Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution
Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remai...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Wu, He [verfasserIn] Dongchen, Wenhua [verfasserIn] Li, Yunbin [verfasserIn] Brown, Sylvia E. [verfasserIn] Wei, Shugu [verfasserIn] Lin, Chun [verfasserIn] Mao, Zichao [verfasserIn] Liu, Zhengjie [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2024 |
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| Schlagwörter: |
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| Anmerkung: |
© The Author(s) 2024 |
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| Übergeordnetes Werk: |
Enthalten in: BMC genomics - BioMed Central, 2000, 25(2024), 1 vom: 12. Sept. |
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| Übergeordnetes Werk: |
volume:25 ; year:2024 ; number:1 ; day:12 ; month:09 |
| Links: |
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| DOI / URN: |
10.1186/s12864-024-10768-3 |
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| Katalog-ID: |
SPR05730789X |
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| 520 | |a Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. | ||
| 520 | |a Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. | ||
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10.1186/s12864-024-10768-3 doi (DE-627)SPR05730789X (SPR)s12864-024-10768-3-e DE-627 ger DE-627 rakwb eng 570 610 VZ 12 ssgn BIODIV DE-30 fid 42.20 bkl 44.48 bkl Wu, He verfasserin aut Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. L. (dpeaa)DE-He213 Mitochondrial genome (dpeaa)DE-He213 Phylogenetic analysis (dpeaa)DE-He213 RNA editing (dpeaa)DE-He213 Energy production system (dpeaa)DE-He213 Dongchen, Wenhua verfasserin aut Li, Yunbin verfasserin aut Brown, Sylvia E. verfasserin aut Wei, Shugu verfasserin aut Lin, Chun verfasserin aut Mao, Zichao verfasserin (orcid)0000-0001-8632-5508 aut Liu, Zhengjie verfasserin aut Enthalten in BMC genomics BioMed Central, 2000 25(2024), 1 vom: 12. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:25 year:2024 number:1 day:12 month:09 https://dx.doi.org/10.1186/s12864-024-10768-3 X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.20 VZ 44.48 VZ AR 25 2024 1 12 09 |
| spelling |
10.1186/s12864-024-10768-3 doi (DE-627)SPR05730789X (SPR)s12864-024-10768-3-e DE-627 ger DE-627 rakwb eng 570 610 VZ 12 ssgn BIODIV DE-30 fid 42.20 bkl 44.48 bkl Wu, He verfasserin aut Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. L. (dpeaa)DE-He213 Mitochondrial genome (dpeaa)DE-He213 Phylogenetic analysis (dpeaa)DE-He213 RNA editing (dpeaa)DE-He213 Energy production system (dpeaa)DE-He213 Dongchen, Wenhua verfasserin aut Li, Yunbin verfasserin aut Brown, Sylvia E. verfasserin aut Wei, Shugu verfasserin aut Lin, Chun verfasserin aut Mao, Zichao verfasserin (orcid)0000-0001-8632-5508 aut Liu, Zhengjie verfasserin aut Enthalten in BMC genomics BioMed Central, 2000 25(2024), 1 vom: 12. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:25 year:2024 number:1 day:12 month:09 https://dx.doi.org/10.1186/s12864-024-10768-3 X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.20 VZ 44.48 VZ AR 25 2024 1 12 09 |
| allfields_unstemmed |
10.1186/s12864-024-10768-3 doi (DE-627)SPR05730789X (SPR)s12864-024-10768-3-e DE-627 ger DE-627 rakwb eng 570 610 VZ 12 ssgn BIODIV DE-30 fid 42.20 bkl 44.48 bkl Wu, He verfasserin aut Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. L. (dpeaa)DE-He213 Mitochondrial genome (dpeaa)DE-He213 Phylogenetic analysis (dpeaa)DE-He213 RNA editing (dpeaa)DE-He213 Energy production system (dpeaa)DE-He213 Dongchen, Wenhua verfasserin aut Li, Yunbin verfasserin aut Brown, Sylvia E. verfasserin aut Wei, Shugu verfasserin aut Lin, Chun verfasserin aut Mao, Zichao verfasserin (orcid)0000-0001-8632-5508 aut Liu, Zhengjie verfasserin aut Enthalten in BMC genomics BioMed Central, 2000 25(2024), 1 vom: 12. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:25 year:2024 number:1 day:12 month:09 https://dx.doi.org/10.1186/s12864-024-10768-3 X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.20 VZ 44.48 VZ AR 25 2024 1 12 09 |
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10.1186/s12864-024-10768-3 doi (DE-627)SPR05730789X (SPR)s12864-024-10768-3-e DE-627 ger DE-627 rakwb eng 570 610 VZ 12 ssgn BIODIV DE-30 fid 42.20 bkl 44.48 bkl Wu, He verfasserin aut Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. L. (dpeaa)DE-He213 Mitochondrial genome (dpeaa)DE-He213 Phylogenetic analysis (dpeaa)DE-He213 RNA editing (dpeaa)DE-He213 Energy production system (dpeaa)DE-He213 Dongchen, Wenhua verfasserin aut Li, Yunbin verfasserin aut Brown, Sylvia E. verfasserin aut Wei, Shugu verfasserin aut Lin, Chun verfasserin aut Mao, Zichao verfasserin (orcid)0000-0001-8632-5508 aut Liu, Zhengjie verfasserin aut Enthalten in BMC genomics BioMed Central, 2000 25(2024), 1 vom: 12. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:25 year:2024 number:1 day:12 month:09 https://dx.doi.org/10.1186/s12864-024-10768-3 X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.20 VZ 44.48 VZ AR 25 2024 1 12 09 |
| allfieldsSound |
10.1186/s12864-024-10768-3 doi (DE-627)SPR05730789X (SPR)s12864-024-10768-3-e DE-627 ger DE-627 rakwb eng 570 610 VZ 12 ssgn BIODIV DE-30 fid 42.20 bkl 44.48 bkl Wu, He verfasserin aut Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2024 Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. L. (dpeaa)DE-He213 Mitochondrial genome (dpeaa)DE-He213 Phylogenetic analysis (dpeaa)DE-He213 RNA editing (dpeaa)DE-He213 Energy production system (dpeaa)DE-He213 Dongchen, Wenhua verfasserin aut Li, Yunbin verfasserin aut Brown, Sylvia E. verfasserin aut Wei, Shugu verfasserin aut Lin, Chun verfasserin aut Mao, Zichao verfasserin (orcid)0000-0001-8632-5508 aut Liu, Zhengjie verfasserin aut Enthalten in BMC genomics BioMed Central, 2000 25(2024), 1 vom: 12. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:25 year:2024 number:1 day:12 month:09 https://dx.doi.org/10.1186/s12864-024-10768-3 X:SPRINGER Resolving-System kostenfrei Volltext SYSFLAG_0 GBV_SPRINGER FID-BIODIV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.20 VZ 44.48 VZ AR 25 2024 1 12 09 |
