Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines
Whole-genome shogun sequence (WGS) data generated by next-generation sequencing (NGS) platforms are a valuable resource for crop improvement. We produced 5–6 × WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes: cabbage, broccoli, cauliflower, kailan, kale,...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
KeAi Communications Co., Ltd.
2021-11-01
|
| Series: | Horticultural Plant Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468014121000315 |
| _version_ | 1827279107595960320 |
|---|---|
| author | Sampath Perumal Nomar Espinosa Waminal Jonghoon Lee Hyun-Jin Koo Boem-soon Choi Jee Young Park Kyounggu Ahn Tae-Jin Yang |
| author_facet | Sampath Perumal Nomar Espinosa Waminal Jonghoon Lee Hyun-Jin Koo Boem-soon Choi Jee Young Park Kyounggu Ahn Tae-Jin Yang |
| author_sort | Sampath Perumal |
| collection | DOAJ |
| description | Whole-genome shogun sequence (WGS) data generated by next-generation sequencing (NGS) platforms are a valuable resource for crop improvement. We produced 5–6 × WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes: cabbage, broccoli, cauliflower, kailan, kale, Brussels sprout, and kohlrabi to systematically evaluate the nuclear and chloroplast (Cp) diversity in the 44 B. oleracea breeding lines. We then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly, annotation of complete chloroplast (Cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences, and copy number variation for major repeats. Nuclear genome diversity analysis has revealed a total of 496 463 SNPs and 37 493 indels in the nuclear genome across the 44 accessions. Interestingly, some SNPs showed subspecies enrichment at certain chromosomal regions. The assembly of complete Cp genomes contained 153 361–153 372 bp with 37 variants including SNPs and indels. The 45S nrDNA transcription unit was 5 802 bp long with a total of 31 SNPs from the 44 lines. The phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli, cauliflower, and kailan in one group and cabbage, Brussels sprout, kale, and kohlrabi in another group. The morphotypes diverged during the last 0.17 million years. The Cp genome diversity reflected the unique cytoplasm of each subspecies, and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process instead. The polymorphic Cp markers provide a classification system for the cytoplasm types in B. oleracea. Furthermore, copy numbers of major transposable elements (TEs) showed high diversity among the 44 accessions, indicating that many TEs have become active recently. Overall, we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse B. oleracea morphotypes. |
| first_indexed | 2024-04-24T08:13:39Z |
| format | Article |
| id | doaj.art-2a7f5fd4e83549d18ee92d466d4ce8db |
| institution | Directory Open Access Journal |
| issn | 2468-0141 |
| language | English |
| last_indexed | 2024-04-24T08:13:39Z |
| publishDate | 2021-11-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Horticultural Plant Journal |
| spelling | doaj.art-2a7f5fd4e83549d18ee92d466d4ce8db2024-04-17T04:38:26ZengKeAi Communications Co., Ltd.Horticultural Plant Journal2468-01412021-11-0176539551Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding linesSampath Perumal0Nomar Espinosa Waminal1Jonghoon Lee2Hyun-Jin Koo3Boem-soon Choi4Jee Young Park5Kyounggu Ahn6Tae-Jin Yang7Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, Saskatoon, SK S7N 4L8, Canada; Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon S7N 0X2, CanadaDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul 01795, Republic of KoreaDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Joeun Seeds. Co., Ltd, Goesan-Gun, Chungcheongbuk-Do 367-833, Republic of KoreaDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of KoreaPhyzen Genomics Institute, 13, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do 13558, Republic of KoreaDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of KoreaJoeun Seeds. Co., Ltd, Goesan-Gun, Chungcheongbuk-Do 367-833, Republic of KoreaDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Corresponding author.Whole-genome shogun sequence (WGS) data generated by next-generation sequencing (NGS) platforms are a valuable resource for crop improvement. We produced 5–6 × WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes: cabbage, broccoli, cauliflower, kailan, kale, Brussels sprout, and kohlrabi to systematically evaluate the nuclear and chloroplast (Cp) diversity in the 44 B. oleracea breeding lines. We then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly, annotation of complete chloroplast (Cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences, and copy number variation for major repeats. Nuclear genome diversity analysis has revealed a total of 496 463 SNPs and 37 493 indels in the nuclear genome across the 44 accessions. Interestingly, some SNPs showed subspecies enrichment at certain chromosomal regions. The assembly of complete Cp genomes contained 153 361–153 372 bp with 37 variants including SNPs and indels. The 45S nrDNA transcription unit was 5 802 bp long with a total of 31 SNPs from the 44 lines. The phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli, cauliflower, and kailan in one group and cabbage, Brussels sprout, kale, and kohlrabi in another group. The morphotypes diverged during the last 0.17 million years. The Cp genome diversity reflected the unique cytoplasm of each subspecies, and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process instead. The polymorphic Cp markers provide a classification system for the cytoplasm types in B. oleracea. Furthermore, copy numbers of major transposable elements (TEs) showed high diversity among the 44 accessions, indicating that many TEs have become active recently. Overall, we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse B. oleracea morphotypes.http://www.sciencedirect.com/science/article/pii/S2468014121000315Brassica oleracea subspeciesChloroplast genomeNuclear ribosomal DNAGenetic diversityPhylogeny |
| spellingShingle | Sampath Perumal Nomar Espinosa Waminal Jonghoon Lee Hyun-Jin Koo Boem-soon Choi Jee Young Park Kyounggu Ahn Tae-Jin Yang Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines Horticultural Plant Journal Brassica oleracea subspecies Chloroplast genome Nuclear ribosomal DNA Genetic diversity Phylogeny |
| title | Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines |
| title_full | Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines |
| title_fullStr | Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines |
| title_full_unstemmed | Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines |
| title_short | Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines |
| title_sort | nuclear and chloroplast genome diversity revealed by low coverage whole genome shotgun sequence in 44 brassica oleracea breeding lines |
| topic | Brassica oleracea subspecies Chloroplast genome Nuclear ribosomal DNA Genetic diversity Phylogeny |
| url | http://www.sciencedirect.com/science/article/pii/S2468014121000315 |
| work_keys_str_mv | AT sampathperumal nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines AT nomarespinosawaminal nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines AT jonghoonlee nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines AT hyunjinkoo nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines AT boemsoonchoi nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines AT jeeyoungpark nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines AT kyoungguahn nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines AT taejinyang nuclearandchloroplastgenomediversityrevealedbylowcoveragewholegenomeshotgunsequencein44brassicaoleraceabreedinglines |