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Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

Clarke TH, Garb JE, Hayashi CY, Arensburger P, Ayoub NA - Genome Biol Evol (2015)

Bottom Line: Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication.We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands.Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Washington & Lee University clarket@wlu.edu.

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Flowchart detailing assembly of multitissue transcriptomes for three species of cobweb weaving spiders. Using RNA collected from multiple tissues (supplementary table S1, Supplementary Material online), cDNA was synthesized, sequenced, and cleaned of low quality and rRNA reads (yellow buttons). Each tissue-specific library was then subject to de novo assembly with Trinity (beige buttons) and these assemblies were combined to create a draft transcriptome (orange buttons). Probable contaminants and chimerics were removed from the draft to obtain the final transcriptomes (purple buttons).
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evv110-F1: Flowchart detailing assembly of multitissue transcriptomes for three species of cobweb weaving spiders. Using RNA collected from multiple tissues (supplementary table S1, Supplementary Material online), cDNA was synthesized, sequenced, and cleaned of low quality and rRNA reads (yellow buttons). Each tissue-specific library was then subject to de novo assembly with Trinity (beige buttons) and these assemblies were combined to create a draft transcriptome (orange buttons). Probable contaminants and chimerics were removed from the draft to obtain the final transcriptomes (purple buttons).

Mentions: Illumina sequence reads were assembled into species-specific transcriptomes using a multistep process (fig. 1). High-quality, nonribosomal RNA reads derived from the same species and tissue were combined and initial transcripts assembled using Trinity with default settings (Grabherr et al. 2011). Trinity produces multiple transcripts (usually interpreted as isoforms) that belong to the same component (interpreted as genes). Only the longest transcript for each component was retained for combination of the tissue-specific assemblies to remove potential isoforms. Tissue-specific assemblies were combined into a single draft transcriptome for each species by comparing the Trinity transcripts using BLAT (Kent 2002), clustering those that matched each other along the boundaries of each transcript by at least 98% identity over the full length of the match (of at least 50 bp). The 98% identity was chosen as the cutoff to allow for mismatches that might arise through sequencing errors. CAP3 was used to generate contiguous sequences (contigs) for each cluster (Huang and Madan 1999). CAP3 did not always combine all the sequences in the cluster. We retained contigs and singletons from each CAP3 assembly for our draft transcriptome.Fig. 1.—


Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

Clarke TH, Garb JE, Hayashi CY, Arensburger P, Ayoub NA - Genome Biol Evol (2015)

Flowchart detailing assembly of multitissue transcriptomes for three species of cobweb weaving spiders. Using RNA collected from multiple tissues (supplementary table S1, Supplementary Material online), cDNA was synthesized, sequenced, and cleaned of low quality and rRNA reads (yellow buttons). Each tissue-specific library was then subject to de novo assembly with Trinity (beige buttons) and these assemblies were combined to create a draft transcriptome (orange buttons). Probable contaminants and chimerics were removed from the draft to obtain the final transcriptomes (purple buttons).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524477&req=5

evv110-F1: Flowchart detailing assembly of multitissue transcriptomes for three species of cobweb weaving spiders. Using RNA collected from multiple tissues (supplementary table S1, Supplementary Material online), cDNA was synthesized, sequenced, and cleaned of low quality and rRNA reads (yellow buttons). Each tissue-specific library was then subject to de novo assembly with Trinity (beige buttons) and these assemblies were combined to create a draft transcriptome (orange buttons). Probable contaminants and chimerics were removed from the draft to obtain the final transcriptomes (purple buttons).
Mentions: Illumina sequence reads were assembled into species-specific transcriptomes using a multistep process (fig. 1). High-quality, nonribosomal RNA reads derived from the same species and tissue were combined and initial transcripts assembled using Trinity with default settings (Grabherr et al. 2011). Trinity produces multiple transcripts (usually interpreted as isoforms) that belong to the same component (interpreted as genes). Only the longest transcript for each component was retained for combination of the tissue-specific assemblies to remove potential isoforms. Tissue-specific assemblies were combined into a single draft transcriptome for each species by comparing the Trinity transcripts using BLAT (Kent 2002), clustering those that matched each other along the boundaries of each transcript by at least 98% identity over the full length of the match (of at least 50 bp). The 98% identity was chosen as the cutoff to allow for mismatches that might arise through sequencing errors. CAP3 was used to generate contiguous sequences (contigs) for each cluster (Huang and Madan 1999). CAP3 did not always combine all the sequences in the cluster. We retained contigs and singletons from each CAP3 assembly for our draft transcriptome.Fig. 1.—

Bottom Line: Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication.We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands.Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Washington & Lee University clarket@wlu.edu.

Show MeSH