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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ftdatacite:10.6084/m9.figshare.c.3610172_d3 2023-05-15T15:58:42+02:00 Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle 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 2016 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 unknown Figshare https://dx.doi.org/10.1186/s40851-016-0039-2 CC BY + CC0 https://creativecommons.org/licenses/by/4.0 CC0 Microbiology FOS Biological sciences Genetics Molecular Biology Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences Plant Biology Computational Biology Paper Text article-journal ScholarlyArticle 2016 ftdatacite https://doi.org/10.6084/m9.figshare.c.3610172_d3 https://doi.org/10.1186/s40851-016-0039-2 2021-11-05T12:55:41Z 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) Report Crassostrea gigas DataCite Metadata Store (German National Library of Science and Technology) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Microbiology FOS Biological sciences Genetics Molecular Biology Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences Plant Biology Computational Biology |
spellingShingle |
Microbiology FOS Biological sciences Genetics Molecular Biology Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences Plant Biology Computational Biology 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 Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle |
topic_facet |
Microbiology FOS Biological sciences Genetics Molecular Biology Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences Plant Biology Computational Biology |
description |
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) |
format |
Report |
author |
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 |
author_facet |
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 |
author_sort |
Takeuchi, Takeshi |
title |
Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle |
title_short |
Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle |
title_full |
Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle |
title_fullStr |
Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle |
title_full_unstemmed |
Additional file 2: of Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle |
title_sort |
additional file 2: of bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle |
publisher |
Figshare |
publishDate |
2016 |
url |
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 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
https://dx.doi.org/10.1186/s40851-016-0039-2 |
op_rights |
CC BY + CC0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC0 |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3610172_d3 https://doi.org/10.1186/s40851-016-0039-2 |
_version_ |
1766394472251260928 |