The comparative studies of complete chloroplast genomes in Actinidia (Actinidiaceae): novel insights into heterogenous variation, clpP gene annotation and phylogenetic relationships
The genus Actinidia , also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species’ relationships, which need further revision throu...
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Published in | Molecular genetics and genomics : MGG Vol. 297; no. 2; pp. 535 - 551 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
Published |
Berlin/Heidelberg
Springer Berlin Heidelberg
01.03.2022
Springer Nature B.V |
Subjects | |
Online Access | Get full text |
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Summary: | The genus
Actinidia
, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual
Actinidia
species’ relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species’ phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes’ sequences derived from 25
Actinidia
taxa. The average genome size is 156,673.38 bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in
Actinidia
were revealed to be the causal agent leading to the chloroplast genome size expansion. The
clpP
gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in
Actinidia
species. Comprehensive sequence analyses indicated the distinct variation at the
clpP
gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e.,
rps16
~
trnQ-UUG
,
rps4
~
trnT-UGU
,
petA
~
psbJ
, and
rps12
~
psbB
) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying
rps12
~
psbB
(including
clpP
gene and its up/downstream noncoding sequence) were identified as variation hot spots in
Actinidia
species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25
Actinidia
taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in
Actinidia
. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among
Actinidia
species. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 1617-4615 1617-4623 |
DOI: | 10.1007/s00438-022-01868-4 |