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Enthalten in BMC genomics 25(2024), 1 vom: 12. Sept. volume:25 year:2024 number:1 day:12 month:09 |
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L. Mitochondrial genome Phylogenetic analysis RNA editing Energy production system |
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The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches.</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. 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Wu, He Dongchen, Wenhua Li, Yunbin Brown, Sylvia E. Wei, Shugu Lin, Chun Mao, Zichao Liu, Zhengjie |
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mitogenomes comparison of 3 species of asparagus l shedding light on their functions due to domestication and adaptative evolution |
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Mitogenomes comparison of 3 species of Asparagus L shedding light on their functions due to domestication and adaptative evolution |
| abstract |
Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. © The Author(s) 2024 |
| abstractGer |
Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. © The Author(s) 2024 |
| abstract_unstemmed |
Background Asparagus L., widely distributed in the old world is a genus under Asparagaceae, Asparagales. The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches. Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus. © The Author(s) 2024 |
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The species of the genus were mainly used as vegetables, traditional medicines as well as ornamental plants. However, the evolution and functions of mitochondrial (Mt) genomes (mitogenomes) remains largely unknown. In this study, the typical herbal medicine A. taliensis and ornamental plant A. setaceus were used to assemble and annotate the mitogenomes, and the resulting mitogenomes were further compared with published mitogenome of A. officinalis for the analysis of their functions in the context of domestication and adaptative evolution. Results The mitochondrial genomes of both A. taliensis and A. setaceus were assembled as complete circular ones. The phylogenetic trees based on conserved protein-coding genes of Mt genomes and whole chloroplast (Cp) genomes showed that, the phylogenetic relationship of the sampled 13 species of Asparagus L. were not exactly consistent. The collinear analyses between the nuclear (Nu) and Mt genomes confirmed the existence of mutual horizontal genes transfers (HGTs) between Nu and Mt genomes within these species. Based on RNAseq data, the Mt RNA editing were predicted and atp1 and ccmB RNA editing of A. taliensis were further confirmed by DNA sequencing. Simultaneously homologous search found 5 Nu coding gene families including pentatricopeptide-repeats (PPRs) involved in Mt RNA editing. Finally, the Mt genome variations, gene expressions and mutual HGTs between Nu and Mt were detected with correlation to the growth and developmental phenotypes respectively. The results suggest that, both Mt and Nu genomes co-evolved and maintained the Mt organella replication and energy production through TCA and oxidative phosphorylation . Conclusion The assembled and annotated complete mitogenomes of both A. taliensis and A. setaceus provide valuable information for their phylogeny and concerted action of Nu and Mt genomes to maintain the energy production system of Asparagus L. in the context of domestication and adaptation to environmental niches.</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Highlights Mitochondrial genomes of A. taliensis and A. setaceus were assembled and annotated, and phylogenetic trees of 13 sampled species in the genus Asparagus based on both mitochondrial and chloroplast genomes showed that A. officinalis, A. taliensis and A. setaceus are represented species of Asparagus L. Independent horizontal gene transfers (HGTs) between the mitochondrial and nuclear genomes were detected with reduction in dioecious species, while Mt RNA editing rate was higher in dioecious species with consistency of their higher copies and higher expression levels of involved nuclear coding RNA editing enzyme genes. Detected different gene copies and expression levels of both pathways of tricarboxylic acid cycle(TCA) and oxidative phosphorylation genes indicates the different efficiency of citric acid accumulation and ATP synthesis due to adaptation and/or domestication among species of A. officinalis, A. taliensis and A. setaceus.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">L.</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Mitochondrial genome</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Phylogenetic analysis</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">RNA editing</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Energy production system</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Dongchen, Wenhua</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Li, Yunbin</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Brown, Sylvia E.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Wei, Shugu</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Lin, Chun</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Mao, Zichao</subfield><subfield code="e">verfasserin</subfield><subfield code="0">(orcid)0000-0001-8632-5508</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Liu, Zhengjie</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">BMC genomics</subfield><subfield code="d">BioMed Central, 2000</subfield><subfield code="g">25(2024), 1 vom: 12. 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