COI Leray fragment of adult and juvenile spiders
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Biodiversity loss is a major problem at the global scale, so bioinventories and monitoring samplings are essential to identify and tackle threats to biodiversity. Arthropods are usually misrepresented in these inventories, despite being the largest component of animal diversity. This is mainly due to the difficulty of identification in some arthropod groups, such as spiders, which can only be morphologically identified to species level at adult stages. Thus, juvenile spiders are usually discarded during sorting despite representing around half of the specimens, but the impact this has on community-level diversity estimates is still unknown. Here, we use a metabarcoding approach to assess the contribution that juvenile stages of spiders collected across the Iberian Peninsula have on diversity estimates, and their effect on diversity patterns across communities. We also compare the proportion of reads and the abundance of each family in the samples to assess the quantitative power of meta..., For adult spiders: Legs of spiders were used for DNA extraction (more information about the specimens in Crespo et al, 2018). Total genomic DNA was extracted using the REDExtract-N-Amp⢠Tissue PCR Kit Protocol from Sigma-Aldrich, following the manufacturerâs protocol and performed in 96 well-plates. We amplified the mitochondrial cytochrome c oxidase (COI). The LCOI1490/ HCO2198 was the preferred combination of primers, while Nancy was used as a replacement for HCOI2198 and Ron as replacement for LCOI1490 (in that order). For problematic amplifications, we used the internal primers mlCOIintF/jgHCOI2198. The polymerase chain reaction (PCR) was performed in 96-well plates using 8 µl REDExtract-N-Amp⢠PCR ReadyMix from Sigma-Aldrich, primers forward and reverse, 4 µl of diluted DNA and ultrapure, distilled water up to a total reaction volume of 20 µl. PCR products were cycle-sequenced in both directions at Macrogen Inc. (Seoul, South Korea). We trimmed the sequences to keep only the Leray ..., , # COI Leray fragment of adult and juvenile spiders [https://doi.org/10.5061/dryad.z08kprrcv](https://doi.org/10.5061/dryad.z08kprrcv) The dataset includes two fasta files, \"Adults.fasta\" and \"Juveniles.fasta\". The file \"Adults.fasta\" contains all the Cytochrome c Oxidase 1 (COI) sequences obtained from adult specimens, which were obtained by Sanger sequencing a variable number of legs. The \"Juveniles.fasta\" file contains all COI sequences obtained from metabarcoding analyses applied to bulk samples of juvenile specimens. All the reads obtained were clustered into MOTU's, which were taxonomically assigned to the deepest possible level. ## Description of the data and file structure Both files are in fasta format. The headers of the Adults.fasta file include the individual code of the specimen (MD-); the number of reads that were artificially included in the analyses of each sequence (count=50000); the taxonomy identifier (taxid) of each species in NCBI; the order name and associated n...
生物多样性丧失是全球性重大问题，因此生物清查与监测采样是识别并应对生物多样性威胁的必要手段。节肢动物尽管是动物多样性中占比最大的类群，但在这类清查中往往代表性不足。这主要源于部分节肢动物类群的鉴定难度较高，例如蜘蛛，仅能通过形态学特征在成虫阶段鉴定至物种水平。因此，尽管幼蛛约占标本总量的一半，但在分拣过程中通常会被丢弃，而其对群落水平多样性评估的影响仍不明朗。 本研究采用元条形码（metabarcoding）方法，评估伊比利亚半岛采集的蜘蛛幼体对多样性评估的贡献，及其对跨群落多样性格局的影响。同时，我们还比对了样本中各科的读段比例与丰度，以评估元... 对于成蛛： 使用蜘蛛的腿部进行DNA提取（标本的更多信息参见Crespo等，2018）。总基因组DNA提取采用Sigma-Aldrich的REDExtract-N-Amp™组织PCR试剂盒方案，严格遵循制造商的操作流程，在96孔板中完成实验。我们扩增了线粒体细胞色素c氧化酶I（COI）基因。首选引物组合为LCO1490/HCO2198，若无法成功扩增，则以Nancy替代HCOI2198、Ron替代LCOI1490（按此顺序）。对于扩增存在问题的样本，我们使用内部引物mlCOIintF/jgHCOI2198。聚合酶链式反应（PCR）在96孔板中进行，反应体系包含8μL Sigma-Aldrich的REDExtract-N-Amp™ PCR ReadyMix、上下游引物、4μL稀释后的DNA，以及超纯水补足至总体积20μL。PCR产物在韩国首尔的Macrogen Inc.公司进行双向循环测序。我们对序列进行修剪，仅保留Leray ... # 成蛛与幼蛛的COI Leray片段 [https://doi.org/10.5061/dryad.z08kprrcv](https://doi.org/10.5061/dryad.z08kprrcv) 本数据集包含两个FASTA文件，分别为"Adults.fasta"与"Juveniles.fasta"。其中"Adults.fasta"包含所有从成蛛标本获得的细胞色素c氧化酶I（COI）序列，这些序列通过对不同数量的腿部组织进行桑格测序（Sanger sequencing）得到。"Juveniles.fasta"文件则包含所有通过对幼蛛标本混合样本进行元条形码分析获得的COI序列。所有获得的读段均被聚类为分子操作分类单元（MOTU, Molecular Operational Taxonomic Unit），并被分类注释至尽可能深的分类层级。 ## 数据与文件结构说明 两个文件均采用FASTA格式。"Adults.fasta"文件的序列头包含标本的个体编码（以MD-开头）、每条序列在分析中人工引入的读段数量（count=50000）、各物种在NCBI的分类学标识符（taxid）、目级分类单元名称及相关n...
