The manuscript describes a draft assembly and annotation for S. aethiopicum genome. Authors estimated the repetitive elements content and proposed that two amplifications of LTR-Rs occurred around 1.25 and 3.5 million years ago, resulting in the expansion of resistance genes. Authors carried out also comparative genomics study in the Solanaceae family and inferred phylogenetic studies as well as the domestication history of S. aethiopicum and LD.

Although S. aethiopicum is an orphan species and therefore I do not expect the use of the most advanced technologies for assembly such as PacBio and chromosome scaffolding with HiC, I would have expected at least the anchoring of scaffolds and contigs to pseudomolecules. I think that generating an F2 mapping population for S. aethiopicum is easy to obtain, which could be thus genotyped using any GBS approach authors want. Although a pan genome of the species was also provided, I think that this paper is not suitable for the publication on this journal. Furthermore, the language needs tightening up and editing for English sense.

More detailed comments Abstract: it is reported that the pan-genome of S. aethiopicum contains 1,345 genes are missing in the reference genome. I cannot find this in the main text. Background Line 8-10: I would add some extra reference to this part "It is reported to have medicinal value and its roots and fruits have been used to treat colic, high blood pressure and uterine complications in Africa" or clearly highlighted the information got from FAO. Furthermore, FAO should be added to reference list

Line 24 is (mansfeld.ipk-gatersleben.de). is it a reference for disease resistance? The link send to a database. I would change it with some references from literature.

line 28: please provide at least a reference for this part:"S. aethiopicum is the second most cultivated eggplant, as an "orphan crop"

Line 40 : the sentence on genome editing sound to me a little bit out of place, as no information on genome editing in scarlet aethiopicum is available. I would point out that genome editing might be used for breeding.

Data description: I would modify "with a genome size of 1.17 Gb" with "expected genome size". You would get a more precise estimate using flow-cytometry. Furthermore, authors generated more than 242Gb of data, but after cleaning, about 50% of the data (128GB) were used for assembly, which is a quite high percentage. This presumably may explain the number of scaffolds obtained (more than 162k). Did the authors filter for scaffolds' size? Did the authors try to assembly the genome sequence with other tools, like SOAP? Any comments? Line 33-39. This sentence "Among these annotated TEs, LTR-Rs were extraordinarily abundant and occupied 719 Mbp, accounting for approximately 70% of the genome, followed by LINEs and SINEs (Supplementary Table S4)." is a repetition of what said at the beginning of the paragraph. I will combine the two sentences.

Line 42 Section protein coding. From table S5 gene features are not so similar to other genomes, especially Pepper and Arabidopsis. Furthermore, why pepper has more than 45k genes? The gene number from Kim et al. 2017 is 35,884

Section Amplification of LTR-Rs: * please add references here "The proportion of Ty3/Gypsy and Ty1/Copia LTR-Rs in S. aethiopicum is also comparable to those reported in other Solanaceae genomes." * Line 19: In this part "they occurred separately in each genome since S. aethiopicum and hot pepper had split about 20 MYA (Figure 1A), and about 4 MYA between S. aethiopicum and tomato (Figure 1A)." authors stated that S. aethiopicum separated from tomato 4 million years ago. This sound strange. S.aethiopicum did not separated from tomato 4 MYA, but only the ancestors of tomato/potato and eggplant/scarlet eggplant, which occurred around 16MYA. Furthermore, the second LTR burst occurred 1.25MYA was also shared by eggplant? Polymorphisms in different S. aethiopicum groups section: Concerning the ADMIXTURE analysis and results, I wonder why authors did not define accessions belonging for less than, let's say 70%, to a group as admixed.

Artificially selected genes in S. aethiopicum I would have expected, at least for the 12 genes in common between Gilo and Shum (and maybe for the 36 selected genes in Shum), some more information. What genes are they? Go enrichments are nice but sometimes it would be better to provide some more details, especially if the number of genes involved are limited.

