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Table 2 Coding potential and SQANTI3 analyses of four Apetala2 genes isoforms of S. chinensis reference genome

From: Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows

Genes Details

 

Isoforms Details

Gene

Size (bp)

Exon count

Average coverage%

Name

Size (bp)

Coding potential

Chr

Structural category

Sub-category

All-canonical

Standard/long

Apetala2-1

12,538

10

18

ISO/171107

2824

complete

chr9

ISM

Intron retention

canonical

Yes

 

ISO/105509

3316

complete

chr9

NIC

Intron retention

canonical

 

Yes

ISO/412095

643

3’ partial

chr9

NIC

mono-exon

NA

 

Yes

ISO/327430

1787

complete

chr9

ISM

3’fragment

canonical

Yes

 

ISO/315531

1880

complete

chr9

NIC

Intron retention

canonical

Yes

 

ISO/222064

2503

complete

chr9

NNIC

Intron retention

canonical

 

Yes

ISO/366229

1420

Non

chr9

Intergenic

mono-exon

NA

 

Yes

ISO/270607

2192

Non

chr9

Intergenic

mono-exon

NA

Yes

 

ISO/100081

3363

complete

chr9

ISM

Intron retention

canonical

 

Yes

ISO/111394

3253

complete

chr9

NIC

Intron retention

canonical

Yes

 

Apetala2-2

5823

9

43

ISO/303053

1970

complete

chr4

NIC

Intron retention

canonical

Yes

 

ISO/257514

2274

5’ partial

chr4

ISM

Intron retention

canonical

Yes

 

ISO/105872

3312

5’ partial

chr4

NIC

Intron retention

canonical

Yes

 

Apetala2-3

8881

11

21

ISO/265232

2225

complete

chr9

NNIC

At least one novel splicesite

canonical

Yes

 

ISO/264460

2218

complete

chr9

ISM

3’ fragment

canonical

Yes

 

ISO/253270

2302

complete

chr9

NIC

Intron retention

canonical

Yes

 

ISO/409273

705

3’ partial

chr9

NIC

mono-exon

NA

 

Yes

ISO/319944

1834

complete

chr9

NNIC

Intron retention

noncanonical

Yes

 

Apetala2-4

7590

11

25

ISO/361458

1476

complete

chr2

ISM

5’ fragment

canonical

Yes

 

ISO/358337

1508

complete

chr2

NNIC

At least one novel splicesite

noncanonical

 

Yes

ISO/382288

1207

complete

chr2

NNIC

At least one novel splicesite

noncanonical

 

Yes

ISO/303247

1969

complete

chr2

ISM

5’ fragment

canonical

Yes

 

ISO/295283

2026

complete

chr2

NNIC

At least one novel splicesite

canonical

Yes

 

ISO/297282

1976

complete

chr2

FSM

At least one novel splicesite

canonical

Yes

 
 

ISO/293887

2035

complete

chr2

NNIC

At least one novel splice site

noncanonical

Yes

 
 

ISO/320398

1844

complete

chr2

Genic

mono-exon

NA

Yes

 
 

ISO/99492

3371

5’ partial

chr2

NNIC

Intron retention

canonical

 

Yes

 

ISO/321893

1832

5’ partial

chr2

FSM

Alternative 3/5 ends

canonical

Yes

 
  1. Coding potential analysis categorize the isoforms into the following categories: complete, 5’ prime (5’ prime), 3’ prime (3’ prime), and no coding potential. SQANTI3 analysis result includes the following information: chromosome number (Chr), structural category, sub-category, and all-canonical. The structural category is divided into intergenic, genic, full-splice match (FSM) incomplete full-splice match (ISM), novel not in catalog (NNIC), and novel in catalog (NIC) transcripts. The sub-category is classified into intron retention (IR), mono-exon, 5’ prime fragment, 3’ prime fragment, Alternative 3end 5end, and at least one novel splice site. Every isoform size and dataset type (standard or long) were determined
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Plant Methods

ISSN: 1746-4811