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Table 1

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Summary of conclusions based on genes with cis- or trans-regulation effects among Nelumbo, Arabidopsis, and cotton

Questions	Results	Interspecific hybrids		Intraspecific hybrid
Questions	Results	Nelumbo	Arabidopsis	Gossypium hirsutum
Do cis- and/or trans-regulation effects have different inheritance modes?	cis-regulatory effect: additive	✓	✓	✓
	trans-regulatory effect: dominance	✓	✓	✓
	Compensatory regulation: transgressive	✓	N/A	✓
Do trans-regulated genes have broader expression breadth?	trans-regulatory: expressed in more tissues	✓	✓	N/A
Do trans-regulated genes have broader expression breadth?	cis-regulatory: expressed in fewer tissues	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	trans-regulatory: higher expression level	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	cis-regulatory: lower expression level	✓	✓	N/A
Do WGD genes tend to have trans-regulatory effects?	Genes with trans-regulatory effects are more divided into genome-wide duplication events	✓	×	×
Are orphan genes unlikely to have any cis- or trans-regulatory effects?	Orphan genes tend to show cis-only and conserved regulatory effects	✓	×	✓

Questions	Results	Interspecific hybrids		Intraspecific hybrid
Questions	Results	Nelumbo	Arabidopsis	Gossypium hirsutum
Do cis- and/or trans-regulation effects have different inheritance modes?	cis-regulatory effect: additive	✓	✓	✓
	trans-regulatory effect: dominance	✓	✓	✓
	Compensatory regulation: transgressive	✓	N/A	✓
Do trans-regulated genes have broader expression breadth?	trans-regulatory: expressed in more tissues	✓	✓	N/A
Do trans-regulated genes have broader expression breadth?	cis-regulatory: expressed in fewer tissues	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	trans-regulatory: higher expression level	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	cis-regulatory: lower expression level	✓	✓	N/A
Do WGD genes tend to have trans-regulatory effects?	Genes with trans-regulatory effects are more divided into genome-wide duplication events	✓	×	×
Are orphan genes unlikely to have any cis- or trans-regulatory effects?	Orphan genes tend to show cis-only and conserved regulatory effects	✓	×	✓

Note: ✓, results were consistent among species; ×, results were inconsistent among species.

N/A: not available.

Table 1

Open in new tab

Summary of conclusions based on genes with cis- or trans-regulation effects among Nelumbo, Arabidopsis, and cotton

Questions	Results	Interspecific hybrids		Intraspecific hybrid
Questions	Results	Nelumbo	Arabidopsis	Gossypium hirsutum
Do cis- and/or trans-regulation effects have different inheritance modes?	cis-regulatory effect: additive	✓	✓	✓
	trans-regulatory effect: dominance	✓	✓	✓
	Compensatory regulation: transgressive	✓	N/A	✓
Do trans-regulated genes have broader expression breadth?	trans-regulatory: expressed in more tissues	✓	✓	N/A
Do trans-regulated genes have broader expression breadth?	cis-regulatory: expressed in fewer tissues	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	trans-regulatory: higher expression level	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	cis-regulatory: lower expression level	✓	✓	N/A
Do WGD genes tend to have trans-regulatory effects?	Genes with trans-regulatory effects are more divided into genome-wide duplication events	✓	×	×
Are orphan genes unlikely to have any cis- or trans-regulatory effects?	Orphan genes tend to show cis-only and conserved regulatory effects	✓	×	✓

Questions	Results	Interspecific hybrids		Intraspecific hybrid
Questions	Results	Nelumbo	Arabidopsis	Gossypium hirsutum
Do cis- and/or trans-regulation effects have different inheritance modes?	cis-regulatory effect: additive	✓	✓	✓
	trans-regulatory effect: dominance	✓	✓	✓
	Compensatory regulation: transgressive	✓	N/A	✓
Do trans-regulated genes have broader expression breadth?	trans-regulatory: expressed in more tissues	✓	✓	N/A
Do trans-regulated genes have broader expression breadth?	cis-regulatory: expressed in fewer tissues	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	trans-regulatory: higher expression level	✓	✓	N/A
Do cis-regulated genes have lower expression levels?	cis-regulatory: lower expression level	✓	✓	N/A
Do WGD genes tend to have trans-regulatory effects?	Genes with trans-regulatory effects are more divided into genome-wide duplication events	✓	×	×
Are orphan genes unlikely to have any cis- or trans-regulatory effects?	Orphan genes tend to show cis-only and conserved regulatory effects	✓	×	✓

Note: ✓, results were consistent among species; ×, results were inconsistent among species.

N/A: not available.