Pan-genome section * Why did the authors get less contigs for Anguivi? The sequencing performance are quite good for the 5 accessions of this species. * I am quite confused on the metrics (Supplementary table S20). In the text, it is reported that 41,626, 22,942 and 17,726 protein-coding genes for "Shum", "Gilo" and "S. anguivi, respectively were predicted, among which accessory gene sets of 29,389, 23,726 and 12,829 for "Shum", "Gilo" and "S. anguivi", respectively were found.

These numbers are not the same in S20 table, presumably two columns were switched. Furthermore in the table S22 for Gilo, a total of 33,194 gene are reported, while in the text the number is 22,942. Accessory genes in the text for Gilo are less than the ones predicted (as reported in the text).

• Table S20, I will add the unit of measurement for length
• I cannot find Supplementary Table S21 and S22

Methods Gene family analysis: References for the 5 proteomes used are missing, as well as the version used

NLR genes: it is not clear to me how the NLR genes were identified. In methods is reported that specific NB-ARC HMM model was constructed, but in the text it is reported that NBS-LRR genes were identified. How did the authors performed the identification of other Motifs (TIR, CC and LRR)?

SNP calling: which parameters did the authors use for SNP identification? Besides MAF and GENO parameters, I would also have considered sequencing depth as a key parameter for the final SNPs set. Population analyses. I would add bootstrap values to the figure 5A Furthermore, is the reference for Itools (80) correct?

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.
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Reviewer #1: The manuscript entitled ""Draft genome sequence of the Solanum aethiopicum provides insight into disease resistance, drought tolerance and evolution"" is a genomic study of Solanum aethiopicum, a close relative of the cultivated eggplant Solanum melongena. Methods are very appropriate to the aims of the study and conclusions are adequately supported by the genomic data.

Could you give more details about the method of: - The high molecular genomic DNA extraction? Response: More details and the cited reference were added. - The selection of high-quality reads? Response: Details have been added.

• The multiplexing? (barcoding?) and the demultiplexing? Response: The delivered reads were already demultiplexed.

• The identification of collinearity blocks (parameters of MCscanX)? Response: Changed to “… gene pairs in MCscanX with default parameters”.

• The RNAseq read filtering and removing of low-quality reads (tools, parameters and threshold)? Response: Details have been added in the text. “SOAPfilter software with the parameters “-M 2, -f 0, -p” was used to filter low quality reads and adapter sequence. Also reads with >=40% low quality bases or with >=10% uncalled bases (“N”) were filtered.”

• The variant calling pipeline? (default parameters in GATK for SNP and SV?) Response: Yes, we used default parameters in GATK pipeline for SNP and SV identified. For quality control, parameters “GENO>0.05, MAF<0.1, HWE test p-value <=0.0001” was used. Detailed parameters have been added.

• The pan-genome reconstruction (parameters and threshold of SOAPdenovo2 and CD-HIT-EST)? Response: We use SOAPdenovo2 and CD-HIT-EST software to construct pan-genome with default parameters.

Minor comments: - Could you describe the eggplant accession used to produce the genome assembly? Response: A brief description had been added.

• You have used a substitution rate of 1.3e-8 year-1site-1 based on works performed on rice genomes. Could you justify this? Response: Generally, the substitution rate varies little among different plants. For example, the substitution rate reported in Arabidopsis is 7 × 10−9 base substitutions per site per generation (Ossowski et al, 2010), which is quite close to that in rice. The use of the rate of rice enables the comparison between our study and another study of hot pepper, in which the same substitution rate was used to infer the ages of LTRs (Kim et al., 2017).

• Could you perform a statistical test to validate the comparison of degeneration of LTR-R activities in different tissues? Response: Unfortunately, statistical test is not allowed without replicates. Instead, we added regression onto the plots.

• An amplification of LTR is found in Solanum aethiopicum and also in Solanum melongena. Could you give us the reference? Response: We searched for LTR in S. melongena genome (Hirakawa et al., 2014) in this study. A same method and criteria were used in both the genomes so that the results are comparable.

