维管植物质体DNA数据在物种和区域上的空缺研究  

A Comprehensive Evaluation of the Plastid DNA Data Gaps of Vascular Plants in Species and Geographic Area

作　　者：邓言 鲁丽敏 张强[4] 陈之端[2,3] 胡海花 Yan Deng;Limin Lu;Qiang Zhang;Zhiduan Chen;Haihua Hu(College of Life Sciences,Guangxi Normal University,Guilin 541006,China;Key Laboratory of Systematic and Evolutionary Botany,State Key Laboratory of Plant Diversity and Specialty Crops,Institute of Botany,Chinese Academy of Sciences,Beijing 100093,China;China National Botanical Garden,Beijing 100093,China;Guangxi Key Laboratory of Plant Con-servation and Restoration Ecology in Karst Terrain,Guangxi Institute of Botany,Chinese Academy of Sciences,Guilin 541006,China)

机构地区：[1]广西师范大学生命科学学院,桂林541006 [2]中国科学院植物研究所,植物多样性与特色经济作物全国重点实验室,系统与进化植物学重点实验室,北京100093 [3]国家植物园,北京100093 [4]广西壮族自治区中国科学院广西植物研究所,广西喀斯特植物保育与恢复生态学重点实验室,桂林541006

出　　处：《植物学报》2025年第1期1-16,共16页Chinese Bulletin of Botany

基　　金：国家自然科学基金(No.32200190,No.32122009)。

摘　　要：在植物大数据时代,测序数据成为众多生物学研究的重要基础,了解测序数据的现状有利于更好地利用这些数据。质体DNA数据因易获取、单亲遗传及变异速率适中而被广泛应用。基于GenBank公共数据库全面评估和分析了全世界维管植物质体DNA数据取样情况,结果表明,仅有33.75%的维管植物种类已测序。已测序物种在不同类群间取样不均衡,缺失率大致与类群多样性呈显著正相关,其中缺失最严重的目和科分别是盔被花目(Paracryphiales)、胡椒目(Piperales)和五桠果目(Dilleniales),以及霉草科(Triuridaceae)、五膜草科(Pentaphragmataceae)和黄眼草科(Xyridaceae)。在地理空间上,维管植物数据缺失程度从赤道向两极递减,且生物多样性高的地区缺失更严重,包括多个生物多样性热点地区。此外,各地区特有种的数据普遍缺失严重。基于上述结果,建议针对分子数据缺失程度较高的类群和生物多样性高的地区进行重点采集和测序,尤其注重对特有种补充取样,以增加这些类群遗传数据的代表性。INTRODUCTION:Molecular data is one of the most important bases for many biological studies,including phylogeny,ecology,and biogeography etc.Incomplete sampling may lead to biased results and inadequate conclusions.However,few studies have evaluated current state of sampling density for sequencing DNA data comprehensively.Plastid DNA sequences have been applied in scientific studies of plants extensively due to their easy accessibility,uniparental inhe-ritance,and moderate rate of mutation.Therefore,it is essential to investigate the current state of sampling density for sequencing plastid DNA data in species and geographic area for researchers to better utilize it.RATIONALE:The GenBank is the biggest and most commonly used database of sequencing DNA data.The data gap of plastid DNA in species and geographic area for vascular plants was investigated based on the GenBank database in this study.Firstly,the plastid DNA data of vascular plant species were downloaded from the GenBank database and cleaned.Secondly,species names were standardized according to the World Checklist of Vascular Plants(WCVP)database.Thirdly,to evaluate the current state of sampling density for plastid DNA data of vascular plants,we counted the number of species with plastid DNA sequenced and the proportion of missing data of lineages representing orders and families.We also mapped the proportion of missing data in each region to evaluate the current state of sampling density of plastid DNA data geographically.To further investigate the potential influencing factors of the plastid DNA data gap,Spearman’s cor-relations between the proportion of missing data and species diversity among major groups of vascular plants or regions were calculated.RESULTS:Only 33.75%vascular plant species have at least one record of DNA in GenBank,covering 139005 vascular plant species(angiosperms:131220 species,gymnosperms:1154 species,and pteridophytes:6631 species).For data gap in species,sequenced species were unevenly sampled among lineages,with the proportio

关 键 词：质体DNA 维管植物 数据缺失 植物大数据 GENBANK 

分 类 号：Q943.2[生物学—植物学]