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

Takeuchi, Takeshi; Koyanagi, Ryo; Gyoja, Fuki; Kanda, Miyuki; Hisata, Kanako; Fujie, Manabu; Goto, Hiroki; Yamasaki, Shinichi; Nagai, Kiyohito; Morino, Yoshiaki; Miyamoto, Hiroshi; Endo, Kazuyoshi; Endo, Hirotoshi; Nagasawa, Hiromichi; Kinoshita, Shigeharu; Asakawa, Shuichi; Watabe, Shugo; Satoh, Noriyuki; Kawashima, Takeshi

doi:10.6084/m9.figshare.c.3610172_D3.v1

40851_2016_39_MOESM2_ESM.pdf (213.23 kB)

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

journal contribution

posted on 2016-02-18, 05:00 authored by Takeshi Takeuchi, Ryo Koyanagi, Fuki Gyoja, Miyuki Kanda, Kanako Hisata, Manabu Fujie, Hiroki Goto, Shinichi Yamasaki, Kiyohito Nagai, Yoshiaki Morino, Hiroshi Miyamoto, Kazuyoshi Endo, Hirotoshi Endo, Hiromichi Nagasawa, Shigeharu Kinoshita, Shuichi Asakawa, Shugo Watabe, Noriyuki Satoh, Takeshi Kawashima

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)