• The number of SNP seems huge. Could you compare with others plant genomes? (Yuan Fu) Response: In this study, we had identified 18,614,838 SNPs in total. The number of SNP is highly dependent on the variations between the accessions used in different studies. The differences of genome sizes also contribute to the varied number of SNP in different species. Actually, it is not fair to compare the number of SNPs between different species and populations. Take tomato, whose genome size (828 Mb) is comparable to S. aethiopicum, as an example, a number of 11,620,517 SNPs and 1,303,213 small indels were identified in a population of 360 accessions (Lin et al., 2014). Furthermore, it is not surprise to have such a large number of SNPs in S. aethiopicum because it is a hypervariable species (Lester et al., 1986).

• ""Artificially selected genes"", what does the term artificial mean? Could you explain/develop? Response: It means the genes preferentially retained by human during the history of domestication.

• Numbers of accessory genes seem huge. Could you check if these values are not overestimate due to the presence of fragmented genes? Response: The genome sequences per se varies greatly among different groups (Lester et al., 1986), several groups were previously recognized as different species. Although we cannot completely exclude the possibility of overestimation caused by the presence of fragmented genes, the degree of overestimation is minor because the length of CDS of accessory genes (921 bp) (Supplementary Table 20) is comparable to that of genes (1104 bp) (Supplementary Table 5) in reference.

• ""Good quality transcripts"" "", what does the term good mean? Could you explain/develop? Response: It has been rephrased to “The mapped reads were then assembled using StringTie”

• Could you justify the choice of e-value thresholds for gene annotations and gene clustering (1e-4 seems very weak)? Response: The cutoff of 1e-4 was used for the identification of NLR. It is actually not that weak and had been used in many other studies (Seo et al., 2016 and Kim et al., 2017). Another reason we use this threshold is to make our results comparable to that reported in pepper (Kim et al., 2017), which used a threshold of e-value <=1e-4.

• Could you explain acronyms (GENO, MAF, HWE)? Response: The full names have been added in the manuscript. They are GENO: Maximum per-SNP missing, MAF: Minor allele frequency, HWE: Hardy-Weinberg disequilibrium p-value.

Reviewer #2: This paper reports the first genome assembly of Solanum aethiopicum. The description is easy to follow and the data would be useful for the breeding programs of eggplant. I recommend the authors to submit the data (genome, genes, protein, annotatoin, sequence variations etc) to Sol Genomics Network so that potential users can access them easily. Response: Thanks. That’s a very good suggestion. We will arrange the submission upon the acceptance of the paper.

Minor comments: The term ""the reference genome"" in the main text should be replaced by ""the reference genome sequence"". Response: Replaced. Thanks.

Abstract: LTR-Rs should be spelled out. Response: Replaced by “long terminal repeat retrotransposons (LTR-Rs)”. Thanks. (P2, L12)

Abstract: ""closely"" is ambiguous. Response: It is 150 kb. It had been indicated in the text.

Introduction: ""We also re-sequenced two ..."". Is this 65 (not two) as mentioned in Abstract and other parts? Response: Changed to “two groups”

Data Description: While a total of 242.6 Gb raw reads were obtained, only 127.83 Gb were used for assembly. I assume that approximately 115 Gb reads were low quality. Correct? Response: Yes, the quality of several of the libraries were poor at the beginning of this work, therefore we added more libraries to make sure the final clean data is sufficient.

Data Description: Only 80.4% complete BUSCOs were found in the assembly, whereas the total length of the assembly was 1.02 Gb covering 87% of the estimated genome size (1.17 Gb). Please clarify the reason for the low BUSCOs. (Yuan Fu, please explain this) Response: We won’t deny that this assembly is only a draft and there must be some genes and sequences missed. In order to keep only the most reliable predictions of gene models, we used much more stringent criteria for gene annotation, compared to many other studies on Solanaceae genomes, resulting in a smaller but more accurate gene set. For example, the genome of Solanum melongena has as many as 85,446 genes (Hirakawa et al, 2014). In fact, the scores of BUSCO assessment can be increased by relaxing the criteria for gene annotation. However, this will also include more inaccurate gene models. We had other version of gene sets with higher scores but we finally selected this one hoping to removing false annotations as many as possible.

