Peer Review #1 of "Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) (v0.2)"

Abstract The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analysed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analysing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesised that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

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THE GENETIC ANALYSIS OF A RECIPROCAL TRANSLOCATION, eT1(III; V), IN CAENORHABDITIS ELEGANS

Genetics ◽

10.1093/genetics/99.3-4.415 ◽

1981 ◽

Vol 99 (3-4) ◽

pp. 415-428

Author(s):

Raja E Rosenbluth ◽

David L Baillie

Keyword(s):

Caenorhabditis Elegans ◽

Genetic Analysis ◽

Gene Order ◽

Reciprocal Translocation ◽

New Order ◽

Linkage Groups ◽

Recombination Rates ◽

Left Half ◽

New Gene ◽

The Right

ABSTRACT The Caenorhabditis elegans mutation e873, which results in a recessive uncoordinated phenotype (formerly named Unc-72) and which had been isolated after 32P t reatment (BRENNER1 974), has now been found to act as a crossover suppressor and to be associated with a translocation between linkage groups (LG's) IIIand V. The translocation has been named, eTl(ZI1; V); eT1acts as a dominant crossover suppressor for both the right half of LGIIIand the left half of LGV,providing a balancer for a total of 39 map units. The uncoordinated e873phenotype has been shown to be a consequence of Eminactive unr- 36111gene. It was possible to demonstrate that, in translocation heterozygotes, eT1chromosomes marked with either sma-3or dpy-11segregate from normal LGIII,while those marked with bli-5, sm-2or unc-42segregate from normal LGV.Since bli-5and sma-2are normally on LGIII,and dpy-11is normally on LGV,it is concluded that: (a) eT1is a reciprocal translocation; (b) there is a breakpoint between sma-3and sma-2in LGIII(the region containing unc- 36)and one between dpy-11and unc-42in LGV;(c) thera is no dominant centromere between sma-2and bli-5on LGIII,since in eT1these genes are not linked to a LGIIIcentromere. Similarly, it is highly unlikely that there is a centromere to the left of dpy-11on LGV.The new gene order in eT1was determined by measuring recombination rates between markers in eT1homozygotes. It is concluded that the new order is: dpy-1 sma-3 (break) dpy-11 unc-60,and bli-5 sma-2 (break) unc-42 unc-51.——Thisis the first analysis of a C. eleganstranslocation with respect to reciprocity, breakpoints and new gene order.

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