Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
BMC Genomics. 2023 Nov 10;24(1):677. doi: 10.1186/s12864-023-09770-y.
Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará.
Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNA, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial).
It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.
亚马逊淡水长臂虾分布广泛，是南美的一种淡水虾，正在经历物种形成过程，因此被称为“亚马逊虾复合体”。线粒体细胞色素 c 氧化酶亚基 I（COI）基因已被用于阐明这种物种形成过程，但已记录到异质体和假基因，这使得分离变得困难。从 cDNA（RNA）而不是基因组 DNA 中获取基因是减轻这两种情况的有效工具。本研究的目的是从栖息在帕拉州的亚马逊沿海地区的 M. amazonicum 的转录组中进行计算机组装线粒体 DNA（mtDNA）。
使用从头开始的方法从对虾的转录组中获得了序列。使用来自性腺、肝胰腺和肌肉组织的六个 cDNA 文库。M. amazonicum 的 mtDNA 长 14960bp。它包含 13 个蛋白质编码基因、21 个完整的转移 RNA，以及核糖体 RNA 的 12S 和 16S 亚基。除了位于重链上的 tRNA 外，所有区域都位于轻链上。未回收控制区（D 环），导致 793bp 的缺口。系统发育树显示形成了定义明确的 Macrobrachium 进化枝，在已建立的分支中具有高支持值（91-100）。mtDNA 编码蛋白的三维空间构象表明，它们中的大多数主要由主要的α-螺旋组成，这些螺旋通常存在于插入膜中的蛋白中（线粒体）。
使用 GenBank 中其他基因组的数据，可以在计算机上组装 M. amazonicum 的线粒体基因组的大部分，并通过与 GenBank 中相同区域的动物的 COI 和 16S 基因的相似性来验证它。将 M. amazonicum mtDNA 序列存入 GenBank 可能有助于解决为该物种记录的分类学问题，此外还提供了候选编码基因的完整序列，可用于生态研究中的生物标志物。