Increased resistance is facilitated by LTR-Rs amplification: What is the definition of ""LTR-Rs captured""? It is unclear why the ""LTR-Rs captured"" genes enhance disease resistance. NLR? Response: The genes located in LTR-Rs were defined as LTR-Rs captured genes. It is likely that these genes were retroposed by the retrotransposition of LTR-Rs. As these genes are overrepresented by NLRs, we speculate that they are beneficial to disease resistance.

Polymorphisms in different S. aethiopicum groups: What's the difference between indels and SVs? Response: In this study, we follow the criteria described in the users’ guide of GATK pipeline (version 4.0), in which SV is considered to be structural variant, while indel is defined as short variants including small deletion or insertions.

Artificially selected genes in S. aethiopicum: What types of selections do the authors mention here? Response: They are the genes preferentially retained by human during the domestication of this crop.

Potential implications: This part can be deleted because this is not based on the data. Response: removed.

Methods: What are the ""standard BGI protocols""? Response: Changed to “The DNA was sheared into small fragments of ~ 200 bp and used to construct paired-end libraries following standard BGI protocols as described in (Mak et al., 2017) and subsequently sequenced on a BGI-500 sequencer. Briefly, the DNA fragments were ligated to BGISEQ-500 compatible adapters, followed by an index PCR amplification, the products of which were then pooled and circularized for sequencing on BGISEQ-500 (BGI, Shenzhen, China).

SNP calling: ""samtools mpileup"" and ""VariantFiltration"" are duplicated. Response: Corrected.

Reviewer #3: The manuscript describes a draft assembly and annotation for S. aethiopicum genome. Authors estimated the repetitive elements content and proposed that two amplifications of LTR-Rs occurred around 1.25 and 3.5 million years ago, resulting in the expansion of resistance genes. Authors carried out also comparative genomics study in the Solanaceae family and inferred phylogenetic studies as well as the domestication history of S. aethiopicum and LD.

Although S. aethiopicum is an orphan species and therefore I do not expect the use of the most advanced technologies for assembly such as PacBio and chromosome scaffolding with HiC, I would have expected at least the anchoring of scaffolds and contigs to pseudomolecules. I think that generating an F2 mapping population for S. aethiopicum is easy to obtain, which could be thus genotyped using any GBS approach authors want. Response: These are very good suggestions. Unfortunately, we do not have extra budget for this at this moment. Of course, the reference will be further improved and updated once these data are available.

Although a pan genome of the species was also provided, I think that this paper is not suitable for the publication on this journal. Furthermore, the language needs tightening up and editing for English sense. Response: The language has been polished.

More detailed comments Abstract: it is reported that the pan-genome of S. aethiopicum contains 1,345 genes are missing in the reference genome. I cannot find this in the main text. Response: The figures in this part have been corrected. Now it has been changed to “A pan-genome of S. aethiopicum with a total of 51,351 protein-coding genes was assembled, of which 24,567 genes are missing in the reference genome sequence.” It has also been added in the text.

Background Line 8-10: I would add some extra reference to this part ""It is reported to have medicinal value and its roots and fruits have been used to treat colic, high blood pressure and uterine complications in Africa"" or clearly highlighted the information got from FAO. Furthermore, FAO should be added to reference list Response: The publication of these orphan crops is very few, we could only find this information on the website of FAO (http://www.fao.org/traditional-crops/africangardenegg/en/?amp%3Butm_medium=social%20media&%3Butm_campaign=unfaopinterest), which had already been added to reference list.

