Biology subjects

Lin, K.-M.

Publications and source records attributed to Lin, K.-M..

3 recordsLinked to original sources

bioRxiv2025

Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacterium Cyanobacterium sp. DS4 from a high-temperature lagoon

BackgroundCyanobacteria have diversified through their long evolutionary history and occupy a wide range of environments on Earth. To advance our understanding of their adaption mechanisms in extreme environments, we performed stress tolerance characterizations, whole genome sequencing, and comparative genomic analyses of a novel heat-tolerant and euryhaline strain of the unicellular cyanobacterium Cyanobacterium sp. Dongsha4 (DS4). This strain was isolated from a lagoon on Dongsha Island in the South China Sea, a habitat with fluctuations in temperature, salinity, light intensity, and nutrient supply. ResultsDS4 cells can tolerate long-term high-temperature up to 50 and salinity from 0 to 6.6 %, which is similar to the results previously obtained for Cyanobacterium aponinum. In contrast, most mesophilic cyanobacteria cannot survive under these extreme conditions. Based on the 16S rRNA gene phylogeny, DS4 is most closely related to Cyanobacterium sp. NBRC 102756 isolated from Iwojima Island, Japan, and Cyanobacterium sp. MCCB114 isolated from Vypeen Island, India. For comparison with strains that have genomic information available, DS4 is most similar to Cyanobacterium aponinum strain PCC 10605 (PCC10605), sharing 81.7% of the genomic segments and 92.9% average nucleotide identity (ANI). Gene content comparisons identified multiple distinct features of DS4. Unlike related strains, DS4 possesses the genes necessary for nitrogen fixation. Other notable genes include those involved in photosynthesis, central metabolisms, cyanobacterial starch metabolisms, stress tolerances, and biosynthesis of novel secondary metabolites. ConclusionsThese findings promote our understanding of the physiology, ecology, evolution, and stress tolerance mechanisms of cyanobacteria. The information is valuable for future functional studies and biotechnology applications of heat-tolerant and euryhaline marine cyanobacteria.

genomics↗

bioRxiv2022

Chinese fir genome and the evolution of gymnosperms

Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families and 70 genera. Their distinctiveness has triggered much debate on their origin, evolution, and phylogenetic placement among seed plants. To better understand the evolution of gymnosperms and their relation to other seed plants, we report here a high-quality genome sequence for a tree species, Chinese fir (Cunninghamia lanceolata), which has excellent timber quality and high aluminum adaptability and is a member of Cupressaceae with high levels of heterozygosity. We assembled an 11.24 Gb genome with a contig N50 value of 2.15 Mb and anchored the 10.89 Gb sequence to 11 chromosomes. Phylogenomic analyses showed that cycads sister to Ginkgo, which place to sister in all gymnosperm lineages, and Gnetales within conifers sister to Pinaceae. Whole-genome duplication (WGD) analysis showed that the ancestor of seed plants has differentiated into angiosperms and gymnosperms after having experienced a WGD event. The ancestor of extant gymnosperm has experienced a gymnosperm-specific WGD event and the extant angiosperms do not share a common WGD before their most recent common ancestor diverged into existing angiosperms lineages. Analysis of the MADS-box gene family of C. lanceolata revealed the developmental mechanism of the reproductive organs in C. lanceolata, which supported the (A)B(C) model of the development of gymnosperms reproductive organs. In addition, astringent seeds and shedding of whole branches (with withered leaves) might be a strategy of C. lanceolata that evolved during long-term adaptation to an aluminum-rich environment. The findings also reveal the molecular regulation mechanism of shade tolerance in C. lanceolata seedlings. Our results improve the resolution of ancestral genomic features within seed plants and the knowledge of genome evolution and diversification of gymnosperms.

genomics↗

bioRxiv2019

Managing congestion at visitor hotspots using park-level use level data: Case study of a Chinese World Heritage site

Tourist congestion at hot spots has been a major management concern for UNESCO World Heritage Sites and other iconic protected areas. A growing number of heritage sites employ technologies, such as cameras and electronic ticket-checking systems, to monitor user levels, but data collected by these monitoring technologies are often under-utilize. In this study, we illustrated how to integrate data from hot spots by camera-captured monitoring and entrance counts to manage use levels at a World Heritage Site in southeastern China. 6,930 photos of a congestion hotspot (scenic outlook on a trail) were collected within the park at a 10-minute interval over 105 days from January to November 2017. The entrance counts were used to predict daily average and maximum use level at the hotspot Average use level at the congestion hotspot did not exceed the use limit mandated by the Chinese park administration agency. However, from 9:20 am to 12:00 pm, the use level at hotspots exceeded visitor preferred use level. Visitor use level was significantly higher at the hotspot during a major Chinese \"golden week\" holiday. The daily entrance counts significantly predicted the average and maximum use level at the hotspot. Based on our findings, we recommend that the number of visitors entering the gate on each day should be less than 28,764 for the hotspots to meet use level mandates, while less than 6,245 to meet visitor preference. The gap manifested the complexity in visitor capacity management at high-use World Heritage Sites and other protected areas and calls for innovative monitoring and management strategies.

ecology↗