Additional file 12: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Additional file 1 of Phylogenomic analysis and development of molecular markers for the determination of twelve plum cultivars (Prunus, Rosaceae)

Yicen Xu (9290163)
Bo Fang (169627)
Jingling Li (729067)
Yuanwei Wang (3219036)
Jingting Liu (2527606)
Chang Liu (35901)
Jie Yu (150626)

November 2022

Additional file 1: TableS1. Summary of sequencing data quality. Table S2. Gene composition in the pl...

Additional file 2: of Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

Margaret Staton (4676)
Tetyana Zhebentyayeva (3421250)
Bode Olukolu (3421247)
Guang Fang (3421244)
Dana Nelson (3421253)
John Carlson (4491)
Albert Abbott (4680)

October 2015

Dot plots comparing each chestnut LG to the set of Populus trichocarpa chromosomes with highlightnig...

Additional file 2: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

Xinxin Wu (1672492)
Ting Shi (3955)
Shahid Iqbal (5632475)
Yong Zhang (5893)
Lin Liu (74495)
Zhihong Gao (127975)

February 2019

The unique reads mapped to various chromosomes (a, b) and the biological replicates correlation coef...

Additional file 11: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S10. Summary of accessions and Illumina short-read data used in whole-genome resequencing anal...

Additional file 5: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S4. Summary of repetitive sequences identified in the draft genome of wild P. yedoensis. (XLSX...

Additional file 2: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S1. Statistics of genome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this study. (X...

Additional file 10: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S9. Over- or under-represented gene families in the wild P. yedoensis genome compared to the P...

Additional file 6: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S5. Statistics of gene models predicted from the draft genome of wild P. yedoensis. (XLSX 10 k...

Additional file 4: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S3. Evaluation of gene space coverage of the wild P. yedoensis genome using transcriptome unig...

Additional file 3: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S2. Statistics of transcriptome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this st...

Additional file 9: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S8. Coverage of individual chromosomes of peach (Pp), sweet cherry (Pa), and Chinese plum (Pm)...

Additional file 1: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Figure S1. K-mer plots of wild P. yedoensis (Pyn) and âYoshino cherryâ (Pxy) accessions. Figure ...

Additional file 8: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S7. Summary of alternative splicing events identified in protein-coding genes. (XLSX 10 kb

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek
Kyung Choi
Goon-Bo Kim
Hee-Ju Yu
Ara Cho
Hoyeol Jang
Changkyun Kim
Hyuk-Jin Kim
Kae Sun Chang
Joo-Hwan Kim
Jeong-Hwan Mun

September 2018

Abstract Background Hybridization is an important evolutionary process that results in increased pla...

Additional file 1 of Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

Lijuan Feng (3746086)
Guopeng Zhao (17585499)
Mengmeng An (17285345)
Chuanzeng Wang (3620984)
Yanlei Yin (7774052)

December 2023

Additional file 1: Fig. S1. Statistical plot of interspersed repeats sequences.The abscissa is the l...

Additional file 1 of Phylogenomic analysis and development of molecular markers for the determination of twelve plum cultivars (Prunus, Rosaceae)

Yicen Xu (9290163)
Bo Fang (169627)
Jingling Li (729067)
Yuanwei Wang (3219036)
Jingting Liu (2527606)
Chang Liu (35901)
Jie Yu (150626)

November 2022

Additional file 1: TableS1. Summary of sequencing data quality. Table S2. Gene composition in the pl...

Additional file 2: of Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

Margaret Staton (4676)
Tetyana Zhebentyayeva (3421250)
Bode Olukolu (3421247)
Guang Fang (3421244)
Dana Nelson (3421253)
John Carlson (4491)
Albert Abbott (4680)

October 2015

Dot plots comparing each chestnut LG to the set of Populus trichocarpa chromosomes with highlightnig...

Additional file 2: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

Xinxin Wu (1672492)
Ting Shi (3955)
Shahid Iqbal (5632475)
Yong Zhang (5893)
Lin Liu (74495)
Zhihong Gao (127975)

February 2019

The unique reads mapped to various chromosomes (a, b) and the biological replicates correlation coef...

Additional file 11: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S10. Summary of accessions and Illumina short-read data used in whole-genome resequencing anal...

Additional file 5: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S4. Summary of repetitive sequences identified in the draft genome of wild P. yedoensis. (XLSX...

Additional file 2: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S1. Statistics of genome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this study. (X...

Additional file 10: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S9. Over- or under-represented gene families in the wild P. yedoensis genome compared to the P...

Additional file 6: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S5. Statistics of gene models predicted from the draft genome of wild P. yedoensis. (XLSX 10 k...

Additional file 4: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S3. Evaluation of gene space coverage of the wild P. yedoensis genome using transcriptome unig...

Additional file 3: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S2. Statistics of transcriptome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this st...

Additional file 9: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S8. Coverage of individual chromosomes of peach (Pp), sweet cherry (Pa), and Chinese plum (Pm)...

Additional file 1: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Figure S1. K-mer plots of wild P. yedoensis (Pyn) and âYoshino cherryâ (Pxy) accessions. Figure ...

Additional file 8: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek (50214)
Kyung Choi (5618495)
Goon-Bo Kim (5718761)
Hee-Ju Yu (553525)
Ara Cho (1736176)
Hoyeol Jang (5718767)
Changkyun Kim (689778)
Hyuk-Jin Kim (5718779)
Kae Chang (5718782)
Joo-Hwan Kim (390936)
Jeong-Hwan Mun (50209)

September 2018

Table S7. Summary of alternative splicing events identified in protein-coding genes. (XLSX 10 kb

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Seunghoon Baek
Kyung Choi
Goon-Bo Kim
Hee-Ju Yu
Ara Cho
Hoyeol Jang
Changkyun Kim
Hyuk-Jin Kim
Kae Sun Chang
Joo-Hwan Kim
Jeong-Hwan Mun

September 2018

Abstract Background Hybridization is an important evolutionary process that results in increased pla...

Additional file 1 of Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

Lijuan Feng (3746086)
Guopeng Zhao (17585499)
Mengmeng An (17285345)
Chuanzeng Wang (3620984)
Yanlei Yin (7774052)

December 2023

Additional file 1: Fig. S1. Statistical plot of interspersed repeats sequences.The abscissa is the l...

Additional file 1 of Phylogenomic analysis and development of molecular markers for the determination of twelve plum cultivars (Prunus, Rosaceae)

Yicen Xu (9290163)
Bo Fang (169627)
Jingling Li (729067)
Yuanwei Wang (3219036)
Jingting Liu (2527606)
Chang Liu (35901)
Jie Yu (150626)

November 2022

Additional file 1: TableS1. Summary of sequencing data quality. Table S2. Gene composition in the pl...

Additional file 2: of Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

Margaret Staton (4676)
Tetyana Zhebentyayeva (3421250)
Bode Olukolu (3421247)
Guang Fang (3421244)
Dana Nelson (3421253)
John Carlson (4491)
Albert Abbott (4680)

October 2015

Dot plots comparing each chestnut LG to the set of Populus trichocarpa chromosomes with highlightnig...

Additional file 2: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

Xinxin Wu (1672492)
Ting Shi (3955)
Shahid Iqbal (5632475)
Yong Zhang (5893)
Lin Liu (74495)
Zhihong Gao (127975)

February 2019

The unique reads mapped to various chromosomes (a, b) and the biological replicates correlation coef...

Additional file 12: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Abstract

Extracted data

Additional file 12: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

Abstract

Extracted data

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