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Table 1 MIP genes in Populus genome identified from the NCBI whole genome shotgun contigs.

From: Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective

Name

NCBI WGS contig accession number

JGI accession number

EST accession

NPA motif (LB)a

NPA motif (LE)a

Chromosome locatione

PtPIP1;1

AARH01004386

724520

DT472648

-

-

X

PtPIP1;2

AARH01003541

656216

BU868142

-

-

VIII

PtPIP1;3

AARH01001832

711735

DT474111

-

-

III

PtPIP1;4

AARH01003029

831918

 

-

-

VI

PtPIP1;5

AARH01006875

835561

 

-

-

XVI

PtPIP2;1

AARH01003794

821084

DT478685

-

-

IX

PtPIP2;2

AARH01002541

648808

DT473513

-

-

IV

PtPIP2;3

AARH01004412

567607

DT474367

-

-

X

PtPIP2;4

AARH01003539

563742

DT472264

-

-

VIII

PtPIP2;5

AARH01008299

826419

BU868919

-

-

*

PtPIP2;6b

AARH01008299

N/A

CV227359

-

-

*

PtPIP2;7

AARH01006751

735495

DT498815

-

-

XVI

PtPIP2;8

AARH01003912

821627

 

-

-

IX

PtPIP2;9c

 

836572

 

-

-

*

PtPIP2;10

AARH01008738

796664

 

-

-

*

PtTIP1;1

AARH01000429

549212

 

-

-

I

PtTIP1;2

AARH01003864

833283

DT499779

-

-

IX

PtTIP1;3

AARH01004405

822504

DT476627

-

-

X

PtTIP1;4

AARH01003540

656044

BU875073

-

-

VIII

PtTIP1;5

AARH01006799

667870

DT497619

-

-

XVI

PtTIP1;6

AARH01008323

589502

DT497300

-

-

*

PtTIP1;7

AARH01003929

558321

 

-

-

IX

PtTIP1;8

AARH01010693

828458

 

-

-

*

PtTIP2;1

AARH01000349

548890

DT496472

-

-

I

PtTIP2;2

AARH01001731

645978

DT488368

-

-

III

PtTIP2;3

AARH01001777

817166

 

-

-

III

PtTIP2;4

AARH01008349

676397

 

-

-

*

PtTIP3;1

AARH01010701

584517

 

-

-

*

PtTIP3;2

AARH01011328

811826

 

-

-

*

PtTIP4;1

AARH01003145

561759

CV233830

-

-

VI

PtTIP5;1d

AARH01001826

414059

 

-

-

III

PtTIP5;2d

AARH01008384

423803

 

-

-

*

PtNIP1;1d

AARH01002108

197507

 

-

-

IV

PtNIP1;2d

AARH01004854

235172

 

-

-

XI

PtNIP1;3

AARH01004327

566501

 

-

-

X

PtNIP1;4c

 

756079

 

-

-

II

PtNIP1;5c

 

754717

 

-

-

II

PtNIP2;1

AARH01007172

577637

 

-

-

XVII

PtNIP3;1

AARH01001861

757987

 

NPS

NPV

III

PtNIP3;2

AARH01000110

797136

 

NPS

NPV

I

PtNIP3;3

AARH01000968

708017

DT488082

-

-

I

PtNIP3;4

AARH01005007

823094

 

-

-

XI

PtNIP3;5

AARH01003691

803915

 

-

-

VIII

PtSIP1;1

AARH01005657

729942

 

NPT

-

XIII

PtSIP1;2

AARH01007966

665418

DT487219

NPT

-

XIX

PtSIP1;3

AARH01001280

755885

 

-

-

II

PtSIP1;4c

 

572968

 

-

-

XIX

PtSIP2;1

AARH01006621

734665

DN491635

NPL

-

XVI

PtSIP2;2

AARH01002935

652505

 

NPL

-

VI

PtXIP1;1

AARH01022440

829126

 

NPI

-

*

PtXIP1;2

AARH01003797

557139

 

NPI

-

IX

PtXIP1;3

AARH01002537

759781

 

NPI

-

IV

PtXIP1;4

AARH01003797

767334

 

NPL

-

IX

PtXIP1;5

AARH01003797

821124

 

-

-

IX

PtXIP2;1

AARH01003797

557138

 

SPV

-

IX

  1. aDeviation of NPA signature motif in loops B and E is reported. '-' indicates that NPA motif is conserved.
  2. bThis gene is not listed in JGI. The coding regions in the NCBI WGS contig are 173376-173676, 173811-174106, 174224-174364, 174465-174584.
  3. cFour PtMIP genes are not found in our TBLASTN search of NCBI database. Their JGI accession codes are given.
  4. dThe sequences for these genes predicted by GeneMark are longer than those found in JGI. GeneMark-predicted sequences have extensions in N- or C-terminus. In this study, we have used GeneMark predicted sequences due to their similarity with Arabidopsis sequences
  5. eThe symbol '*' indicates that these genes are located on a scaffold not yet assigned to a chromosome.
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BMC Plant Biology

ISSN: 1471-2229

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