Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

Figure S1. Histograms of sequence coverage depth of each contig. (a) Contig coverage distribution in the initial assembly. The peak at lower coverage (near 26.5x) indicates redundant contigs caused by the heterozygotic nature of the Pinctada fucata genome. The red line shows the fitted normal distri...

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Bibliographic Details
Main Authors: Takeuchi, Takeshi, Koyanagi, Ryo, Fuki Gyoja, Kanda, Miyuki, Hisata, Kanako, Fujie, Manabu, Goto, Hiroki, Yamasaki, Shinichi, Kiyohito Nagai, Morino, Yoshiaki, Miyamoto, Hiroshi, Endo, Kazuyoshi, Endo, Hirotoshi, Nagasawa, Hiromichi, Shigeharu Kinoshita, Asakawa, Shuichi, Shugo Watabe, Satoh, Noriyuki, Kawashima, Takeshi
Format: Report
Language:unknown
Published: Figshare 2016
Subjects:
Microbiology
FOS Biological sciences
Genetics
Molecular Biology
Ecology
69999 Biological Sciences not elsewhere classified
110309 Infectious Diseases
FOS Health sciences
Plant Biology
Computational Biology
Crassostrea gigas
Online Access:https://dx.doi.org/10.6084/m9.figshare.c.3610172_d3
https://springernature.figshare.com/articles/journal_contribution/Additional_file_2_of_Bivalve-specific_gene_expansion_in_the_pearl_oyster_genome_implications_of_adaptation_to_a_sessile_lifestyle/4359890
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Summary:Figure S1. Histograms of sequence coverage depth of each contig. (a) Contig coverage distribution in the initial assembly. The peak at lower coverage (near 26.5x) indicates redundant contigs caused by the heterozygotic nature of the Pinctada fucata genome. The red line shows the fitted normal distribution, where μ = 26.5 and σ = 3. (b) The histogram of contig coverage depth after redundant contigs were removed. (c) The histogram of scaffold coverage depth. These data indicate that redundant sequences in the genome assembly were effectively removed by a sequence similarity and coverage-based method. Figure S2. The numbers of genes corresponding to grouped gene families presented in Fig. 2a and b in the main text. (a–c) The numbers of genes that were assigned by OrthoMCL DB; (a) Pinctada fucata, (b) Crassostrea gigas, and (c) Lottia gigantea. (d–f) The numbers of genes that were not assigned by OrthoMCL DB, while detected in comparisons among three mollusc genomes; (d) P. fucata, (e) C. gigas, and (f) L. gigantea. Mollusc-specific genes shared by all three molluscs are much less abundant than lineage-specific genes. (PDF 213 kb)

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