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Heterosigma akashiwo is a eukaryotic, cosmopolitan, and uni-cellular alga (class: Raphidophyceae), and produces fish -killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information en-ables researchers to characterize organisms using modern molecular technology. In the present study, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assem-bly of 84,693,530 high-quality deduplicated short-read se-quences. Obtained RNA reads were assembled by Trinity assembler and 144,777 contigs were identified with N 50 values of 1085. Total 60,877 open reading frames with the length of 150 bp or greater were predicted. For further analy-ses, top Gene Ontology terms, pfam hits, and blast hits were annotated for all the predicted genes. The raw data were deposited in the NCBI SRA database (BioProject PR - JDB6241 and PRJDB15108), and the assemblies are available in NCBI TSA database (ICRV01). The annotation information can be obtained in Dryad and can be accessed via doi: 10.5061/dryad.m0cfxpp56.

Heterosigma akashiwo is a eukaryotic, cosmopolitan, and uni-cellular alga (class: Raphidophyceae), and produces fish -killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information en-ables researchers to characterize organisms using modern molecular technology. In the present study, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assem-bly of 84,693,530 high-quality deduplicated short-read se-quences. Obtained RNA reads were assembled by Trinity assembler and 144,777 contigs were identified with N 50 values of 1085. Total 60,877 open reading frames with the length of 150 bp or greater were predicted. For further analy-ses, top Gene Ontology terms, pfam hits, and blast hits were annotated for all the predicted genes. The raw data were deposited in the NCBI SRA database (BioProject PR - JDB6241 and PRJDB15108), and the assemblies are available in NCBI TSA database (ICRV01). The annotation information can be obtained in Dryad and can be accessed via doi: 10.5061/dryad.m0cfxpp56.

Rhinogobius fishes (Gobiidae) are distributed widely in East and Southeast Asia, and represent the most species-rich group of freshwater gobies with diversified life histories (i.e., amphidromous, fluvial, and lentic). To reveal their phylogenetic relationships and life history evolution patterns, we sequenced six nuclear and three mitochondrial DNA (mtDNA) loci from 18 species, mainly from the mainland of Japan and the Ryukyu Archipelago. Our phylogenetic tree based on nuclear genes resolved three major clades, including several distinct subclades. The mtDNA and nuclear DNA phylogenies showed large discordance, which strongly suggested mitochondrial introgression through large-scale interspecific hybridization in these regions. On the basis of the molecular dating using geological data as calibration points, the hybridization occurred in the early to middle Pleistocene. Reconstruction of the ancestral states of life history traits based on nuclear DNA phylogeny suggests that the evolutionary change from amphidromous to freshwater life, accompanied by egg size change, occurred independently in at least three lineages. One of these lineages showed two life history alterations, i.e., from amphidromous (small egg) to fluvial (large egg) to lentic (small egg). Although more inclusive analysis using species outside Japan should be further conducted, the present results suggest the importance of the life history evolution associated with high adaptability to freshwater environments in the remarkable species diversification in this group. Such life history divergences may have contributed to the development of reproductive isolation.

Aim: Phylogeographical signatures of past population fragmentation and demographic change have been reported in several African rain forest trees. These signatures have usually been interpreted in the light of the Pleistocene forest refuge hypothesis, although dating these events has remained impracticable because of inadequate genetic markers. We assess the timing of interspecific and intraspecific genetic differentiation and demographic changes within two rain forest Erythrophleum tree species (Fabaceae: Caesalpinioideae). Location: Tropical forests of Upper Guinea (West Africa) and Lower Guinea (Atlantic Central Africa). Methods: Six single-copy nuclear genes were used to characterize the phylogeographical patterns of the parapatric sister species Erythrophleum suaveolens (characteristic of semi-deciduous or gallery forests) and Erythrophleum ivorense (characteristic of evergreen forests). The number of gene pools within each species was determined and the timings of their divergence and past demographic changes were estimated using Bayesian-based coalescent approaches. Results: Three geographically separated gene pools were identified within E. suaveolens, and a single gene pool was inferred in E. ivorense. All gene pools show signatures of demographic bottlenecks concomitant with the last glacial period (c. 120-12 ka). Species-tree inferences show that the two species diverged c. 600 ka, whereas the divergence between E. suaveolens gene pools was dated to the late Pleistocene (first divergence c. 120 ka, second c. 60 ka). Main conclusions: (1) Molecular dating of demographic changes of two African tropical forest tree species is consistent with the Pleistocene forest refuge hypothesis. (2) Tree species from Guinean evergreen tropical forests might have been less affected by past climate change than semi-deciduous species. (3) Our phylogeographical data support a recent date (Holocene) of the last opening of the Dahomey Gap., SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

