Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae

Abstract

The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA)–Eastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomiaheterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (EST-SSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.

Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset

“…In the genome era, large scale SNP data have been developed by using next-generation high throughput sequencing technologies at unprecedented speed [59,60], and this makes SNP markers the most frequent and convenient tool to study phylogenetic relationship of organisms [61,62]. Besides above molecular markers, the single copy orthologues genes also regarded as excellent markers to study the phylogenetic relationship of diploid or polyploid individuals between intra-and inter-species [63,64]. The sources of blueberry cultivars are complex, so clarifications by phylogenetic relationships are meaningful for the identification, protection and breeding of blueberry germplasm.…”

“…In the recent years, single copy genes have attracted many researchers because of excellent application in genetics, for example, single copy gene is a good molecular tool to construct the phylogenetic tree of species [73]. Logically, without duplication copy, the single copy homologous genes could be regarded as orthologs, and paralogs don't disturb the evolutionary analysis, which made the single copy genes as the merit research object for the molecular mechanism of selection effect and speciation of organism [27,34,36,55,64,73,74]. In this study, we also only test the single copy unigenes to identify the molecular footprints of selection effects by using the method of Ka/Ks.…”

“…Nonsynonymous substitution rate (Ka), synonymous substitution rate (Ks) of T1, T2, and T3, and Ka/Ks of all single copy homologous gene pairs (orthologs) of T1 versus T2, T1 versus T3, and T2 versus T3 were estimated by KaKs_Calculator Toolbox with the standard genetic code table (version 2.0) [7]. We filtered the single copy orthologs with no applicable values of Ka or Ks or Ks values > 0.1 (the benchmark of potential paralogs) as done by previous reports [74,78,96].…”

“…The low values of Ka/Ks for most of the non-synonymous mutations are harmful, and single-copy homologous gene make organisms less tolerant to harmful mutations because they have no copies. So, in order to find out the unigenes which underwent positive selection but might be neutralized (or covered) by a large number of harmful mutant sites, we defined single copy orthologs with Ka/Ks > 1 as strong positive selection, the Ka/Ks values between 0.5 and 1 as weak positive selection, and with Ka/Ks < 0.1 as negatively selected (purifying selection) according to previous reports [74,[79][80][81]. GO and KEGG enrichment analyses were performed by using GOseq [98] and KOBAS [99] of the orthologs sets with strong positive, weak positive and negative positive selection in three blueberry species, respectively.…”

Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements

“…Repeat sequences played a significant role in the rearrangement of the mitogenome (Cole et al, 2018). Extensive gene repeat sequences have been observed in Stemonaceae species, including S. mairei (Lu et al, 2018a), C. japonica (Lu et al, 2018b), and S. parviflora (Wei and Li, 2022). The repeats analysis indicated the presence of microsatellites (SSRs), tandem repeats, and dispersed repeats within the S. sessilifolia mitogenome.…”