Gene transfer and nucleotide sequence evolution by Gossypium cytoplasmic genomes indicates novel evolutionary characteristics.

KEY MESSAGE: The DNA fragments transferred among cotton cytoplasmic genomes are highly differentiated. The wild D group cotton species have undergone much greater evolution compared with cultivated AD group. Cotton (Gossypium spp.) is one of the most economically important fiber crops worldwide. Gene transfer, nucleotide evolution, and the codon usage preferences in cytoplasmic genomes are important evolutionary characteristics of high plants. In this study, we analyzed the nucleotide sequence evolution, codon usage, and transfer of cytoplasmic DNA fragments in Gossypium chloroplast (cp) and mitochondrial (mt) genomes, including the A genome group, wild D group, and cultivated AD group of cotton species. Our analyses indicated that the differences in the length of transferred cytoplasmic DNA fragments were not significant in mitochondrial and chloroplast sequences. Analysis of the transfer of tRNAs found that trnQ and nine other tRNA genes were commonly transferred between two different cytoplasmic genomes. The Codon Adaptation Index values showed that Gossypium cp genomes prefer A/T-ending codons. Codon preference selection was higher in the D group than the other two groups. Nucleotide sequence evolution analysis showed that intergenic spacer sequences were more variable than coding regions and nonsynonymous mutations were clearly more common in cp genomes than mt genomes. Evolutionary analysis showed that the substitution rate was much higher in cp genomes than mt genomes. Interestingly, the D group cotton species have undergone much faster evolution compared with cultivated AD groups, possibly due to the selection and domestication of diverse cotton species. Our results demonstrate that gene transfer and differential nucleotide sequence evolution have occurred frequently in cotton cytoplasmic genomes.

Characterization of the complete mitochondrial genome of Morchella eohespera.

Morchella eohespera Beug, Voitk & O'Donnell is a typical black morel species. In this study, using the Nanopore sequencing platform, we characterized its whole mitochondrial (mt) genome sequence. Mt genome of M. eohespera is composed of circular DNA molecules of 243,963 bp, which encoded 102 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), and 31 transfer RNA (tRNA) genes. The base composition of M. eohespera mitogenome is as follows: A (30.40%), T (29.30%), G (20.8%), and C (19.5%). The phylogenetic analysis suggested that M. eohespera was closely related to the congeneric M. importuna.

Whole plastid genome of Anemone taipaiensis (Ranunculaceae), an endemic herb plant in China.

Anemone taipaiensis W. T. Wang is an endemic herb species in Shaanxi province (China). Here, we first characterized its whole plastid genome via pair-end sequencing method. The whole chloroplast genome was 156,659 bp in size, including a large single-copy (LSC) region of 78,439 bp, a small single-copy (SSC) region of 16,178 bp, and two repeat regions (IRs) of 31,021 bp. A total of 135 genes, including 91 protein-coding genes, 36 tRNA, and 8 rRNA genes were identified in A. taipaiensis. The phylogenetic analysis showed that A. taipaiensis have a close relationship with congeneric species A. trullifolia.

Characterization of the complete plastid genome of Acer tsinglingense, an endemic tree species in China.

Acer tsinglingense is an ecologically and economically important tree species in China. In this study, we characterized its whole plastid genome sequence using the Illumina sequencing platform. The complete plastid genome size of A. tsinglingense is 156,039 bp in length, including a large single-copy [LSC] region of 85,760 bp, a small single-copy [SSC] region of 18,139 bp, and a pair of inverted repeats [IRs] of 26,070 bp. The genome contains 137 genes, including 89 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The GC contents in chloroplast genome, LSC region, SSC region, and IR region were 38.0%, 36.2%, 32.4%, and 42.9%, respectively. The phylogenetic analysis based on the plastid genomes showed that A. tsinglingense was more closely related with the congeneric A. laevigatum, A. palmatum, A. wilsonii, and A. buergerianum, these species were clustered into a monophyletic clade with high bootstrap support.