Aim: Phylogeographical signatures of past population fragmentation and demographic change have been reported in several African rain forest trees. These signatures have usually been interpreted in the light of the Pleistocene forest refuge hypothesis, although dating these events has remained impracticable because of inadequate genetic markers. We assess the timing of interspecific and intraspecific genetic differentiation and demographic changes within two rain forest Erythrophleum tree species (Fabaceae: Caesalpinioideae). Location: Tropical forests of Upper Guinea (West Africa) and Lower Guinea (Atlantic Central Africa). Methods: Six single-copy nuclear genes were used to characterize the phylogeographical patterns of the parapatric sister species Erythrophleum suaveolens (characteristic of semi-deciduous or gallery forests) and Erythrophleum ivorense (characteristic of evergreen forests). The number of gene pools within each species was determined and the timings of their divergence and past demographic changes were estimated using Bayesian-based coalescent approaches. Results: Three geographically separated gene pools were identified within E. suaveolens, and a single gene pool was inferred in E. ivorense. All gene pools show signatures of demographic bottlenecks concomitant with the last glacial period (c. 120-12 ka). Species-tree inferences show that the two species diverged c. 600 ka, whereas the divergence between E. suaveolens gene pools was dated to the late Pleistocene (first divergence c. 120 ka, second c. 60 ka). Main conclusions: (1) Molecular dating of demographic changes of two African tropical forest tree species is consistent with the Pleistocene forest refuge hypothesis. (2) Tree species from Guinean evergreen tropical forests might have been less affected by past climate change than semi-deciduous species. (3) Our phylogeographical data support a recent date (Holocene) of the last opening of the Dahomey Gap., SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

The phylogeny of lampreys is controversial, because they possess few taxon-distinctive morphological characters. This is especially true of the relationships among the genus Lethenteron and the closely related genera Eudontomyzon and Lampetra. Thus, the first objective of this thesis was to use DNA sequences of the mitochondrial cytochrome b gene and two nuclear gene introns to infer the phylogeny among these three genera. I found that: 1) Lethenteron plus Eudontomyzon morii without Lethenteron ninae, Lethenteron zanandreai, and Lethenteron sp. S (a distinct cryptic species in the Lethenteron reissneri complex) was monophyletic; 2) Lampetra from the Pacific drainage of North America and Lampetra aepyptera should each be separated, as distinct genera, from Lampetra (including Lethenteron ninae and Lethenteron zanandreai) from the Atlantic drainage of Eurasia; and 3) the remaining Eudontomyzon and the Atlantic Lampetra clustered together in all analyses. The second objective of this thesis was to resolve the relationship among closely related Lethenteron species. Lampreys are either parasitic or non-parasitic, and each non-parasitic (satellite) species is believed to have been derived independently from the parasitic (stem) ancestor. In the phylogenetic analysis, the parasitic Arctic lamprey Lethenteron camtschaticum and its four satellite species were not reciprocally monophyletic. Since network methods are generally more useful for closely related haplotypes than bifurcating trees, a haplotype network of these five Lethenteron species was generated using the cytochrome b gene sequences; Lethenteron appendix showed haplotype frequency distribution differences but there was little support for recognizing the other four taxa as distinct species.

The phylogeny of lampreys is controversial, because they possess few taxon-distinctive morphological characters. This is especially true of the relationships among the genus Lethenteron and the closely related genera Eudontomyzon and Lampetra. Thus, the first objective of this thesis was to use DNA sequences of the mitochondrial cytochrome b gene and two nuclear gene introns to infer the phylogeny among these three genera. I found that: 1) Lethenteron plus Eudontomyzon morii without Lethenteron ninae, Lethenteron zanandreai, and Lethenteron sp. S (a distinct cryptic species in the Lethenteron reissneri complex) was monophyletic; 2) Lampetra from the Pacific drainage of North America and Lampetra aepyptera should each be separated, as distinct genera, from Lampetra (including Lethenteron ninae and Lethenteron zanandreai) from the Atlantic drainage of Eurasia; and 3) the remaining Eudontomyzon and the Atlantic Lampetra clustered together in all analyses. The second objective of this thesis was to resolve the relationship among closely related Lethenteron species. Lampreys are either parasitic or non-parasitic, and each non-parasitic (satellite) species is believed to have been derived independently from the parasitic (stem) ancestor. In the phylogenetic analysis, the parasitic Arctic lamprey Lethenteron camtschaticum and its four satellite species were not reciprocally monophyletic. Since network methods are generally more useful for closely related haplotypes than bifurcating trees, a haplotype network of these five Lethenteron species was generated using the cytochrome b gene sequences; Lethenteron appendix showed haplotype frequency distribution differences but there was little support for recognizing the other four taxa as distinct species.

Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato. The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum and 8 derived from hybridization processes) were morphologically and genetically using the SolCap platform (7,414 SNPs). The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from Mesoamer

We have cloned and sequenced three different cDNAs from sunflower seed-stored mRNA. Sequence similarities and response to heat-shock identified one of the cDNAs as a low-molecular-weight heat-shock protein (lmw-HSP). The other two clones showed significant sequence similarity to the cotton and carrot late-embryogenesis-abundant (Lea) proteins D-113 and Emb-1, respectively. The three cDNAs showed similar expression patterns during zygotic embryo development, as well as in vegetative tissues of 3-day-old seedlings in response to stress. Maximal accumulation of all three mRNAs was detected in dry seeds and during embryo mid-maturation stage, in the absence of exogenous stress. In seedlings, mRNAs accumulated to lower levels in response to osmotic stress and exogenous abscisic acid (ABA) treatments. A differential time course of response to osmotic stress was observed: lmw-HSP mRNA accumulation was induced earlier than that of Lea mRNAs. The coordinate accumulation of Lea and lmw-HSP transcripts during embryo development and in response to stress and ABA suggests the existence of common regulatory elements for Lea and lmw-HSP genes, and supports the notion that HSPs might have alternative functions in the plant cell.