A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of Flexistyly
Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strat...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2021-08-01
|
Series: | Genes |
Subjects: | |
Online Access: | https://www.mdpi.com/2073-4425/12/9/1297 |
id |
doaj-bcac32c059344e2098e471706c622bca |
---|---|
record_format |
Article |
spelling |
doaj-bcac32c059344e2098e471706c622bca2021-09-26T00:12:46ZengMDPI AGGenes2073-44252021-08-01121297129710.3390/genes12091297A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of FlexistylySurabhi Ranavat0Hannes Becher1Mark F. Newman2Vinita Gowda3Alex D. Twyford4Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UKInstitute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UKRoyal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UKDepartment of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, IndiaInstitute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UKAngiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a <i>de novo</i> assembly of the genome of <i>Alpinia nigra</i> using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high F<sub>ST</sub> values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype.https://www.mdpi.com/2073-4425/12/9/1297flexistyly<i>Alpinia</i>stylar polymorphismZingiberaceaePool-seqgenome assembly |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Surabhi Ranavat Hannes Becher Mark F. Newman Vinita Gowda Alex D. Twyford |
spellingShingle |
Surabhi Ranavat Hannes Becher Mark F. Newman Vinita Gowda Alex D. Twyford A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of Flexistyly Genes flexistyly <i>Alpinia</i> stylar polymorphism Zingiberaceae Pool-seq genome assembly |
author_facet |
Surabhi Ranavat Hannes Becher Mark F. Newman Vinita Gowda Alex D. Twyford |
author_sort |
Surabhi Ranavat |
title |
A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of Flexistyly |
title_short |
A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of Flexistyly |
title_full |
A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of Flexistyly |
title_fullStr |
A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of Flexistyly |
title_full_unstemmed |
A Draft Genome of the Ginger Species <i>Alpinia nigra</i> and New Insights into the Genetic Basis of Flexistyly |
title_sort |
draft genome of the ginger species <i>alpinia nigra</i> and new insights into the genetic basis of flexistyly |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2021-08-01 |
description |
Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a <i>de novo</i> assembly of the genome of <i>Alpinia nigra</i> using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high F<sub>ST</sub> values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype. |
topic |
flexistyly <i>Alpinia</i> stylar polymorphism Zingiberaceae Pool-seq genome assembly |
url |
https://www.mdpi.com/2073-4425/12/9/1297 |
work_keys_str_mv |
AT surabhiranavat adraftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT hannesbecher adraftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT markfnewman adraftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT vinitagowda adraftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT alexdtwyford adraftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT surabhiranavat draftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT hannesbecher draftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT markfnewman draftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT vinitagowda draftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly AT alexdtwyford draftgenomeofthegingerspeciesialpinianigraiandnewinsightsintothegeneticbasisofflexistyly |
_version_ |
1717366705168056320 |