Biology subjects

Shigita, G.

Publications and source records attributed to Shigita, G..

3 recordsLinked to original sources

bioRxiv2024

Polyphyletic domestication and inter-lineage hybridization magnified genetic diversity of cultivated melon, Cucumis melo L.

A total of 212 melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9 mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp. melo and the East Asian subsp. agrestis were characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence in both nuclear and cytoplasm genomes. In contrast, in South and Southeast Asia, in addition to the Europe/US and East Asian types, recombinant types were also frequently found, indicating unclear genetic differentiation in South and Southeast Asia. Such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types of melon. Seed length was intermediate, between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib in Momordica, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp. agrestis of the Ic type proved to be endemic to Africa, indicating its African origin.

evolutionary biology↗

bioRxiv2024

Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East

The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber. Key messageGenotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia.

plant biology↗

bioRxiv2023

A novel phylogenomics pipeline reveals complex pattern of reticulate evolution in Cucurbitales

High-throughput sequencing data, such as target capture, RNA-Seq, genome skimming, and high-depth whole genome sequencing, are used for phylogenomic analyses. Integrating these mixed data types into a single phylogenomic dataset requires several bioinformatic tools and significant computational resources. Here, we present CAPTUS, a novel pipeline to analyze mixed data efficiently. CAPTUS assembles these data types, searches for loci of interest, and produces paralog-filtered alignments. If reference target loci are not available for the studied taxon, CAPTUS can also be used to discover new putative homologs via sequence clustering. Compared to other software, CAPTUS allows the recovery of a greater number of more complete loci across more species. We apply CAPTUS to assemble a comprehensive dataset, comprising the four types of sequencing data for the angiosperm order Cucurbitales, a clade of about 3,100 species in eight mainly tropical plant families, including begonias (Begoniaceae) and gourds (Cucurbitaceae). Our phylogenomic results support the currently accepted circumscription of Cucurbitales except for the position of the holoparasitic Apodanthaceae, which group with Rafflesiaceae in Malpighiales. A subset of mitochondrial gene regions supports the earlier divergence of Apodanthaceae in Cucurbitales. However, the nuclear regions and majority of mitochondrial regions place Apodanthaceae in Malpighiales. Within Cucurbitaceae, we confirm the monophyly of all currently accepted tribes but also reveal hybridization and incomplete lineage sorting both in Cucurbitales and within Cucurbitaceae. We show that contradicting results among earlier phylogenetic studies in Cucurbitales can be reconciled when accounting for gene tree conflict and demonstrate the efficiency of CAPTUS for complex datasets.

bioinformatics↗