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Table 3 Introns in Scenedesmus cpDNA and homologous introns at identical gene locations in other green algal cpDNAs

From: The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands

Scenedesmus introns

Homologous introns

Designation

Subgroupa

ORF locationb

ORF typec

Green algad/Intron numbere

Accession no.

So.L(uaa).1

IC3

Bryopsis plumosa (U)

[GenBank:M61159]

    

Chlorella vulgaris (T)

[GenBank:NC_001865]

So.psaB.1

IA1

Chlamydomonas moewusii (C)

[GenBank: M90641]

So.psbA.1

IA1

L5

H-N-H

-

So.psbA.2

IA1

-

So.psbA.3

IA1

L5

H-N-H

Pseudendoclonium akinetum i6 (U)

[GenBank: AY835431]

So.rrl.1

IB4

L6

LAGLIDADG

Chlamydomonas eugametos i5 (C)

[GenBank: Z17234]

So.rrl.2

IA3

L6

LAGLIDADG

Chlamydomonas reinhardtii (C)

[GenBank: NC_005353]

    

Chlorella vulgaris (T)

[GenBank: NC_001865]

    

Oltmannsiellopsis viridis i3 (U)

[GenBank: DQ291132]

    

Pseudendoclonium akinetum (U)

[GenBank: AY835431]

So.petD.1

IIA

DIV

RT-X-Zn

So.psaA.1

IIB

Chlamydomonas reinhardtii i2 (C)

[GenBank: NC_005353]

  1. a Group I introns were classified according to Michel and Westhof [66], whereas classification of group II introns was according to Michel et al. [65].
  2. b L followed by a number refers to the loop extending the base-paired region identified by the number; D refers to a domain of group II intron secondary structure.
  3. c For group I intron ORFs, the conserved motif in the predicted homing endonuclease is given; for the petD intron ORF, RT, X and Zn refer to the reverse transcriptase, maturase and nuclease domains of reverse transcriptases, respectively.
  4. d For the two rrl introns, only the homologues identified in completely sequenced genomes are given. The complete lists of introns homologous to So. rrl.1 and So.rrl.2 can be obtained in Turmel et al. [35] and Pombert et al. [13], respectively. The letter in parentheses indicates the chlorophyte lineage comprising the green alga indicated. U, Ulvophyceae; T, Trebouxiophyceae; C, Chlorophyceae.
  5. e The intron number is given when more than one intron is present.