Melon Microsynteny

The sequence of the melon region around the nsv locus reveals high microsynteny with model plant species

The work

1. Summary
   1. Melon BAC (92kb - 13 genes - 2 TEs )- analysed with Arabidopsis, Medicago and Populus
   2. Melon close to Arabidopsis then to Populus then to Medicago (30%)
2. Introduction
   1. The approach. Model system->annotated genes->Find the synteny region->Make use of it
   2. eg: nsv locus that confers resistance to the melon necrotic spot virus was identified this way in 2006.
   3. So these guys did 92kb BAC sequencing and compared
3. Materials and Methods
   1. BAC clone->encompassing nsv locus->shotgun sub cloning sequencing->1152 clones->768 sequenced (5fold coverage)+54 clones further sequenced to resolve the gaps
   2. BAC seq -> TBlastX -> ab initio gene prediction programes
   3. Putative protein analysis (TBlastN, BlastP), compared the predicted protein with the melon database for ESTs
   4. Melon protein -> TBlastN -> Arabidopsis -> Syntenic regions were defined as contiguous regions containing two or more homologous genes in A. thaliana and C. melo, irrespective of the orientation and exact order of the genes.
   5. C. melo and M. truncatula -> TBlastN
   6. melo and P. trichocarpa -> BlastP of Blast2
   7. Synteny quality -> %
4. Results
   1. TPS gene:
   2. catalytic domain - supported by mediacago EST
   3. Unknown function -> close to Arabidopsis
   4. exonuclease -> close to Arabidopsis
   5. nsv gene -> gene prediction supported by 2 full length EST ->close to Arabidopsis -> 5 exons
   6. 15d_03-C10 -> supported by melon EST, but a noval gene
   7. Src homology-3 (SH3) domain:
   8. transposase:
   9. AWPM19 like protein: membrane proteins - 4 exons
   10. Repetitive sequences:
   11. SSRs
   12. Palindromic sequences
   13. sysnteny melo<->populus:
5. Discussion

Review

Ideas

1. Table in graphical view
2. Need for gene density calculations??? Though justified, it is beyond the scope of this article
3. The reason to search for synteny of melon with chromosome1 and 2?? It should be 4 and 13

Review of MGG-07-00024
(*) Summary of the Review
	1. Is the content appropriate for MGG?		Yes
	2. Are the findings original?			No
	3. Do the findings represent a significant 
	   contribution that is likely to be cited 
	   by others in the field?			Yes
	4. Do the experimental findings justify the
	   conclusions drawn?				Yes
	5. Is the previous work adequately referenced?	Yes
	6. Are the Figures and Tables		
	  (a) sufficient to illustrate the data?	Yes
	  (b) excessive in number or in content?	No
	7. Is the text clear, readable and succinct?	Yes

(*) The paper as a whole:
	[ ] Outstanding
	[*] Above average
	[ ] Average
	[ ] Below average

(*) Recommendation:
	[ ] Accept 
	[*] Revise 
	[ ] Reject

(*) Comments to the Editor: The paper may be accepted following the recommended changes as described in the comments to author section.

(*) Comments to the Author: The paper analyses micro-synteny of Melon (Cucumis melo L.) with Arabidopsis thaliana, Medicago truncatula and Populus trichocarpa using 92kb of BAC, 1-21-10 sequences encompassing nsv locus that confers resistance to the melon necrotic spot virus (MNSV). The study covers an interesting topic for researchers interested in gene structure of Melon MNSV locus and its relative position in Eurosid I clade with reference to Medicago and Populus, besides description of 13 genes with detailed annotation. The paper also describes two novel genes, 15d_03_C10 and 15d_01_G03 that could be potentially exploited.

In the discussion, authors discuss in length about the estimation and comparison of gene density in Melon with other genomes in the study. However the gene estimates were based on one 92kb stretch of BAC 1-21-10 sequences, which may not represent the true gene density in the whole genome. Therefore it is not worthwhile to compare the gene densities of fully sequenced genome Arabidopsis and Populus. In addition, the the gene density estimates were based on one BAC as described in the materials, but mentioned as 3 BACs in the discussion. There is no information on the remaining 2 BACs that were included in the analysis.

in the discussion of one per 7.7kb estimates was based only on one BAC sequences,