Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)
Abstract Background Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsonia...
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| Format: | Article |
| Language: | English |
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BMC
2021-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07566-6 |
| _version_ | 1818598219605606400 |
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| author | Duo Chen Peng-Cheng Yan Yan-Ping Guo |
| author_facet | Duo Chen Peng-Cheng Yan Yan-Ping Guo |
| author_sort | Duo Chen |
| collection | DOAJ |
| description | Abstract Background Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently. Results We conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to “defense response”. Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors. Conclusion Two independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids. |
| first_indexed | 2024-12-16T12:00:13Z |
| format | Article |
| id | doaj.art-b11bb214f2734e188ea5aea5744f5aa7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-16T12:00:13Z |
| publishDate | 2021-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b11bb214f2734e188ea5aea5744f5aa72022-12-21T22:32:28ZengBMCBMC Genomics1471-21642021-04-0122111210.1186/s12864-021-07566-6Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)Duo Chen0Peng-Cheng Yan1Yan-Ping Guo2Key Laboratory of Biodiversity Science and Ecological Engineering of the Ministry of Education, and College of Life Sciences, Beijing Normal UniversityBeijing Tangtang Tianxia Biotechnology Co., LtdKey Laboratory of Biodiversity Science and Ecological Engineering of the Ministry of Education, and College of Life Sciences, Beijing Normal UniversityAbstract Background Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently. Results We conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to “defense response”. Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors. Conclusion Two independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids.https://doi.org/10.1186/s12864-021-07566-6Allopolyploid speciationRNA-sequencingInheritance of gene expressionHomeolog express biasAchillea |
| spellingShingle | Duo Chen Peng-Cheng Yan Yan-Ping Guo Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae) BMC Genomics Allopolyploid speciation RNA-sequencing Inheritance of gene expression Homeolog express bias Achillea |
| title | Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae) |
| title_full | Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae) |
| title_fullStr | Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae) |
| title_full_unstemmed | Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae) |
| title_short | Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae) |
| title_sort | imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species achillea asteraceae |
| topic | Allopolyploid speciation RNA-sequencing Inheritance of gene expression Homeolog express bias Achillea |
| url | https://doi.org/10.1186/s12864-021-07566-6 |
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