<b>Genetic and functional traits limit the success of colonisation by arbuscular mycorrhizal fungi in a tomato wild relative</b>

This folder contains relevant datasets generated in the study:Chialva, M., Stelluti, S., Novero, M., Masson, S., Bonfante, P. &amp; Lanfranco, L. (2024) Genetic and functional traits limit the success of colonisation by arbuscular mycorrhizal fungi in a tomato wild relative. <i>Plant, Cell &amp; </i><i>Environment </i>47 (11), 4275-4292. https://doi.org/10.1111/pce.15007<b><i>RNA-seq dataset and </i></b><b><i>Orthogroups inference</i></b>SLY_raw_counts.tsv &gt; raw mRNA-seq reads counts obtained by pseudo-aligning reads of the 'M82' cultivar roots on the <i>Solanum lycopersicum</i> reference transcriptome (SL3.0, ITAG3.2) using Salmon software and summarised using 'tximport' library in R.SPE_raw_counts.tsv &gt; Raw mRNA-seq reads counts obtained by pseudo-aligning <i>Solanum pennellii</i> LA5240 reads from roots on the reference transcriptome (Spenn_v2.0) using Salmon software and summarised using 'tximport' library in R.SLY_vst_counts.tsv &gt; vst-normalised mRNA-seq counts for <i>S. lycopersicum</i> 'M82' obtained by filtering low-expressed transcripts and by removing unwanted variation using RUV-seq R package (RUVg normalization, k=2).SPE_vst_counts.tsv &gt; vst-normalised mRNA-seq counts obtained by filtering low-expressed transcripts and by removing unwanted variation using RUV-seq R package (RUVg normalization, k=2).SL3.00_pennellii_orthologs_all.tsv &gt; Orthogroups predicted by Orthofinder (v.2.2.7) on <i>S. pennellii</i> (Spenn_v2.0) and <i>S. lycopersicum </i>(SL3.0, ITAG3.2) proteomesSL3.00_pennellii_orthologs_pairs.tsv &gt; Single-copy orthogroup predicted by Orthofinder (v.2.2.7) on <i>S. pennellii</i> and <i>S. lycopersicum</i> proteomes<br><br><br>

本文件夹包含本研究生成的相关数据集：Chialva, M.、Stelluti, S.、Novero, M.、Masson, S.、Bonfante, P. 与 Lanfranco, L.（2024）《遗传与功能性状限制丛枝菌根真菌（arbuscular mycorrhizal fungi）在番茄野生近缘种中的定殖成功率》，发表于*Plant, Cell & Environment* 47卷第11期，页码4275-4292，DOI: 10.1111/pce.15007。

***RNA测序（RNA-seq）数据集与直系同源组（Orthogroups）推断***：
SLY_raw_counts.tsv > 为通过Salmon软件将‘M82’栽培种根系的测序读段（reads）与番茄（*Solanum lycopersicum*）参考转录组（SL3.0，ITAG3.2）进行伪比对后得到的原始mRNA测序（mRNA-seq）读段计数，并通过R语言的‘tximport’库汇总所得。
SPE_raw_counts.tsv > 为通过Salmon软件将潘那利番茄（*Solanum pennellii*）LA5240的根系测序读段与参考转录组（Spenn_v2.0）进行伪比对后得到的原始mRNA测序读段计数，并通过R语言的‘tximport’库汇总所得。
SLY_vst_counts.tsv > 为番茄‘M82’的vst标准化mRNA测序读段计数，通过过滤低表达转录本，并使用RUV-seq R包去除无关变异（RUVg标准化，k=2）得到。
SPE_vst_counts.tsv > 为潘那利番茄的vst标准化mRNA测序读段计数，通过过滤低表达转录本，并使用RUV-seq R包去除无关变异（RUVg标准化，k=2）得到。
SL3.00_pennellii_orthologs_all.tsv > 为通过Orthofinder（v.2.2.7）对潘那利番茄（Spenn_v2.0）与番茄（SL3.0，ITAG3.2）的蛋白质组进行预测得到的直系同源组。
SL3.00_pennellii_orthologs_pairs.tsv > 为通过Orthofinder（v.2.2.7）对潘那利番茄与番茄蛋白质组进行预测得到的单拷贝直系同源组。

搜集汇总

背景与挑战

背景概述

该数据集包含与番茄野生近缘种Solanum pennellii中丛枝菌根真菌定植限制因素研究相关的RNA-seq数据和直系同源群组推断。具体包括番茄栽培品种'M82'和S. pennellii的原始及归一化mRNA-seq读数计数文件，以及通过Orthofinder预测的直系同源群组文件，用于分析基因表达和进化关系。数据集支持植物基因组学、转录组学和可持续农业发展等领域的研究。