Accelerating moss identification through the development of specific DNA barcodes based on the whole chloroplast genome

Mosses represent the most species-diverse clade of bryophytes and are among the earliest land plants. These diminutive organisms possess considerable ecological significance and diverse applications. However, their study, development, and utilization are impeded by the complex identification process and scarcity of researchers specializing in moss taxonomy. The advancement of DNA barcoding technology presents an opportunity for precise moss identification. While several chloroplast DNA barcodes have been proposed for mosses, these molecular markers primarily originate from angiosperm research and may not be optimal for moss species. This study aims to identify suitable DNA barcodes for mosses at the chloroplast genome level. Utilizing 61 complete chloroplast genome datasets of mosses, this research presented the first construction of a reliable phylogenetic tree at the family level of mosses using whole chloroplast genomes, enabling accurate identification of most samples. Based on nucleotide polymorphism in the complete chloroplast genome, 12 highly variable regions were selected as candidate DNA barcodes for mosses. Experimental validation of newly designed primer universality demonstrated high universality (>90%) for the primers developed in this study. The resolution verification experiment, employing DNA barcodes from 103 samples representing 21 families and 48 genera, confirmed the efficacy of atpB-rbcL, psaI-accD, ycf2, ycf1, matK, rpoB-trnC, and clpP as reliable DNA barcodes for mosses. The study also revealed inconsistencies in the chloroplast genome structures of mosses submitted to public databases, which hinder subsequent research. Consequently, we recommend that researchers upload data with a designated reference genome (such as Bryum argenteum) in future submissions.

藓类（mosses）是苔藓植物（bryophytes）中物种多样性最高的演化支，同时也是最早登陆的陆生植物类群之一。这类体型微小的生物兼具重要的生态学价值与多样化的应用场景。然而，其研究、开发与利用却因鉴定流程复杂、苔藓分类学（taxonomy）专业研究者稀缺而受到阻碍。DNA条形码（DNA barcoding）技术的发展为精准的藓类物种鉴定提供了契机。尽管已有多项研究提出适用于藓类的叶绿体DNA条形码，但这类分子标记大多源自被子植物（angiosperm）研究，未必是藓类物种的最优选择。本研究旨在从叶绿体基因组（chloroplast genome）层面筛选适用于藓类的DNA条形码。本研究利用61组藓类完整叶绿体基因组数据集，首次基于全叶绿体基因组构建了可信度较高的藓类科级系统发育树（phylogenetic tree），可实现多数样本的精准鉴定。基于完整叶绿体基因组的核苷酸多态性，本研究筛选出12个高变区域作为藓类候选DNA条形码。对新设计引物开展的通用性实验验证结果显示，本研究开发的引物具备极高的通用性（>90%）。本研究利用涵盖21科、48属的103份样本的DNA条形码开展分辨率验证实验，证实atpB-rbcL、psaI-accD、ycf2、ycf1、matK、rpoB-trnC及clpP可作为藓类可靠的DNA条形码。本研究同时发现，提交至公共数据库的藓类叶绿体基因组结构存在不一致性，这会对后续研究造成阻碍。因此，我们建议研究者在未来提交数据时，指定参考基因组（例如银叶真藓Bryum argenteum）以完成数据上传。

搜集汇总

背景与挑战

背景概述

该数据集旨在解决苔藓植物鉴定复杂的问题，通过开发基于叶绿体基因组的特定DNA条形码，提高了鉴定的准确性和效率。研究不仅构建了苔藓科水平的系统发育树，还验证了多个DNA条形码的实用性，为苔藓植物的研究和应用提供了重要工具。