Line 24 is (mansfeld.ipk-gatersleben.de). is it a reference for disease resistance? The link send to a database. I would change it with some references from literature. Response: The full address is http://mansfeld.ipk-gatersleben.de/apex/f?p=185:46:448783208481::NO::module,mf_use,source,akzanz,rehm,akzname,taxid:mf,,botnam,0,,Solanum%20aethiopicum%20Aculeatum%20Group,5898, which is too long and only the website of home page was shown. Now, we changed it to “Aculeatum is used as ornamentals (Prohens et al., 2012; Plazas et al., 2014) or rootstocks (mansfeld.ipk-gatersleben.de) due to its excellent disease resistance nature (Toppino et al., 2008)”

line 28: please provide at least a reference for this part:""S. aethiopicum is the second most cultivated eggplant, as an ""orphan crop"" Response: This statement has been changed to “Although S. aethiopicum is one of the most important cultivated eggplants in Africa, it remains an “orphan crop” because research and breeding investments are substantially lagging behind in comparison with other Solanaceae relatives such as tomato, potato and eggplant.”

Line 40 : the sentence on genome editing sound to me a little bit out of place, as no information on genome editing in scarlet aethiopicum is available. I would point out that genome editing might be used for breeding. Response: We noticed that there is no report of genome editing in S. aethiopicum so far. This is because very few efforts have been paid to it. However, we believe that these techniques, just like many other advanced techniques, can eventually be applied into this species to speed the progress of breeding. When these platforms are ready, the sequence of genome would be very essential for the identification of genes to be edited, as well as for the design of guide RNAs. This strategy had been proved to be very efficient in a report on Physalis pruinose, another orphan crop also in Solanaceae (Lemmon et al., 2018. Nat. Plants), before which there is not available genome editing example either.

Data description: I would modify ""with a genome size of 1.17 Gb"" with ""expected genome size"". You would get a more precise estimate using flow-cytometry. Response: Changed.

Furthermore, authors generated more than 242Gb of data, but after cleaning, about 50% of the data (128GB) were used for assembly, which is a quite high percentage. This presumably may explain the number of scaffolds obtained (more than 162k). Did the authors filter for scaffolds' size? Did the authors try to assembly the genome sequence with other tools, like SOAP? Any comments? Response: Yes, the quality of several of the libraries were poor, therefore we added more libraries to make sure the final clean data is sufficient. We also had tried to assembly the genome using other tools including SOAPdenovo and selected the best assembly for downstream analyses. The assembler automatically filtered out the scaffolds smaller than 100 bp, and all the resulted scaffolds were retained.

Line 33-39. This sentence ""Among these annotated TEs, LTR-Rs were extraordinarily abundant and occupied 719 Mbp, accounting for approximately 70% of the genome, followed by LINEs and SINEs (Supplementary Table S4)."" is a repetition of what said at the beginning of the paragraph. I will combine the two sentences. Response: We have deleted this sentence. Thanks.

Line 42 Section protein coding. From table S5 gene features are not so similar to other genomes, especially Pepper and Arabidopsis. Furthermore, why pepper has more than 45k genes? The gene number from Kim et al. 2017 is 35,884 Response: Arabidopsis is relatively distant to S. aethiopicum. As for the data of Pepper, the data in this table was collected from NCBI (version GCA_000710875.1), which has a total of 45,131 protein-coding genes. The data now has been replaced by Kim’s data (Kim et al, 2017).

Section Amplification of LTR-Rs: * please add references here ""The proportion of Ty3/Gypsy and Ty1/Copia LTR-Rs in S. aethiopicum is also comparable to those reported in other Solanaceae genomes."" Response: The references were added. The sentence was rephrased to “The proportion of Ty3/Gypsy in S. aethiopicum is also comparable to what is reported in the hot pepper genome (87.7% of Ty3/Gypsy in hot pepper)”.

