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Table 2 Type, localization and characteristics of repeated elements in the RGA08 locus of M. balbisiana

From: Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana)

Name

Type

ID

Location

Length

5' LTR

3'LTR

TSD

Divergence time

   

(bp)

(bp)

length

TG

CA

length

TG

CA

 

(MY)

RE1

Copia-like element

MbP032N20c_te030

129477

2855

-

-

-

-

-

-

-

-

RE1

 

MbP036B13_te010

100745

2882

-

-

-

-

-

-

-

-

Clio

LARD

MbP032N20c_te010

28466

4441

382

TG

CA

382

TG

CA

ATAC/ATAC

0.294

Clio

 

MbP032N20c_te040

148954

4441

382

TG

CA

382

TG

CA

GGAG/GGAG

1.189

Clio

 

MbP036B13_te020

120343

4441

382

TG

CA

382

TG

CA

GGAG/-

 

Clio*

 

MbP036B13_te030

124784

1606

-

-

-

-

-

-

-

 

Mooz

Copia-like element

MbP032N20c_te050

166534

3849

115

-

-

112

-

-

-

-

Mooz

 

MbP032N20c_te060

225945

3346

231

-

-

447

TG

CA

-

-

Mooz

 

MbP036B13_te050

185390

3688

447

TG

CA

447

TG

CA

CTTTG/CTTTC

2.183

Mooz*

 

MbP036B13_te040

181339

2464

447

TG

CA

-

-

-

CTTTG/-

 

RE5

Copia-like element

MbP032N20c_te020

124026

4301

94

TG

-

171

TG

CA

ACCAC/ACCAC

-

  1. LTR features (length, presence of TG and CA at their ends) and Target Site Duplication (TSD) were determined using LTR_FINDER followed by manual annotation. For complete elements with clearly identified TSD and with LTR length exceeding the empirical limit of 300 bp, divergence time was calculated based on the Kimura-2 parameter distance between LTRs with a substitution rate of 0.9 × 10-8 mutation per site per year. Stars indicate TE fragments. MY, million years.
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BMC Plant Biology

ISSN: 1471-2229

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