Summary of PAR observations taken from a subsample of 14 caves.

<p>Observation taken parallel to leaf surface at points at which vascular plants were growing. Means are of 3 observations taken in each zone.</p

Yangzi cave, Guangxi, China.

<p>The cave entrance is approximately 70 m wide, 15 m high and the depth of the entrance cavern supporting vascular plants 170 m. This cave is type locality for 8 vascular plant species.</p

Light levels recorded in the entrance and twilight zones of caves compared to other previously documented low-light vascular plant habitats.

<p>Numbers in square brackets refer to reference used to source of data, * refers to this study.</p

Summary of human disturbance observed in the 61 caves surveyed.

<p>Grey (no disturbance), pale blue (tourism), yellow (storage of cattle), pale green (cultivation of herbs), dark grey (harvesting of plants), white (temporary mausoleum) and dark blue (drawing water).</p

Species accumulation curves.

<p>All species (red), angiosperms (blue) and ferns (green).</p

Distribution and species-richness of study caves across SW China.

<p>The diameter of the point corresponds to species-richness.</p

A comprehensive profiling of T- and B-lymphocyte receptor repertoires from a Chinese-origin rhesus macaque by high-throughput sequencing

<div><p>Due to the close genetic background, high similarity of physiology, and susceptibility to infectious and metabolic diseases with humans, rhesus macaques have been widely used as an important animal model in biomedical research, especially in the study of vaccine development and human immune-related diseases. In recent years, high-throughput sequencing based immune repertoire sequencing (IR-SEQ) has become a powerful tool to study the dynamic adaptive immune responses. Several previous studies had analyzed the responses of B cells to HIV-1 trimer vaccine or T cell repertoire of rhesus macaques using this technique, however, there are little studies that had performed a comprehensive analysis of immune repertoire of rhesus macaques, including T and B lymphocytes. Here, we did a comprehensive analysis of the T and B cells receptor repertoires of a Chinese rhesus macaque based on the 5’—RACE and IR-SEQ. The detailed analysis includes the distribution of CDR3 length, the composition of amino acids and nucleotides of CDR3, V, J and V-J combination usage, the insertion and deletion length distribution and somatic hypermutation rates of the framework region 3 (FR3). In addition, we found that several positions of FR3 region have high mutation frequencies, which may indicate the existence of new genes/alleles that have not been discovered and/or collected into IMGT reference database. We believe that a comprehensive profiling of immune repertoire of rhesus macaque will facilitate the human immune-related diseases studies.</p></div

The usage frequencies of all possible distinct functional V-J pairing in TCRB and IGH repertoires.

<p>(a-b) The frequencies of all possible distinct functional V-J pairing in TCRB and IGH repertoires, respectively. The x axis represents all functional J genes and the y axis represents all functional V genes. The area of the circle is proportional to the frequency of a V-J pairing.</p

The usage frequency of each functional V/J gene for TCRB and IGH repertoires.

<p>(a-b) The usage frequency of each functional V gene in TCRB and IGH repertoires, respectively. (c-d) The usage frequency of each functional J gene in TCRB and IGH repertoire, respectively.</p

The mutation characteristics of FR3.

<p>(a) The overall mutation rates of FR3 in IGH, IGK, and IGL repertoires. NT represents the nucleotide and AA represents the amino acid. (b) The average mutation rates of FR3 among different functional V genes in IGH repertoire. (c-d) The distribution of mutation frequencies at each position of FR3 among functional V genes in IGH repertoire, at amino acid level (c) and nucleotide level (d). The grey rectangle indicates that no nucleotide was sequenced at that position or the number of nucleotide was less than or equal to 30 at that position.</p