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An analysis of genetic changes during the divergence of Drosophila species.

Sousa-Neves R, Rosas A - PLoS ONE (2010)

Bottom Line: We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster.Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America. rui.sousaneves@case.edu

ABSTRACT

Background: It has been long appreciated that speciation involves changes in body plans and establishes genetic, reproductive, developmental and behavioral incompatibilities between populations. However, little is still known about the genetic components involved in these changes or the sequence and scale of events that lead to the differentiation of species.

Principal findings: In this paper, we investigated the genetic changes in three closely related species of Drosophila by making pair-wise comparisons of their genomes. We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster. Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.

Conclusions: Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

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Overview of the data collection and sorting.A) Exons of coding sequence were extracted from the annotated genome of D. melanogaster using Extractor and electronically joined using Analyst to obtain complete coding sequences. These coding sequences were then automatically blasted against the genome of D. melanogaster, D. simulans and D. sechellia with Megablast. Analyst scanned the resulting alignments for the best hits and assembled the coding sequences in the three species from them. B) Analyst also calculated the coverage, the percentage not covered, the divergence in sim-sec, sim-mel, sec-mel as well as the control mel-mel and organized this data in a table. C) To minimize artifacts due to incomplete clone representation in the genomic libraries, the coding sequences were filtered and only genes with the same coverage in D. simulans and D. sechellia retrieved. To avoid genes truncated by Megablast (i.e. usually genes with small exons), only genes with a mismatch up to 1% in the control mel-mel were retrieved. After these two filters were applied, a new table like the one exemplified in C) was generated for each chromosome.
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pone-0010485-g001: Overview of the data collection and sorting.A) Exons of coding sequence were extracted from the annotated genome of D. melanogaster using Extractor and electronically joined using Analyst to obtain complete coding sequences. These coding sequences were then automatically blasted against the genome of D. melanogaster, D. simulans and D. sechellia with Megablast. Analyst scanned the resulting alignments for the best hits and assembled the coding sequences in the three species from them. B) Analyst also calculated the coverage, the percentage not covered, the divergence in sim-sec, sim-mel, sec-mel as well as the control mel-mel and organized this data in a table. C) To minimize artifacts due to incomplete clone representation in the genomic libraries, the coding sequences were filtered and only genes with the same coverage in D. simulans and D. sechellia retrieved. To avoid genes truncated by Megablast (i.e. usually genes with small exons), only genes with a mismatch up to 1% in the control mel-mel were retrieved. After these two filters were applied, a new table like the one exemplified in C) was generated for each chromosome.

Mentions: To begin addressing this issue, we extracted and compared the annotated coding sequences of D. melanogaster to the sequence of computationally predicted coding sequences of D. simulans and D. sechellia (Fig. 1A). A total of 13,740 predicted coding sequences were assembled from D. simulans and D. sechellia genomes: 2,226 on the X chromosome, 5,355 on the second chromosome, 6,074 on the third chromosome and 85 on the fourth chromosome.


An analysis of genetic changes during the divergence of Drosophila species.

Sousa-Neves R, Rosas A - PLoS ONE (2010)

Overview of the data collection and sorting.A) Exons of coding sequence were extracted from the annotated genome of D. melanogaster using Extractor and electronically joined using Analyst to obtain complete coding sequences. These coding sequences were then automatically blasted against the genome of D. melanogaster, D. simulans and D. sechellia with Megablast. Analyst scanned the resulting alignments for the best hits and assembled the coding sequences in the three species from them. B) Analyst also calculated the coverage, the percentage not covered, the divergence in sim-sec, sim-mel, sec-mel as well as the control mel-mel and organized this data in a table. C) To minimize artifacts due to incomplete clone representation in the genomic libraries, the coding sequences were filtered and only genes with the same coverage in D. simulans and D. sechellia retrieved. To avoid genes truncated by Megablast (i.e. usually genes with small exons), only genes with a mismatch up to 1% in the control mel-mel were retrieved. After these two filters were applied, a new table like the one exemplified in C) was generated for each chromosome.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2864749&req=5

pone-0010485-g001: Overview of the data collection and sorting.A) Exons of coding sequence were extracted from the annotated genome of D. melanogaster using Extractor and electronically joined using Analyst to obtain complete coding sequences. These coding sequences were then automatically blasted against the genome of D. melanogaster, D. simulans and D. sechellia with Megablast. Analyst scanned the resulting alignments for the best hits and assembled the coding sequences in the three species from them. B) Analyst also calculated the coverage, the percentage not covered, the divergence in sim-sec, sim-mel, sec-mel as well as the control mel-mel and organized this data in a table. C) To minimize artifacts due to incomplete clone representation in the genomic libraries, the coding sequences were filtered and only genes with the same coverage in D. simulans and D. sechellia retrieved. To avoid genes truncated by Megablast (i.e. usually genes with small exons), only genes with a mismatch up to 1% in the control mel-mel were retrieved. After these two filters were applied, a new table like the one exemplified in C) was generated for each chromosome.
Mentions: To begin addressing this issue, we extracted and compared the annotated coding sequences of D. melanogaster to the sequence of computationally predicted coding sequences of D. simulans and D. sechellia (Fig. 1A). A total of 13,740 predicted coding sequences were assembled from D. simulans and D. sechellia genomes: 2,226 on the X chromosome, 5,355 on the second chromosome, 6,074 on the third chromosome and 85 on the fourth chromosome.

Bottom Line: We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster.Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America. rui.sousaneves@case.edu

ABSTRACT

Background: It has been long appreciated that speciation involves changes in body plans and establishes genetic, reproductive, developmental and behavioral incompatibilities between populations. However, little is still known about the genetic components involved in these changes or the sequence and scale of events that lead to the differentiation of species.

Principal findings: In this paper, we investigated the genetic changes in three closely related species of Drosophila by making pair-wise comparisons of their genomes. We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster. Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.

Conclusions: Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

Show MeSH