what are the main files that I should prepare when submitting my paper to journals?

After writing my paper and making submissions to journals I found that they need files that I do not know like graphical abstracts, and highlights. so, what files should I prepare before submitting the paper? 
Agriculture Aquatic toxicology Cell biology Ecotoxicology Pathology
- (Concise) cover letter stating all authors confirm submission and material not considered elsewhere at this moment.
- Ethical statement, if appropriate.

- Usually as one file (but submission systems may ask for sections):
--- Concise and very informative (= elaborated) abstract to allow the reader fast decision on scope and findings.
--- Main body of the manuscript text
--- Reference list
--- Tables and Figures
--- Supplementary material

Specialities, submission systems differ on the extras they want or offer to be submitted
- fixed sections in the abstract
- highlights
- grafical abstract
- video explanation
- cover grafics
- etc. etc.
You have to check the submission guidelines (sorry, no standard advice possible)
Practical lesson learnt:
Submit the standards package.
You will be asked by the Editorial office to add if any of the "specials" is mandatory in the first round of peer-review. Anything else will be asked/oferred once your submission made it through to acceptance.
I'm surprised there are specific responses to your question because each journal has specific requirements that must be followed or risk rejection upon initial submission. Some of the requirements are rather unusual for a certain journal, therefore you must craft your submission in a unique manner compliant with a certain journal. Good luck.  
1. Precise cover letter to the editor highlighting the significant outcome of the manuscript.
2. Title page: Title of the manuscript, authors list, and corresponding author contact details.
3. Abstract: Precise information about the findings, their importance, and a way forward message. 
4. Introduction about the topic.
5. Materials & Methods: Detailed information about the tools and techniques employed in the study.
6. Results: Detailed outcome of the research work with Figures and Tables.
7. Discussion: This section covers a comparative analysis of the findings with the existing studies and future prospects.
8. References: Literature citations
9. Figure legends & Figures
10. Tables
1- Manuscript File (title, authors, abstract, introduction, methodology, results, discussion, conclusion, declarations, references). In some journals, you need a title page (title, authors and affiliation) and a blind manuscript (with no author information).
2- Cover Letter
3- Suggested Reviewers
4- Supplementary material (when applicable)
5- Graphical abstract (when applicable)
7-Higlights (when applicable)

In summary, talways read INSTRUCTION TO AUTHORS because it changes from journal to journal.

Muhammad Tayyab
This can vary depending on the type of peer review used. An anonymized version of your article is required for double-blind peer review.

To submit your article, you will need the following files:

Your manuscript (including a title page with names of all authors and co-authors)
A main document file containing an abstract, keywords, main text, and references.
Figure files
Table files
Any additional files, such as supplemental materials or biographical notes
on top of all the items mentioned by the others above, you might need to provide the alignment file of gene sequences for some journals.
First, visit the websites of some standard journals *in your discipline*.  Each discipline and journal specify different requirements.
Some of them might even provide templates for different *types* of articles.  Decide on which type of article you want to submit to which journal.  Now, even if you don't intend to submit to that specific journal, the template is a useful guide to prepare your manuscript.  Note that most journals also permit online supplementary information for large amounts of data.
Other than that, you should always have handy an abstract and a cover letter (and an outline, particularly if you are proposing a review).  Beyond that, all bets are off.
The basic files are:

The manuscript
Supplementary files

Other additional files depends on the journal you are submitting to:

Cover letter
Graphical abstract
Audio files
Twitter statement
Cover letter
Manuscript file
Graphical abstract
Supplementary files

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