨酸(Phe)(4.77%),异亮氨酸(Ile)(4.71%),赖氨酸(Lys)(4.26%),而精氨酸(Arg)(0.32%),很少发现组氨酸(His)(0.42%)。简单序列重复(SSR)分析显示,在条状芽孢杆菌的mt基因组中总共鉴定出114个SSR,占整个mt基因组的0.35%。单体重复是SSR的大多数类型,占SSR总数的91.89%。此外,总共有1948次穿插重复(158次向前,147回文,在H.crispatamt基因组中鉴定出长度从30bp到14,945bp的5个反向重复序列),并且30-39bp的重复序列是最丰富的类型。基因转移分析表明,在条件成熟的cp和mt基因组之间共发现了12个同源片段。占总cp和mt基因组的0.93%和2.48%,分别。系统进化树显示,柳树是柳树的姐妹。Ka/Ks分析结果表明,大多数PCG,除了atp6基因,在进化过程中进行纯化选择。我们的研究提供了关于H.crispatamt基因组特征的广泛信息,并将有助于解开进化关系,以及黄质植物中的分子鉴定。
Huperzia crispata is a traditional Chinese herb plant and has attracted special attention in recent years for its products Hup A can serve as an acetylcholinesterase inhibitor (AChEI). Although the chloroplast (cp) genome of H. crispata has been studied, there are no reports regarding the Huperzia mitochondrial (mt) genome since the previously reported H. squarrosa has been revised as Phlegmariurus squarrosus. The mt genome of H. crispata was sequenced using a combination of long-read nanopore and Illumina sequencing platforms. The entire H. crispata mt genome was assembled in a circular with a length of 412,594 bp and a total of 91 genes, including 45 tRNAs, 6 rRNAs, 37 protein-coding genes (PCGs), and 3 pseudogenes. Notably, the rps8 gene was present in P. squarrosus and a pseudogene rps8 was presented in H. crispata, which was lacking in most of Pteridophyta and Gymnospermae. Intron-encoded maturase (mat-atp9i85 and mat-cobi787) genes were present in H. crispata and P. squarrosus, but lost in other examined lycophytes, ferns, and Gymnospermae plants. Collinearity analysis showed that the mt genome of H. crispata and P. squarrossus is highly conservative compared to other ferns. Relative synonymous codon usage (RSCU) analysis showed that the amino acids most frequently found were phenylalanine (Phe) (4.77%), isoleucine (Ile) (4.71%), lysine (Lys) (4.26%), while arginine (Arg) (0.32%), and histidine (His) (0.42%) were rarely found. Simple sequence repeats (SSR) analysis revealed that a total of 114 SSRs were identified in the mt genome of H. crispata and account for 0.35% of the whole mt genome. Monomer repeats were the majority types of SSRs and represent 91.89% of the total SSRs. In addition, a total of 1948 interspersed repeats (158 forward, 147 palindromic, and 5 reverse repeats) with a length ranging from 30 bp to 14,945 bp were identified in the H. crispata mt genome and the 30-39-bp repeats were the most abundant type. Gene transfer analysis indicated that a total of 12 homologous fragments were discovered between the cp and mt genomes of H. crispata, accounting for 0.93% and 2.48% of the total cp and mt genomes, respectively. The phylogenetic trees revealed that H. crispata was the sister of P. squarrosus. The Ka/Ks analysis results suggested that most PCGs, except atp6 gene, were subject to purification selection during evolution. Our study provides extensive information on the features of the H. crispata mt genome and will help unravel evolutionary relationships, and molecular identification within lycophytes.