Teixeira Daniel Fonseca, Hilário Heron Oliveira, Santos Gilmar Bastos, Carvalho Daniel Cardoso
Post-Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte Brazil.
Post-Graduate Program in Genetics Federal University of Minas Gerais Belo Horizonte Brazil.
Ecol Evol. 2023 Oct 20;13(10):e10649. doi: 10.1002/ece3.10649. eCollection 2023 Oct.
The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost-effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp - NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%-87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker-dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR-dependent protocols.
浮游鱼类的研究对于理解鱼类群落的繁殖动态至关重要。DNA宏条形码技术已作为一种快速、经济高效且准确的分类工具得到应用，它能够同时鉴定多个个体。然而，使用DNA宏条形码技术仍存在重大挑战，例如根据分类分辨率和待测序片段长度选择分子标记、引物偏差、参考数据库不完整以及定性推断不一致等问题。在此，利用DNA宏条形码技术对从一条新热带河流采集的30个浮游鱼类样本池进行分子水平鉴定，以比较三种分子标记的分辨率、灵敏度、特异性和相对读数丰度（RRA）恢复情况：标准COI片段（650 pb，两端分别进行分析）和两个短的12S rRNA基因标记（约200 bp - NeoFish和MiFish标记）。三种标记的联合使用使属的检测率提高了25% - 87.5%，从而增加了分类覆盖范围，并能对复杂的新热带浮游鱼类群落进行可靠的分类鉴定。RRA依赖于标记，这表明在使用基于PCR的方案根据DNA宏条形码数据推断物种丰度时仍需谨慎。
