Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

被引：33

作者：

Abdullah ^{[1
]}

Henriquez, Claudia L. ^{[2
]}

Mehmood, Furrukh ^{[1
,4
]}

Shahzadi, Iram ^{[1
]}

Ali, Zain ^{[1
,5
]}

Waheed, Mohammad Tahir ^{[1
]}

Croat, Thomas B. ^{[3
]}

Poczai, Peter ^{[4
]}

Ahmed, Ibrar ^{[5
]}

机构：

[1] Quaid I Azam Univ, Fac Biol Sci, Dept Biochem, Islamabad 45320, Pakistan

[2] Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA

[3] Missouri Bot Garden, 4344 Shaw Blvd, St Louis, MO 63110 USA

[4] Univ Helsinki, Bot Unit, Finnish Museum Nat Hist, POB 7, FI-00014 Helsinki, Finland

[5] Alpha Genom Private Ltd, Islamabad 45710, Pakistan

来源：

PLANTS-BASEL | 2020年 / 9卷 / 06期

关键词：

Araceae; chloroplast genome; substitutions; gene evolution; inverted repeats; contraction and expansion; phylogenetics; PLASTID GENOMES; MATERNAL INHERITANCE; SEQUENCE; GENES; ALIGNMENT; DNA; IDENTIFICATION; ORGANIZATION; ANGIOSPERMS; EVOLUTION;

D O I：

10.3390/plants9060737

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17-18 genes are duplicated in the inverted repeat (IR) regions, comprising 6-7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf 2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

引用

页码：1 / 16

页数：16

共 82 条

[1] Complete Chloroplast Genomes ofAnthurium huixtlenseandPothos scandens(Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution [J].