• Line 19: In this part ""they occurred separately in each genome since S. aethiopicum and hot pepper had split about 20 MYA (Figure 1A), and about 4 MYA between S. aethiopicum and tomato (Figure 1A)."" authors stated that S. aethiopicum separated from tomato 4 million years ago. This sound strange. S.aethiopicum did not separated from tomato 4 MYA, but only the ancestors of tomato/potato and eggplant/scarlet eggplant, which occurred around 16MYA. Response: Changed to “they occurred separately in each genome since the ancestor of S. aethiopicum had diverged from that of hot pepper and tomato about 20 MYA and 4 MYA, respectively”.

Furthermore, the second LTR burst occurred 1.25MYA was also shared by eggplant? Response: No, but eggplant has a burst more recently, about 0.5 MYA (Figure 2A)

Polymorphisms in different S. aethiopicum groups section: Concerning the ADMIXTURE analysis and results, I wonder why authors did not define accessions belonging for less than, let's say 70%, to a group as admixed. Response: The accessions were clustered using ADMIXTURE following the methods previously described in (Mathieson et al. 2017; Olalde et al., 2017; Mittnik et al., 2017), and we did not see an example in which accessions were grouped as suggested.

Artificially selected genes in S. aethiopicum I would have expected, at least for the 12 genes in common between Gilo and Shum (and maybe for the 36 selected genes in Shum), some more information. What genes are they? Response: The functional descriptions have been listed in a new table, Supplementary Table 18.

Go enrichments are nice but sometimes it would be better to provide some more details, especially if the number of genes involved are limited. Response: Added

Pan-genome section * Why did the authors get less contigs for Anguivi? The sequencing performance are quite good for the 5 accessions of this species. Response: The contigs were assembled separately for each individual, Anguivi had fewer contigs only because the number of Anguivi accessions used in this study is small (5 for Anguivi, and 24 for Gilo and 36 for Shum)

• I am quite confused on the metrics (Supplementary table S20). In the text, it is reported that 41,626, 22,942 and 17,726 protein-coding genes for ""Shum"", ""Gilo"" and ""S. anguivi, respectively were predicted, among which accessory gene sets of 29,389, 23,726 and 12,829 for ""Shum"", ""Gilo"" and ""S. anguivi"", respectively were found. These numbers are not the same in S20 table, presumably two columns were switched. Furthermore in the table S22 for Gilo, a total of 33,194 gene are reported, while in the text the number is 22,942. Accessory genes in the text for Gilo are less than the ones predicted (as reported in the text).

• Table S20, I will add the unit of measurement for length

• I cannot find Supplementary Table S21 and S22 Response: The two columns were switched in Supplementary table 21 (previous supplementary table 20) and we forgot to add supplementary table 22 and 23. We have corrected the errors and add the unit of measurement for length.

Methods Gene family analysis: References for the 5 proteomes used are missing, as well as the version used

Response: The references and version of the data have been added.

NLR genes: it is not clear to me how the NLR genes were identified. In methods is reported that specific NB-ARC HMM model was constructed, but in the text it is reported that NBS-LRR genes were identified. How did the authors performed the identification of other Motifs (TIR, CC and LRR)? Response: The “NBS-LRR gene” in the text was supposed to be “NB-containing genes”. We counted the number of “NB-containing genes” because, even without LRR motif, NB-containing genes can also function in plant immunity (Nandety et al., 2013).

SNP calling: which parameters did the authors use for SNP identification? Besides MAF and GENO parameters, I would also have considered sequencing depth as a key parameter for the final SNPs set. Response: Yes, sequencing depth is critical. Actually, the depth had been considered, and it is not a problem because the sequencing depth for each accession is averagely higher than 60 X in our work.

Population analyses. I would add bootstrap values to the figure 5A Response: As the branches in the figure are too short, we added the phylogenetic tree with bootstrap in supplementary figure 4.

Furthermore, is the reference for Itools (80) correct? Response: The software itools used in our research has been changed to a new name, called ReSeqTools. We have changed it to the correct software name in our article.

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published.
I agree to the open peer review policy of the journal.