Bony fish 12S rRNA sequencing data from coastal water samples in gulf of Maine

Ecosystems in coastal waters of Gulf of Maine (GOM) are undergoing environmental challenges in response to climate change and anthropogenic stressors.  eDNA metabarcoding, a powerful tool for assessing fish community structure, was used to identify fish communities in three types of GOM aquatic environments (sand, macroalgae, and eelgrass) in Maine and New Hampshire, USA. The available 12S rRNA fish universal primer analysis system was modified using nested PCR (MiFish and 12S-V5) to improve targeting of fish products and reduce to non-target products.  The nested PCR strategy allowed successful amplification of 12S rRNA genes in fishes without production of non-target products and identified 28 fish groups at the genus level. Presence/Absence data and Relative Abundance showed significant differences among locales but not among habitats.  Myoxocephalus sp. were found at all sampling sites.  Relative Abundance data revealed that Menidia menidia and Brevoortia sp. wer..., Water samples were collected from 3 habitat types (sand, ellgrass, and macroalgae) in four different GOM locations: New Castle (NC) in New Hampshire, Fort Foster (FF), Kennebunk Port (KB), and Goosefare (GF) in Maine.  Three-liter samples were collected ~1 meter above the seafloor, either manually by divers carrying Niskin bottles (3´1L), or by using a Van Dorn sampler and filling 3 Niskin bottles aboard the sampling vessel.  All 36 samples were collected between June and October in 2022.  Total DNA was extracted using the DNeasy PowerSoil Pro™ kit (Qiagen) after fitration. Nested PCR based on 12S rRNA was performed to amplify fish DNA. Three PCR replicates were conducted for each DNA sample and then pooled for sequencing analysis after confirmation of no contamination in both negative controls.  Final amplicons were purified with AMPure XP SPRI™ reagent  to remove remnant primers and dNTPs. The purified amplicons were indexed by barcode and sequenced on the Ill..., , # Bony fish 12S rRNA sequencing data from coastal water samples in gulf of Maine

[https://doi.org/10.5061/dryad.47d7wm3q6](https://doi.org/10.5061/dryad.47d7wm3q6)

## Description of the data and file structure

**Sequence_data.zip**

This folder includes paired-end raw sequencing data generated by NovaSeq6000 for 36 samples. 

**mdat.v3.tsv**

This is metadata file of 36 sample water samples collected for this study.

**V4-gs.csv**

This is the sequence abundance file that used for R-analysis.
### Files and variables

#### File: mdat.v3.tsv

**Description:** 

##### Variables

* sampleid:  sample name
* Site: Four locales that samples were collected: New Castle (NC), Fort Foster (FF), Kennebunk Port (BK), Goosefare (GF)
* Habitat: Three habitats that samples were collected: Sand (S), eelgrass (Eg): macroalgae (Ma)
* Replicate: number of sample replicates
* Date Collected : Date that Sample collected
* year: All samples were collected in 2002
* month: month that samples were collec...,

缅因湾（Gulf of Maine, GOM）近岸水域生态系统正面临气候变化与人为胁迫带来的环境挑战。环境DNA宏条形码（eDNA metabarcoding）作为评估鱼类群落结构的有力工具，被用于鉴定美国缅因州与新罕布什尔州境内三类缅因湾水生环境（沙质生境、大型藻类生境与鳗草生境）中的鱼类群落。研究对已有的12S rRNA鱼类通用引物分析体系进行优化，采用嵌套式聚合酶链式反应（nested PCR，MiFish与12S-V5）以提升鱼类靶序列扩增效率，减少非靶序列产物。该嵌套PCR策略可成功扩增鱼类12S rRNA基因且无额外非靶产物生成，最终在属水平上鉴定出28个鱼类类群。存在/缺失数据与相对丰度数据显示，鱼类群落在不同采样地点间存在显著差异，但在不同生境间无显著差异。所有采样点均检测到绵鲉属（Myoxocephalus sp.）物种。相对丰度分析显示，美洲银汉鱼（Menidia menidia）与短体沙丁鱼属（Brevoortia sp.）……

本研究在缅因湾的4个采样地点收集了3类生境的水样：新罕布什尔州的纽卡斯尔（NC）、缅因州的福特·福斯特（FF）、肯纳邦克港（KB）与古斯费尔（GF）。水样采集于距海底约1米处，采集方式包括潜水员携带尼斯金采水器（Niskin bottles）手动采集3份1升样本，或使用范多恩采水器（Van Dorn sampler）在采样船上分装至3个尼斯金采水器中。所有36份样本均于2022年6月至10月间采集。过滤后使用DNeasy PowerSoil Pro™试剂盒（Qiagen）提取总DNA。基于12S rRNA的嵌套PCR用于扩增鱼类DNA，每份DNA样本设置3次PCR重复，在确认阴性对照无污染后，将重复产物混合用于测序分析。最终扩增产物使用AMPure XP SPRI™试剂纯化，以去除残留引物与脱氧核苷三磷酸（dNTPs）。纯化后的扩增产物通过条形码进行索引，随后在Illumina测序平台上完成测序……

# 缅因湾近岸水样硬骨鱼12S rRNA测序数据
https://doi.org/10.5061/dryad.47d7wm3q6

## 数据与文件结构
**Sequence_data.zip**
该文件夹包含由NovaSeq6000测序平台生成的36份样本的双端原始测序数据。

**mdat.v3.tsv**
本研究收集的36份水样的元数据文件。

**V4-gs.csv**
用于R语言分析的序列丰度文件。

### 文件与变量
#### 文件：mdat.v3.tsv
**描述：**
##### 变量
* sampleid：样本名称
* Site：样本采集的4个地点：纽卡斯尔（NC）、福特·福斯特（FF）、肯纳邦克港（BK）、古斯费尔（GF）
* Habitat：样本采集的3类生境：沙质生境（S）、鳗草生境（Eg）、大型藻类生境（Ma）
* Replicate：样本重复次数
* Date Collected：样本采集日期
* year：所有样本均采集于2002年
* month：样本采集月份……