Investigating Host and Parasitic Plant Interaction by Tissue-Specific Gene Analyses on Tomato and Cuscuta campestris Interface at Three Haustorial Developmental Stages.

Parasitic weeds cause billions of dollars in agricultural losses each year worldwide. Cuscuta campestris (C. campestris), one of the most widespread and destructive parasitic plants in the United States, severely reduces yield in tomato plants. Reducing the spread of parasitic weeds requires understanding the interaction between parasites and hosts. Several studies have identified factors needed for parasitic plant germination and haustorium induction, and genes involved in host defense responses. However, knowledge of the mechanisms underlying the interactions between host and parasitic plants, specifically at the interface between the two organisms, is relatively limited. A detailed investigation of the crosstalk between the host and parasite at the tissue-specific level would enable development of effective parasite control strategies. To focus on the haustorial interface, we used laser-capture microdissection (LCM) with RNA-seq on early, intermediate and mature haustorial stages. In addition, the tomato host tissue that immediately surround the haustoria was collected to obtain tissue- resolution RNA-Seq profiles for C. campestris and tomato at the parasitism interface. After conducting RNA-Seq analysis and constructing gene coexpression networks (GCNs), we identified CcHB7, CcPMEI, and CcERF1 as putative key regulators involved in C. campestris haustorium organogenesis, and three potential regulators, SlPR1, SlCuRe1-like, and SlNLR, in tomatoes that are involved in perceiving signals from the parasite. We used host-induced gene silencing (HIGS) transgenic tomatoes to knock-down the candidate genes in C. campestris and produced CRISPR transgenic tomatoes to knock out candidate genes in tomatoes. The interactions of C. campestris with these transgenic lines were tested and compared with that in wild-type tomatoes. The results of this study reveal the tissue-resolution gene regulatory mechanisms at the parasitic plant-host interface and provide the potential of developing a parasite-resistant system in tomatoes

Eleven strategies for making reproducible research and open science training the norm at research institutions

Across disciplines, researchers increasingly recognize that open science and reproducible research practices may accelerate scientific progress by allowing others to reuse research outputs and by promoting rigorous research that is more likely to yield trustworthy results. While initiatives, training programs, and funder policies encourage researchers to adopt reproducible research and open science practices, these practices are uncommon inmanyfields. Researchers need training to integrate these practicesinto their daily work. We organized a virtual brainstorming event, in collaboration with the German Reproducibility Network, to discuss strategies for making reproducible research and open science training the norm at research institutions. Here, weoutline eleven strategies, concentrated in three areas:(1)offering training, (2)adapting research assessment criteria and program requirements, and (3) building communities. We provide a brief overview of each strategy, offer tips for implementation,and provide links to resources. Our goal is toencourage members of the research community to think creatively about the many ways they can contribute and collaborate to build communities,and make reproducible research and open sciencetraining the norm. Researchers may act in their roles as scientists, supervisors, mentors, instructors, and members of curriculum, hiring or evaluation committees. Institutionalleadership and research administration andsupport staff can accelerate progress by implementing change across their institution

Eleven strategies for making reproducible research and open science training the norm at research institutions

Across disciplines, researchers increasingly recognize that open science and reproducible research practices may accelerate scientific progress by allowing others to reuse research outputs and by promoting rigorous research that is more likely to yield trustworthy results. While initiatives, training programs, and funder policies encourage researchers to adopt reproducible research and open science practices, these practices are uncommon inmanyfields. Researchers need training to integrate these practicesinto their daily work. We organized a virtual brainstorming event, in collaboration with the German Reproducibility Network, to discuss strategies for making reproducible research and open science training the norm at research institutions. Here, weoutline eleven strategies, concentrated in three areas:(1)offering training, (2)adapting research assessment criteria and program requirements, and (3) building communities. We provide a brief overview of each strategy, offer tips for implementation,and provide links to resources. Our goal is toencourage members of the research community to think creatively about the many ways they can contribute and collaborate to build communities,and make reproducible research and open sciencetraining the norm. Researchers may act in their roles as scientists, supervisors, mentors, instructors, and members of curriculum, hiring or evaluation committees. Institutionalleadership and research administration andsupport staff can accelerate progress by implementing change across their institution

The Major Qualitative Characteristics of Olive (Olea europaea L.) Cultivated in Southwest China

Olive trees, originated from Mediterranean, have been cultivated in China for decades and show great adaption to local environment. However, research on this topic is limited. In this study, the major qualitative characteristics and changes of olive grown in southwest China were investigated. The results showed that oil accumulated during fruit development and reached its maximum value when fruit had fully ripened. Phenolic and flavonoid contents increase rapidly in the early growth stage (0–90 DAFB) and then begin to decrease as fruit ripens. Compared with olive from the Mediterranean, olive from China has special characteristics: higher moisture content in the fruit combined with lower percentages of unsaturated fatty acids and oil content. This is due to southwest China's climate which is wetter and cooler compared to the Mediterranean. Our study suggests that southwest China's higher annual rainfall might contribute to higher fruit moisture content while its low temperatures would be conducive to higher unsaturated fatty acid levels in the fruit

S_DGE.FQ1.tar.gz

Compressed file containing Tomato SAM RNA-seq reads from BrAd-seq DGE libraries (S_DGE_A5.fastq, S_DGE_A6.fastq, S_DGE_B7.fastq, S_DGE_C7.fastq

L_DGE.FQ1.tar.gz

Compressed file containing Tomato leaf RNA-seq reads from BrAd-seq DGE libraries (L_DGE_B5.fastq, L_DGE_C6.fastq, L_DGE_D7.fastq

SHO.FQ.tar.gz

Compressed file containing Tomato RNA-seq reads from BrAD-seq shotgun (SHO) type strand-specific libraries (SHO_22.fastq, SHO_23.fastq, SHO_24.fastq)

S_HTR.FQ.tar.gz

Compressed file containing Tomato SAM RNA-seq reads from HTR-method libraries (S_HTR_A5.fastq, S_HTR_A6.fastq, S_HTR_B6.fastq, S_HTR_B7.fastq

S_DGE.FQ2.tar.gz

Compressed file containing Tomato SAM RNA-seq reads from BrAd-seq DGE libraries (S_DGE_D8.fastq, S_DGE_E1.fastq, S_DGE_F2.fastq