First de novo draft genome sequence of Oryza coarctata , the only halophytic species in the genus Oryza [version 2; peer review: 3 approved]

Oryza coarctata plant, collected from Sundarban delta of West Bengal, India, has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 % and deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417


Amendments from Version 1
In this revision, we have addressed all the issues raised by the referee. In additions, we have made few grammatical corrections. We revised the manuscript as a result of reanalysis of the data. We have also improved clarity in the Methods regarding assembly of the genome. Further, as per the suggestions of the referee as well as requirement, we incorporated 6 more references.

Introduction
Soil salinity is a major abiotic stress of rice cultivation globally (Molla et al., 2015), and rice cultivation areas under soil salinity stress are increasing gradually. Genetic potential for salt tolerance of rice that exists among the natural population has been largely exploited, and alternative useful alleles may further enhance salinity tolerance. Wild species are a potential source of many useful genes and QTLs that may not be present in the primary gene pool of the domesticated species.
Oryza coarctata, known as Asian wild rice, grows naturally in the coastal region of South-East Asian countries. It flowers and set seeds under as high as 40 E.Ce dS m -1 saline soil (Bal & Dutt, 1986). It is the only species in the genus Oryza that is halophyte in nature. However, with the exception of one transcriptomic (Garg et al., 2014) and one miRNA (Mondal et al., 2015) experiment, no large scale generation of any other genomic resource is available for this important species, although several pinitol biosynthesis pathway genes have been cloned to study the functional genomics (Sengupta & Majumder, 2009).

Methods
The plant was collected from its native place, Sundarban delta of West Bengal, India (21°.36'N and 88°.15' E) and established at our institute Net house through clonal propagation. To determine the genome size, 20 mg of young leaf tissue from Net house grown plants was chopped into small pieces and stained with RNase containing propidium iodide (50 μg/ml) (BD Science, India) as per the protocol of Dolezel et al. It has been calculated that data contain very small amount of non-ATGC character. Further, we also found that the 19.89% of the assembled genome is repetitive in nature. We also identified approximately 5512 different non-coding RNAs and around 230,968 SSRs. Gene ontology analysis identified several salt responsive genes.

Data availability
Raw sequence data are available at NCBI SRA under the BioProject ID: PRJNA396417.

Competing interests
No competing interests were disclosed.

Grant information
The author(s) declared that no grants were involved in supporting this work.
Open Peer Review data.
The genome sequencing methods seems good enough but authors have discussed very little about the annotation of the genome data. I can understand that there is word limit under Data Note in F1000Research, but still by looking at the discussion, I think analysis portion is weak point in this paper. Authors should provide a comparative note on the genome of Oryza sativa and Oryza coarctata. How this species is tolerating such a high saline conditions, which kind of genes/osmoregulators are involved in this adaptation should be discussed along with comparison to O. sativa. How many different genes were predicted should be mentioned. Authors found approximately 1605 non-coding RNAs? I am not sure, what are trying to tell here, this number should be high as per my opinion.
There are some minor mistakes like; in the affiliation the word "Delhi" is not required. The word, "Primary" should be inserted in the first paragraph last line of Introduction. So the correct sentence will be "...in the primary gene pool...". © 2017 Das S. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Sandip Das
Department of Botany, University of Delhi, Delhi, India The authors report a draft genome sequence of a halophyte Oryza species collected from Sunderbans, and provides a glimpse into the adaptive strategies employed by Oryza against salinity stress. Undoubtedly, it will be an useful resource for future functional characterization, comparative genomic studies, and developing salinity tolerance in rice. I understand that the present format is only for reporting, and look forward to reading the full manuscript with all the analysis. There are small language edits that that authors need to incorporate.
Comments: Please add a reference or sufficient information for general readers as to how genome types of rice (for instance, KKLL in case of O. coarctata) was assigned. expertise to confirm that it is of an acceptable scientific standard.
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